simple_moves¶

Bindings for protocols::simple_moves namespace

class pyrosetta.rosetta.protocols.simple_moves.AddCavitiesMover¶

Bases: Mover

add_suckers(self: pyrosetta.rosetta.protocols.simple_moves.AddCavitiesMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::simple_moves::AddCavitiesMover::add_suckers(class core::pose::Pose &) –> void

apply(self: pyrosetta.rosetta.protocols.simple_moves.AddCavitiesMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::simple_moves::AddCavitiesMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.AddCavitiesMover, : pyrosetta.rosetta.protocols.simple_moves.AddCavitiesMover) → pyrosetta.rosetta.protocols.simple_moves.AddCavitiesMover¶: C++: protocols::simple_moves::AddCavitiesMover::operator=(const class protocols::simple_moves::AddCavitiesMover &) –> class protocols::simple_moves::AddCavitiesMover &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clear_suckers(self: pyrosetta.rosetta.protocols.simple_moves.AddCavitiesMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::simple_moves::AddCavitiesMover::clear_suckers(class core::pose::Pose &) –> void

clone(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶

Return a clone of the Mover object.

C++: protocols::moves::Mover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶

Generates a new Mover object freshly created with the default ctor.

C++: protocols::moves::Mover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_cavities(self: pyrosetta.rosetta.protocols.simple_moves.AddCavitiesMover, pose: pyrosetta.rosetta.core.pose.Pose, nbdis: float, nbcount: int, minsep: float) → pyrosetta.rosetta.utility.vector1_core_scoring_packstat_CavityBall¶: C++: protocols::simple_moves::AddCavitiesMover::get_cavities(const class core::pose::Pose &, double, int, double) –> class utility::vector1<class core::scoring::packstat::CavityBall, class std::allocator<class core::scoring::packstat::CavityBall> >

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.simple_moves.AddCavitiesMover) → str¶: C++: protocols::simple_moves::AddCavitiesMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.

C++: protocols::moves::Mover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.simple_moves.AddChainMover¶

Bases: Mover

add_new_chain(self: pyrosetta.rosetta.protocols.simple_moves.AddChainMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::simple_moves::AddChainMover::add_new_chain(class core::pose::Pose &) const –> void

apply(self: pyrosetta.rosetta.protocols.simple_moves.AddChainMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::simple_moves::AddChainMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.AddChainMover, : pyrosetta.rosetta.protocols.simple_moves.AddChainMover) → pyrosetta.rosetta.protocols.simple_moves.AddChainMover¶: C++: protocols::simple_moves::AddChainMover::operator=(const class protocols::simple_moves::AddChainMover &) –> class protocols::simple_moves::AddChainMover &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.simple_moves.AddChainMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::AddChainMover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fname(*args, **kwargs)¶

Overloaded function.

fname(self: pyrosetta.rosetta.protocols.simple_moves.AddChainMover, f: str) -> None

C++: protocols::simple_moves::AddChainMover::fname(const std::string &) –> void

fname(self: pyrosetta.rosetta.protocols.simple_moves.AddChainMover) -> str

C++: protocols::simple_moves::AddChainMover::fname() const –> std::string

fresh_instance(self: pyrosetta.rosetta.protocols.simple_moves.AddChainMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::AddChainMover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.simple_moves.AddChainMover) → str¶: C++: protocols::simple_moves::AddChainMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static mover_name() → str¶: C++: protocols::simple_moves::AddChainMover::mover_name() –> std::string

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

new_chain(*args, **kwargs)¶

Overloaded function.

new_chain(self: pyrosetta.rosetta.protocols.simple_moves.AddChainMover, n: bool) -> None

C++: protocols::simple_moves::AddChainMover::new_chain(const bool) –> void

new_chain(self: pyrosetta.rosetta.protocols.simple_moves.AddChainMover) -> bool

C++: protocols::simple_moves::AddChainMover::new_chain() const –> bool

parse_my_tag(self: pyrosetta.rosetta.protocols.simple_moves.AddChainMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::simple_moves::AddChainMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::AddChainMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

random_access(*args, **kwargs)¶

Overloaded function.

random_access(self: pyrosetta.rosetta.protocols.simple_moves.AddChainMover) -> bool

C++: protocols::simple_moves::AddChainMover::random_access() const –> bool

random_access(self: pyrosetta.rosetta.protocols.simple_moves.AddChainMover, b: bool) -> None

C++: protocols::simple_moves::AddChainMover::random_access(const bool) –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

scorefxn(*args, **kwargs)¶

Overloaded function.

scorefxn(self: pyrosetta.rosetta.protocols.simple_moves.AddChainMover, s: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None

C++: protocols::simple_moves::AddChainMover::scorefxn(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void

scorefxn(self: pyrosetta.rosetta.protocols.simple_moves.AddChainMover) -> pyrosetta.rosetta.core.scoring.ScoreFunction

C++: protocols::simple_moves::AddChainMover::scorefxn() const –> class std::shared_ptr<class core::scoring::ScoreFunction>

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

spm_reference_name(self: pyrosetta.rosetta.protocols.simple_moves.AddChainMover) → str¶: C++: protocols::simple_moves::AddChainMover::spm_reference_name() const –> std::string

swap_chain(self: pyrosetta.rosetta.protocols.simple_moves.AddChainMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::simple_moves::AddChainMover::swap_chain(class core::pose::Pose &) const –> void

swap_chain_number(*args, **kwargs)¶

Overloaded function.

swap_chain_number(self: pyrosetta.rosetta.protocols.simple_moves.AddChainMover, wc: int) -> None

C++: protocols::simple_moves::AddChainMover::swap_chain_number(const unsigned long) –> void

swap_chain_number(self: pyrosetta.rosetta.protocols.simple_moves.AddChainMover) -> int

C++: protocols::simple_moves::AddChainMover::swap_chain_number() const –> unsigned long

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

update_PDBInfo(*args, **kwargs)¶

Overloaded function.

update_PDBInfo(self: pyrosetta.rosetta.protocols.simple_moves.AddChainMover, n: bool) -> None

C++: protocols::simple_moves::AddChainMover::update_PDBInfo(const bool) –> void

update_PDBInfo(self: pyrosetta.rosetta.protocols.simple_moves.AddChainMover) -> bool

C++: protocols::simple_moves::AddChainMover::update_PDBInfo() const –> bool

class pyrosetta.rosetta.protocols.simple_moves.AddChainMoverCreator¶

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.simple_moves.AddChainMoverCreator, : pyrosetta.rosetta.protocols.simple_moves.AddChainMoverCreator) → pyrosetta.rosetta.protocols.simple_moves.AddChainMoverCreator¶: C++: protocols::simple_moves::AddChainMoverCreator::operator=(const class protocols::simple_moves::AddChainMoverCreator &) –> class protocols::simple_moves::AddChainMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.simple_moves.AddChainMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::AddChainMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.simple_moves.AddChainMoverCreator) → str¶: C++: protocols::simple_moves::AddChainMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.simple_moves.AddChainMoverCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::AddChainMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.simple_moves.AddJobPairData¶

Bases: Mover

Add an arbitrary piece of data to the current Job, which will be output in the silent file, database, etc. This is useful for adding metadata to keep track of data generated using multiple experimental conditions. Currently ONLY RosettaScript interface supported.

The data appended to the Job consists of a key and a value. The key is a string, and the value can be either a real or string.

apply(self: pyrosetta.rosetta.protocols.simple_moves.AddJobPairData, : pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::simple_moves::AddJobPairData::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.AddJobPairData, : pyrosetta.rosetta.protocols.simple_moves.AddJobPairData) → pyrosetta.rosetta.protocols.simple_moves.AddJobPairData¶: C++: protocols::simple_moves::AddJobPairData::operator=(const class protocols::simple_moves::AddJobPairData &) –> class protocols::simple_moves::AddJobPairData &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.simple_moves.AddJobPairData) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::AddJobPairData::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.simple_moves.AddJobPairData) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::AddJobPairData::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.simple_moves.AddJobPairData) → str¶: C++: protocols::simple_moves::AddJobPairData::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static mover_name() → str¶: C++: protocols::simple_moves::AddJobPairData::mover_name() –> std::string

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.simple_moves.AddJobPairData, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::simple_moves::AddJobPairData::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::AddJobPairData::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.simple_moves.AddJobPairDataCreator¶

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.simple_moves.AddJobPairDataCreator, : pyrosetta.rosetta.protocols.simple_moves.AddJobPairDataCreator) → pyrosetta.rosetta.protocols.simple_moves.AddJobPairDataCreator¶: C++: protocols::simple_moves::AddJobPairDataCreator::operator=(const class protocols::simple_moves::AddJobPairDataCreator &) –> class protocols::simple_moves::AddJobPairDataCreator &

create_mover(self: pyrosetta.rosetta.protocols.simple_moves.AddJobPairDataCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::AddJobPairDataCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.simple_moves.AddJobPairDataCreator) → str¶: C++: protocols::simple_moves::AddJobPairDataCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.simple_moves.AddJobPairDataCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::AddJobPairDataCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.simple_moves.AddPDBInfoMover¶

Bases: Mover

apply(self: pyrosetta.rosetta.protocols.simple_moves.AddPDBInfoMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::simple_moves::AddPDBInfoMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.AddPDBInfoMover, : pyrosetta.rosetta.protocols.simple_moves.AddPDBInfoMover) → pyrosetta.rosetta.protocols.simple_moves.AddPDBInfoMover¶: C++: protocols::simple_moves::AddPDBInfoMover::operator=(const class protocols::simple_moves::AddPDBInfoMover &) –> class protocols::simple_moves::AddPDBInfoMover &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.simple_moves.AddPDBInfoMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::AddPDBInfoMover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.simple_moves.AddPDBInfoMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::AddPDBInfoMover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.simple_moves.AddPDBInfoMover) → str¶: C++: protocols::simple_moves::AddPDBInfoMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static mover_name() → str¶: C++: protocols::simple_moves::AddPDBInfoMover::mover_name() –> std::string

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.simple_moves.AddPDBInfoMover, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::simple_moves::AddPDBInfoMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::AddPDBInfoMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.simple_moves.AddPDBInfoMoverCreator¶

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.simple_moves.AddPDBInfoMoverCreator, : pyrosetta.rosetta.protocols.simple_moves.AddPDBInfoMoverCreator) → pyrosetta.rosetta.protocols.simple_moves.AddPDBInfoMoverCreator¶: C++: protocols::simple_moves::AddPDBInfoMoverCreator::operator=(const class protocols::simple_moves::AddPDBInfoMoverCreator &) –> class protocols::simple_moves::AddPDBInfoMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.simple_moves.AddPDBInfoMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::AddPDBInfoMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.simple_moves.AddPDBInfoMoverCreator) → str¶: C++: protocols::simple_moves::AddPDBInfoMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.simple_moves.AddPDBInfoMoverCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::AddPDBInfoMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.simple_moves.AddResidueCouplingConstraint¶

Bases: Mover

The mover is designed to improve the design process by using information from co-evolutionary correlation matrices. These matrices can be created by different methods, e.g. GREMLIN or plmDCA. The matrices get input as tensor of the shape [N, A, N, A] where N is the length of the protein and A is the length of the alphabet (typically 21 amino acids + 1 for gaps).

GRELIN alphabet order: ARNDCQEGHILKMFPSTWYV- plmDCA alphabet order: ACDEFGHIKLMNPQRSTVWY-

The order of the alphabet used can be defined by the user. To access the measure of co-evolution between, e.g., residue 1 (ALA) and residue 2 (ARG) the tensor lookup would be [1, 0, 2, 1] (using the GREMLIN alphabet order). The co-evolution strength is multiplied by a user defined strength factor (default=1) and then added as new term to the scoring function.

apply(self: pyrosetta.rosetta.protocols.simple_moves.AddResidueCouplingConstraint, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::simple_moves::AddResidueCouplingConstraint::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.AddResidueCouplingConstraint, : pyrosetta.rosetta.protocols.simple_moves.AddResidueCouplingConstraint) → pyrosetta.rosetta.protocols.simple_moves.AddResidueCouplingConstraint¶: C++: protocols::simple_moves::AddResidueCouplingConstraint::operator=(const class protocols::simple_moves::AddResidueCouplingConstraint &) –> class protocols::simple_moves::AddResidueCouplingConstraint &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.simple_moves.AddResidueCouplingConstraint) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::AddResidueCouplingConstraint::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶

Generates a new Mover object freshly created with the default ctor.

C++: protocols::moves::Mover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.simple_moves.AddResidueCouplingConstraint) → str¶: C++: protocols::simple_moves::AddResidueCouplingConstraint::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static mover_name() → str¶: C++: protocols::simple_moves::AddResidueCouplingConstraint::mover_name() –> std::string

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.simple_moves.AddResidueCouplingConstraint, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::simple_moves::AddResidueCouplingConstraint::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::AddResidueCouplingConstraint::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.simple_moves.AddResidueCouplingConstraintCreator¶

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.simple_moves.AddResidueCouplingConstraintCreator, : pyrosetta.rosetta.protocols.simple_moves.AddResidueCouplingConstraintCreator) → pyrosetta.rosetta.protocols.simple_moves.AddResidueCouplingConstraintCreator¶: C++: protocols::simple_moves::AddResidueCouplingConstraintCreator::operator=(const class protocols::simple_moves::AddResidueCouplingConstraintCreator &) –> class protocols::simple_moves::AddResidueCouplingConstraintCreator &

create_mover(self: pyrosetta.rosetta.protocols.simple_moves.AddResidueCouplingConstraintCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::AddResidueCouplingConstraintCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.simple_moves.AddResidueCouplingConstraintCreator) → str¶: C++: protocols::simple_moves::AddResidueCouplingConstraintCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.simple_moves.AddResidueCouplingConstraintCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::AddResidueCouplingConstraintCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.simple_moves.AddResidueLabelMover¶

Bases: Mover

apply(self: pyrosetta.rosetta.protocols.simple_moves.AddResidueLabelMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::simple_moves::AddResidueLabelMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.AddResidueLabelMover, : pyrosetta.rosetta.protocols.simple_moves.AddResidueLabelMover) → pyrosetta.rosetta.protocols.simple_moves.AddResidueLabelMover¶: C++: protocols::simple_moves::AddResidueLabelMover::operator=(const class protocols::simple_moves::AddResidueLabelMover &) –> class protocols::simple_moves::AddResidueLabelMover &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.simple_moves.AddResidueLabelMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::AddResidueLabelMover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.simple_moves.AddResidueLabelMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::AddResidueLabelMover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.simple_moves.AddResidueLabelMover) → str¶: C++: protocols::simple_moves::AddResidueLabelMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.simple_moves.AddResidueLabelMover, tag: pyrosetta.rosetta.utility.tag.Tag, data_map: pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::simple_moves::AddResidueLabelMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.simple_moves.AddResidueLabelMoverCreator¶

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.simple_moves.AddResidueLabelMoverCreator, : pyrosetta.rosetta.protocols.simple_moves.AddResidueLabelMoverCreator) → pyrosetta.rosetta.protocols.simple_moves.AddResidueLabelMoverCreator¶: C++: protocols::simple_moves::AddResidueLabelMoverCreator::operator=(const class protocols::simple_moves::AddResidueLabelMoverCreator &) –> class protocols::simple_moves::AddResidueLabelMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.simple_moves.AddResidueLabelMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::AddResidueLabelMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.simple_moves.AddResidueLabelMoverCreator) → str¶: C++: protocols::simple_moves::AddResidueLabelMoverCreator::keyname() const –> std::string

static mover_name() → str¶: C++: protocols::simple_moves::AddResidueLabelMoverCreator::mover_name() –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.simple_moves.AddResidueLabelMoverCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::AddResidueLabelMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.simple_moves.AddSapConstraintMover¶

Bases: Mover

Adds variant types to selected residues

apply(self: pyrosetta.rosetta.protocols.simple_moves.AddSapConstraintMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::simple_moves::AddSapConstraintMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.AddSapConstraintMover, ot: pyrosetta.rosetta.protocols.simple_moves.AddSapConstraintMover) → pyrosetta.rosetta.protocols.simple_moves.AddSapConstraintMover¶: C++: protocols::simple_moves::AddSapConstraintMover::operator=(const class protocols::simple_moves::AddSapConstraintMover &) –> class protocols::simple_moves::AddSapConstraintMover &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.simple_moves.AddSapConstraintMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::AddSapConstraintMover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.simple_moves.AddSapConstraintMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::AddSapConstraintMover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.simple_moves.AddSapConstraintMover) → str¶: C++: protocols::simple_moves::AddSapConstraintMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static mover_name() → str¶: C++: protocols::simple_moves::AddSapConstraintMover::mover_name() –> std::string

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.simple_moves.AddSapConstraintMover, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::simple_moves::AddSapConstraintMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::AddSapConstraintMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_full_accuracy_when_scoring(self: pyrosetta.rosetta.protocols.simple_moves.AddSapConstraintMover, full_accuracy: bool) → None¶: C++: protocols::simple_moves::AddSapConstraintMover::set_full_accuracy_when_scoring(bool) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_name(self: pyrosetta.rosetta.protocols.simple_moves.AddSapConstraintMover, name: str) → None¶: C++: protocols::simple_moves::AddSapConstraintMover::set_name(const std::string &) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_packing_correction(self: pyrosetta.rosetta.protocols.simple_moves.AddSapConstraintMover, correction: float) → None¶: C++: protocols::simple_moves::AddSapConstraintMover::set_packing_correction(double) –> void

set_penalty_per_sap(self: pyrosetta.rosetta.protocols.simple_moves.AddSapConstraintMover, penalty: float) → None¶: C++: protocols::simple_moves::AddSapConstraintMover::set_penalty_per_sap(double) –> void

set_sap_calculate_selector(self: pyrosetta.rosetta.protocols.simple_moves.AddSapConstraintMover, selector_in: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) → None¶: C++: protocols::simple_moves::AddSapConstraintMover::set_sap_calculate_selector(const class std::shared_ptr<const class core::select::residue_selector::ResidueSelector> &) –> void

set_sap_goal(self: pyrosetta.rosetta.protocols.simple_moves.AddSapConstraintMover, goal: float) → None¶: C++: protocols::simple_moves::AddSapConstraintMover::set_sap_goal(double) –> void

set_sap_lb_goal(self: pyrosetta.rosetta.protocols.simple_moves.AddSapConstraintMover, goal: float) → None¶: C++: protocols::simple_moves::AddSapConstraintMover::set_sap_lb_goal(double) –> void

set_sasa_selector(self: pyrosetta.rosetta.protocols.simple_moves.AddSapConstraintMover, selector_in: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) → None¶: C++: protocols::simple_moves::AddSapConstraintMover::set_sasa_selector(const class std::shared_ptr<const class core::select::residue_selector::ResidueSelector> &) –> void

set_score_selector(self: pyrosetta.rosetta.protocols.simple_moves.AddSapConstraintMover, selector_in: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) → None¶

Set the ResidueSelector used by this mover.

C++: protocols::simple_moves::AddSapConstraintMover::set_score_selector(const class std::shared_ptr<const class core::select::residue_selector::ResidueSelector> &) –> void

set_speed(self: pyrosetta.rosetta.protocols.simple_moves.AddSapConstraintMover, speed: str) → None¶: C++: protocols::simple_moves::AddSapConstraintMover::set_speed(const std::string &) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.simple_moves.AddSapConstraintMoverCreator¶

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.simple_moves.AddSapConstraintMoverCreator, : pyrosetta.rosetta.protocols.simple_moves.AddSapConstraintMoverCreator) → pyrosetta.rosetta.protocols.simple_moves.AddSapConstraintMoverCreator¶: C++: protocols::simple_moves::AddSapConstraintMoverCreator::operator=(const class protocols::simple_moves::AddSapConstraintMoverCreator &) –> class protocols::simple_moves::AddSapConstraintMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.simple_moves.AddSapConstraintMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::AddSapConstraintMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.simple_moves.AddSapConstraintMoverCreator) → str¶: C++: protocols::simple_moves::AddSapConstraintMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.simple_moves.AddSapConstraintMoverCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::AddSapConstraintMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.simple_moves.AddSapMathConstraintMover¶

Bases: Mover

Adds variant types to selected residues

add_constraint(self: pyrosetta.rosetta.protocols.simple_moves.AddSapMathConstraintMover, weight: float, name: str) → None¶: C++: protocols::simple_moves::AddSapMathConstraintMover::add_constraint(double, const std::string &) –> void

apply(self: pyrosetta.rosetta.protocols.simple_moves.AddSapMathConstraintMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::simple_moves::AddSapMathConstraintMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.AddSapMathConstraintMover, ot: pyrosetta.rosetta.protocols.simple_moves.AddSapMathConstraintMover) → pyrosetta.rosetta.protocols.simple_moves.AddSapMathConstraintMover¶: C++: protocols::simple_moves::AddSapMathConstraintMover::operator=(const class protocols::simple_moves::AddSapMathConstraintMover &) –> class protocols::simple_moves::AddSapMathConstraintMover &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.simple_moves.AddSapMathConstraintMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::AddSapMathConstraintMover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.simple_moves.AddSapMathConstraintMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::AddSapMathConstraintMover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.simple_moves.AddSapMathConstraintMover) → str¶: C++: protocols::simple_moves::AddSapMathConstraintMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static mover_name() → str¶: C++: protocols::simple_moves::AddSapMathConstraintMover::mover_name() –> std::string

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.simple_moves.AddSapMathConstraintMover, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::simple_moves::AddSapMathConstraintMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::AddSapMathConstraintMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_lower_bound(self: pyrosetta.rosetta.protocols.simple_moves.AddSapMathConstraintMover, lower: float) → None¶: C++: protocols::simple_moves::AddSapMathConstraintMover::set_lower_bound(double) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_penalty_per_unit(self: pyrosetta.rosetta.protocols.simple_moves.AddSapMathConstraintMover, penalty: float) → None¶: C++: protocols::simple_moves::AddSapMathConstraintMover::set_penalty_per_unit(double) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

set_upper_bound(self: pyrosetta.rosetta.protocols.simple_moves.AddSapMathConstraintMover, upper: float) → None¶: C++: protocols::simple_moves::AddSapMathConstraintMover::set_upper_bound(double) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.simple_moves.AddSapMathConstraintMoverCreator¶

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.simple_moves.AddSapMathConstraintMoverCreator, : pyrosetta.rosetta.protocols.simple_moves.AddSapMathConstraintMoverCreator) → pyrosetta.rosetta.protocols.simple_moves.AddSapMathConstraintMoverCreator¶: C++: protocols::simple_moves::AddSapMathConstraintMoverCreator::operator=(const class protocols::simple_moves::AddSapMathConstraintMoverCreator &) –> class protocols::simple_moves::AddSapMathConstraintMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.simple_moves.AddSapMathConstraintMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::AddSapMathConstraintMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.simple_moves.AddSapMathConstraintMoverCreator) → str¶: C++: protocols::simple_moves::AddSapMathConstraintMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.simple_moves.AddSapMathConstraintMoverCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::AddSapMathConstraintMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.simple_moves.AlignChainMover¶

Bases: Mover

Align a chain in the working pose to a chain. CA superposition

source_chain: the chain number in the working pose. 0 means the entire pose. target_chain: the chain number in the target pose. 0 means the entire pose. **target and source chains must have the same length of residues.

apply(self: pyrosetta.rosetta.protocols.simple_moves.AlignChainMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::simple_moves::AlignChainMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.AlignChainMover, : pyrosetta.rosetta.protocols.simple_moves.AlignChainMover) → pyrosetta.rosetta.protocols.simple_moves.AlignChainMover¶: C++: protocols::simple_moves::AlignChainMover::operator=(const class protocols::simple_moves::AlignChainMover &) –> class protocols::simple_moves::AlignChainMover &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.simple_moves.AlignChainMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::AlignChainMover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.simple_moves.AlignChainMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::AlignChainMover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.simple_moves.AlignChainMover) → str¶: C++: protocols::simple_moves::AlignChainMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static mover_name() → str¶: C++: protocols::simple_moves::AlignChainMover::mover_name() –> std::string

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.simple_moves.AlignChainMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::simple_moves::AlignChainMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

pose(*args, **kwargs)¶

Overloaded function.

pose(self: pyrosetta.rosetta.protocols.simple_moves.AlignChainMover) -> pyrosetta.rosetta.core.pose.Pose

C++: protocols::simple_moves::AlignChainMover::pose() const –> class std::shared_ptr<class core::pose::Pose>

pose(self: pyrosetta.rosetta.protocols.simple_moves.AlignChainMover, pose: pyrosetta.rosetta.core.pose.Pose) -> None

C++: protocols::simple_moves::AlignChainMover::pose(class std::shared_ptr<class core::pose::Pose>) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::AlignChainMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

source_chain(*args, **kwargs)¶

Overloaded function.

source_chain(self: pyrosetta.rosetta.protocols.simple_moves.AlignChainMover) -> int

C++: protocols::simple_moves::AlignChainMover::source_chain() const –> unsigned long

source_chain(self: pyrosetta.rosetta.protocols.simple_moves.AlignChainMover, s: int) -> None

C++: protocols::simple_moves::AlignChainMover::source_chain(const unsigned long) –> void

target_chain(*args, **kwargs)¶

Overloaded function.

target_chain(self: pyrosetta.rosetta.protocols.simple_moves.AlignChainMover) -> int

C++: protocols::simple_moves::AlignChainMover::target_chain() const –> unsigned long

target_chain(self: pyrosetta.rosetta.protocols.simple_moves.AlignChainMover, s: int) -> None

C++: protocols::simple_moves::AlignChainMover::target_chain(const unsigned long) –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.simple_moves.AlignChainMoverCreator¶

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.simple_moves.AlignChainMoverCreator, : pyrosetta.rosetta.protocols.simple_moves.AlignChainMoverCreator) → pyrosetta.rosetta.protocols.simple_moves.AlignChainMoverCreator¶: C++: protocols::simple_moves::AlignChainMoverCreator::operator=(const class protocols::simple_moves::AlignChainMoverCreator &) –> class protocols::simple_moves::AlignChainMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.simple_moves.AlignChainMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::AlignChainMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.simple_moves.AlignChainMoverCreator) → str¶: C++: protocols::simple_moves::AlignChainMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.simple_moves.AlignChainMoverCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::AlignChainMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.simple_moves.AtomHash¶

Bases: pybind11_object

add_point(self: pyrosetta.rosetta.protocols.simple_moves.AtomHash, residx: int, xyz: pyrosetta.rosetta.numeric.xyzVector_double_t) → None¶: C++: protocols::simple_moves::AtomHash::add_point(unsigned long, class numeric::xyzVector<double>) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.AtomHash, : pyrosetta.rosetta.protocols.simple_moves.AtomHash) → pyrosetta.rosetta.protocols.simple_moves.AtomHash¶: C++: protocols::simple_moves::AtomHash::operator=(const class protocols::simple_moves::AtomHash &) –> class protocols::simple_moves::AtomHash &

get_neighborcount(self: pyrosetta.rosetta.protocols.simple_moves.AtomHash, xyz: pyrosetta.rosetta.numeric.xyzVector_double_t, dlim: float) → int¶: C++: protocols::simple_moves::AtomHash::get_neighborcount(class numeric::xyzVector<double>, double) –> unsigned long

npoints(self: pyrosetta.rosetta.protocols.simple_moves.AtomHash) → int¶: C++: protocols::simple_moves::AtomHash::npoints() –> int

reset_and_get_clusters(self: pyrosetta.rosetta.protocols.simple_moves.AtomHash, clusters: pyrosetta.rosetta.utility.vector1_utility_vector1_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t, dredundant: float, dcluster: float) → None¶: C++: protocols::simple_moves::AtomHash::reset_and_get_clusters(class utility::vector1<class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > >, class std::allocator<class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > > > > &, double, double) –> void

trim_to_heterogeneous_clusters(self: pyrosetta.rosetta.protocols.simple_moves.AtomHash, dlim: float) → None¶: C++: protocols::simple_moves::AtomHash::trim_to_heterogeneous_clusters(double) –> void

class pyrosetta.rosetta.protocols.simple_moves.AtomHashNode¶

Bases: pybind11_object

property idx¶

property residx¶

property xyz¶

class pyrosetta.rosetta.protocols.simple_moves.BBConRotMover¶

Bases: BBGaussianMover

apply(self: pyrosetta.rosetta.protocols.simple_moves.BBConRotMover, : pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::simple_moves::BBConRotMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.BBConRotMover, : pyrosetta.rosetta.protocols.simple_moves.BBConRotMover) → pyrosetta.rosetta.protocols.simple_moves.BBConRotMover¶: C++: protocols::simple_moves::BBConRotMover::operator=(const class protocols::simple_moves::BBConRotMover &) –> class protocols::simple_moves::BBConRotMover &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::BBGaussianMover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

factorA(self: pyrosetta.rosetta.protocols.simple_moves.BBConRotMover, fA: float) → None¶: C++: protocols::simple_moves::BBConRotMover::factorA(const double) –> void

factorB(self: pyrosetta.rosetta.protocols.simple_moves.BBConRotMover, fB: float) → None¶: C++: protocols::simple_moves::BBConRotMover::factorB(const double) –> void

factorC(self: pyrosetta.rosetta.protocols.simple_moves.BBConRotMover, fC: float) → None¶: C++: protocols::simple_moves::BBConRotMover::factorC(const double) –> void

finalize_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, pose: pyrosetta.rosetta.core.pose.Pose, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover) → None¶

Callback executed after all Monte Carlo trials are completed.

C++: protocols::canonical_sampling::ThermodynamicMover::finalize_simulation(class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover &) –> void

fresh_instance(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶

Generates a new Mover object freshly created with the default ctor.

C++: protocols::moves::Mover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_A(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover) → None¶: C++: protocols::simple_moves::BBGaussianMover::get_A() –> void

get_G(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover) → None¶: C++: protocols::simple_moves::BBGaussianMover::get_G() –> void

get_L_move(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, : pyrosetta.rosetta.core.pose.Pose) → float¶

calculate L matrix and update pose

C++: protocols::simple_moves::BBGaussianMover::get_L_move(class core::pose::Pose &) –> double

get_L_prime(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover) → float¶

calculate L’, update last_proposal_density

C++: protocols::simple_moves::BBGaussianMover::get_L_prime() –> double

get_VdRdPhi(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, : pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::simple_moves::BBGaussianMover::get_VdRdPhi(const class core::pose::Pose &) –> void

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.simple_moves.BBConRotMover) → str¶: C++: protocols::simple_moves::BBConRotMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

init(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover) → None¶: C++: protocols::simple_moves::BBGaussianMover::init() –> void

init_kic_loop(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, looplength: int, mm: pyrosetta.rosetta.core.kinematics.MoveMap) → None¶: C++: protocols::simple_moves::BBGaussianMover::init_kic_loop(unsigned long, class std::shared_ptr<const class core::kinematics::MoveMap>) –> void

initialize_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, pose: pyrosetta.rosetta.core.pose.Pose, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover, cycle: int) → None¶

Callback executed before any Monte Carlo trials are attempted.

C++: protocols::canonical_sampling::ThermodynamicMover::initialize_simulation(class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover &, unsigned long) –> void

is_multi_trial(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → bool¶

Return true if the move performs multiple trials on each apply.

last_inner_score_delta_over_temperature()

metropolis_hastings_mover()

set_metropolis_hastings_mover()

C++: protocols::canonical_sampling::ThermodynamicMover::is_multi_trial() –> bool

last_inner_score_delta_over_temperature(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → float¶

If this is a multi-trial move, return the change in internal

score/temperature caused by the last call to apply().

is_multi_trial()

C++: protocols::canonical_sampling::ThermodynamicMover::last_inner_score_delta_over_temperature() –> double

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover) → float¶

get the ratio of proposal densities for the last move

C++: protocols::simple_moves::BBGaussianMover::last_proposal_density_ratio() –> double

metropolis_hastings_mover(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → pyrosetta.rosetta.std.weak_ptr_protocols_canonical_sampling_MetropolisHastingsMover_t¶

If this is a multi-trial move, return the MetropolisHastingsMover

being used internally.

is_multi_trial()

C++: protocols::canonical_sampling::ThermodynamicMover::metropolis_hastings_mover() –> class std::weak_ptr<class protocols::canonical_sampling::MetropolisHastingsMover>

movemap(*args, **kwargs)¶

Overloaded function.

movemap(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, : pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.core.kinematics.MoveMap

Generates the movemap used by this mover for the given pose

C++: protocols::simple_moves::BBGaussianMover::movemap(const class core::pose::Pose &) const –> class std::shared_ptr<const class core::kinematics::MoveMap>

movemap(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, new_movemap: pyrosetta.rosetta.core.kinematics.MoveMap) -> None

C++: protocols::simple_moves::BBGaussianMover::movemap(class std::shared_ptr<const class core::kinematics::MoveMap>) –> void

movemap_factory(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, new_movemap_factory: pyrosetta.rosetta.core.select.movemap.MoveMapFactory) → None¶

The movemap_factory will be used to generate a movemap, if an explcit one hasn’t already been set.

C++: protocols::simple_moves::BBGaussianMover::movemap_factory(class std::shared_ptr<const class core::select::movemap::MoveMapFactory>) –> void

static mover_name() → str¶: C++: protocols::simple_moves::BBGaussianMover::mover_name() –> std::string

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

observe_after_metropolis(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover) → None¶

Callback executed after the Metropolis criterion is evaluated.

C++: protocols::canonical_sampling::ThermodynamicMover::observe_after_metropolis(const class protocols::canonical_sampling::MetropolisHastingsMover &) –> void

parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.

C++: protocols::moves::Mover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

preserve_detailed_balance(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover) → bool¶

get whether detailed balance is preserved (i.e. no Ramachandran biasing)

C++: protocols::simple_moves::BBGaussianMover::preserve_detailed_balance() const –> bool

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::BBGaussianMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

resize(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, : int, : int, : int) → None¶: C++: protocols::simple_moves::BBGaussianMover::resize(unsigned long, unsigned long, unsigned long) –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_metropolis_hastings_mover(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, metropolis_hastings_mover: pyrosetta.rosetta.std.weak_ptr_protocols_canonical_sampling_MetropolisHastingsMover_t) → None¶

If this is a multi-trial move, set the MetropolisHastingsMover to

be used internally.

is_multi_trial()

C++: protocols::canonical_sampling::ThermodynamicMover::set_metropolis_hastings_mover(class std::weak_ptr<class protocols::canonical_sampling::MetropolisHastingsMover>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_preserve_detailed_balance(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, preserve_detailed_balance: bool) → None¶

set whether detailed balance is preserved (i.e. no Ramachandran biasing)

C++: protocols::simple_moves::BBGaussianMover::set_preserve_detailed_balance(bool) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

torsion_id_ranges(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, : pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_core_id_TorsionID_Range¶

dummy

C++: protocols::simple_moves::BBGaussianMover::torsion_id_ranges(class core::pose::Pose &) –> class utility::vector1<class core::id::TorsionID_Range, class std::allocator<class core::id::TorsionID_Range> >

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

update_counting_last_PDR(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, : float) → None¶: C++: protocols::simple_moves::BBGaussianMover::update_counting_last_PDR(double) –> void

class pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover¶

Bases: Mover

Mover interface to BBDihedralSampler ( 1D ). Samples using BBDihedralSamplers randomly using residues set in the movemap. If multiple samplers are given, will randomly sample on them.

add_sampler(self: pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover, sampler: protocols::simple_moves::bb_sampler::BBDihedralSampler) → None¶

Add a sampler to this mover.

C++: protocols::simple_moves::BBDihedralSamplerMover::add_sampler(class std::shared_ptr<class protocols::simple_moves::bb_sampler::BBDihedralSampler>) –> void

apply(self: pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::simple_moves::BBDihedralSamplerMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover, : pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover) → pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover¶: C++: protocols::simple_moves::BBDihedralSamplerMover::operator=(const class protocols::simple_moves::BBDihedralSamplerMover &) –> class protocols::simple_moves::BBDihedralSamplerMover &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover) → pyrosetta.rosetta.protocols.moves.Mover¶

required in the context of the parser/scripting scheme

C++: protocols::simple_moves::BBDihedralSamplerMover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover) → pyrosetta.rosetta.protocols.moves.Mover¶

required in the context of the parser/scripting scheme

C++: protocols::simple_moves::BBDihedralSamplerMover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover) → str¶: C++: protocols::simple_moves::BBDihedralSamplerMover::get_name() const –> std::string

get_name_of_last_sampler_used(self: pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover) → str¶

Return the name of the last sampler used during the last apply

C++: protocols::simple_moves::BBDihedralSamplerMover::get_name_of_last_sampler_used() –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

parse XML tag (to use this Mover in Rosetta Scripts)

C++: protocols::simple_moves::BBDihedralSamplerMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide the citation.

C++: protocols::simple_moves::BBDihedralSamplerMover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_dihedral_mask(self: pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover, mask: pyrosetta.rosetta.std.map_unsigned_long_utility_vector1_unsigned_long_std_allocator_unsigned_long_t_std_allocator_std_pair_const_unsigned_long_utility_vector1_unsigned_long_std_allocator_unsigned_long_t) → None¶

Limit the torsions that are sampled using a mask.

Mask is a vector of torsions we are allowed to sample at each residue.: NOT every residue must be present - only the ones we need to mask. This helps for carbohydrates, since not every residue has all possible dihedrals, even if we have samplers to use.

C++: protocols::simple_moves::BBDihedralSamplerMover::set_dihedral_mask(class std::map<unsigned long, class utility::vector1<unsigned long, class std::allocator<unsigned long> >, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, class utility::vector1<unsigned long, class std::allocator<unsigned long> > > > >) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_residue_selector(self: pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) → None¶

Sets residues from a residue selector.

C++: protocols::simple_moves::BBDihedralSamplerMover::set_residue_selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

set_sampler(self: pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover, sampler: protocols::simple_moves::bb_sampler::BBDihedralSampler) → None¶

Set a single sampler this mover will use.

C++: protocols::simple_moves::BBDihedralSamplerMover::set_sampler(class std::shared_ptr<class protocols::simple_moves::bb_sampler::BBDihedralSampler>) –> void

set_single_resnum(self: pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover, resnum: int) → None¶

Set a single resnum instead of a movemap.

C++: protocols::simple_moves::BBDihedralSamplerMover::set_single_resnum(unsigned long) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover) -> None
show(self: pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover, output: pyrosetta.rosetta.std.ostream) -> None

C++: protocols::simple_moves::BBDihedralSamplerMover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMoverCreator¶

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMoverCreator, : pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMoverCreator) → pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMoverCreator¶: C++: protocols::simple_moves::BBDihedralSamplerMoverCreator::operator=(const class protocols::simple_moves::BBDihedralSamplerMoverCreator &) –> class protocols::simple_moves::BBDihedralSamplerMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::BBDihedralSamplerMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMoverCreator) → str¶: C++: protocols::simple_moves::BBDihedralSamplerMoverCreator::keyname() const –> std::string

static mover_name() → str¶: C++: protocols::simple_moves::BBDihedralSamplerMoverCreator::mover_name() –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.moves.MoverCreator, xsd: utility::tag::XMLSchemaDefinition) → None¶

Describe the schema for the Mover that this Creator is responsible for

C++: protocols::moves::MoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover¶

Bases: BBGaussianMover

a particular gaussian mover from the original paper

using 8 torsion angles as DOF, 3 atoms (Ca,C,O) as end

apply(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::simple_moves::BBGaussianMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover, : pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover) → pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover¶: C++: protocols::simple_moves::BBG8T3AMover::operator=(const class protocols::simple_moves::BBG8T3AMover &) –> class protocols::simple_moves::BBG8T3AMover &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::BBG8T3AMover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

factorA(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, fA: float) → None¶: C++: protocols::simple_moves::BBGaussianMover::factorA(const double) –> void

factorB(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, fB: float) → None¶: C++: protocols::simple_moves::BBGaussianMover::factorB(const double) –> void

finalize_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, pose: pyrosetta.rosetta.core.pose.Pose, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover) → None¶

Callback executed after all Monte Carlo trials are completed.

C++: protocols::canonical_sampling::ThermodynamicMover::finalize_simulation(class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover &) –> void

fresh_instance(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶

Generates a new Mover object freshly created with the default ctor.

C++: protocols::moves::Mover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_A(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover) → None¶: C++: protocols::simple_moves::BBGaussianMover::get_A() –> void

get_G(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover) → None¶: C++: protocols::simple_moves::BBGaussianMover::get_G() –> void

get_L_move(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, : pyrosetta.rosetta.core.pose.Pose) → float¶

calculate L matrix and update pose

C++: protocols::simple_moves::BBGaussianMover::get_L_move(class core::pose::Pose &) –> double

get_L_prime(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover) → float¶

calculate L’, update last_proposal_density

C++: protocols::simple_moves::BBGaussianMover::get_L_prime() –> double

get_VdRdPhi(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, : pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::simple_moves::BBGaussianMover::get_VdRdPhi(const class core::pose::Pose &) –> void

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover) → str¶: C++: protocols::simple_moves::BBG8T3AMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

init(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover) → None¶: C++: protocols::simple_moves::BBGaussianMover::init() –> void

init_kic_loop(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, looplength: int, mm: pyrosetta.rosetta.core.kinematics.MoveMap) → None¶: C++: protocols::simple_moves::BBGaussianMover::init_kic_loop(unsigned long, class std::shared_ptr<const class core::kinematics::MoveMap>) –> void

initialize_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, pose: pyrosetta.rosetta.core.pose.Pose, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover, cycle: int) → None¶

Callback executed before any Monte Carlo trials are attempted.

C++: protocols::canonical_sampling::ThermodynamicMover::initialize_simulation(class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover &, unsigned long) –> void

is_multi_trial(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → bool¶

Return true if the move performs multiple trials on each apply.

last_inner_score_delta_over_temperature()

metropolis_hastings_mover()

set_metropolis_hastings_mover()

C++: protocols::canonical_sampling::ThermodynamicMover::is_multi_trial() –> bool

last_inner_score_delta_over_temperature(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → float¶

If this is a multi-trial move, return the change in internal

score/temperature caused by the last call to apply().

is_multi_trial()

C++: protocols::canonical_sampling::ThermodynamicMover::last_inner_score_delta_over_temperature() –> double

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover) → float¶

get the ratio of proposal densities for the last move

C++: protocols::simple_moves::BBGaussianMover::last_proposal_density_ratio() –> double

metropolis_hastings_mover(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → pyrosetta.rosetta.std.weak_ptr_protocols_canonical_sampling_MetropolisHastingsMover_t¶

If this is a multi-trial move, return the MetropolisHastingsMover

being used internally.

is_multi_trial()

C++: protocols::canonical_sampling::ThermodynamicMover::metropolis_hastings_mover() –> class std::weak_ptr<class protocols::canonical_sampling::MetropolisHastingsMover>

movemap(*args, **kwargs)¶

Overloaded function.

movemap(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, : pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.core.kinematics.MoveMap

Generates the movemap used by this mover for the given pose

C++: protocols::simple_moves::BBGaussianMover::movemap(const class core::pose::Pose &) const –> class std::shared_ptr<const class core::kinematics::MoveMap>

movemap(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, new_movemap: pyrosetta.rosetta.core.kinematics.MoveMap) -> None

C++: protocols::simple_moves::BBGaussianMover::movemap(class std::shared_ptr<const class core::kinematics::MoveMap>) –> void

movemap_factory(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, new_movemap_factory: pyrosetta.rosetta.core.select.movemap.MoveMapFactory) → None¶

The movemap_factory will be used to generate a movemap, if an explcit one hasn’t already been set.

C++: protocols::simple_moves::BBGaussianMover::movemap_factory(class std::shared_ptr<const class core::select::movemap::MoveMapFactory>) –> void

static mover_name() → str¶: C++: protocols::simple_moves::BBGaussianMover::mover_name() –> std::string

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

observe_after_metropolis(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover) → None¶

Callback executed after the Metropolis criterion is evaluated.

C++: protocols::canonical_sampling::ThermodynamicMover::observe_after_metropolis(const class protocols::canonical_sampling::MetropolisHastingsMover &) –> void

parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.

C++: protocols::moves::Mover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

preserve_detailed_balance(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover) → bool¶

get whether detailed balance is preserved (i.e. no Ramachandran biasing)

C++: protocols::simple_moves::BBGaussianMover::preserve_detailed_balance() const –> bool

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::BBGaussianMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

resize(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, : int, : int, : int) → None¶: C++: protocols::simple_moves::BBGaussianMover::resize(unsigned long, unsigned long, unsigned long) –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_metropolis_hastings_mover(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, metropolis_hastings_mover: pyrosetta.rosetta.std.weak_ptr_protocols_canonical_sampling_MetropolisHastingsMover_t) → None¶

If this is a multi-trial move, set the MetropolisHastingsMover to

be used internally.

is_multi_trial()

C++: protocols::canonical_sampling::ThermodynamicMover::set_metropolis_hastings_mover(class std::weak_ptr<class protocols::canonical_sampling::MetropolisHastingsMover>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_preserve_detailed_balance(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, preserve_detailed_balance: bool) → None¶

set whether detailed balance is preserved (i.e. no Ramachandran biasing)

C++: protocols::simple_moves::BBGaussianMover::set_preserve_detailed_balance(bool) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

torsion_id_ranges(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, : pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_core_id_TorsionID_Range¶

dummy

C++: protocols::simple_moves::BBGaussianMover::torsion_id_ranges(class core::pose::Pose &) –> class utility::vector1<class core::id::TorsionID_Range, class std::allocator<class core::id::TorsionID_Range> >

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

update_counting_last_PDR(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, : float) → None¶: C++: protocols::simple_moves::BBGaussianMover::update_counting_last_PDR(double) –> void

class pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover¶

Bases: ThermodynamicMover

the basic class for implementing Gaussian Perturbation of bb

“Monte Carlo update for chain molecules: Biased Gaussian steps in torsional space” “The Journal of Chemical Physics, Vol. 114, No. 18. (2001), pp. 8154-8158.” Two steps for perturbing the backbone and keeping the geometry constrain Step 1: Gaussian Biased steps in torsional space: the end atoms of the moving segment should be choosen by user and to keep the geometry constrain(6), the DOF of the moving segment > 6 Step 2: “pivot” update the bb conformation, or followed by a chainclosure method (BBConRot)

apply(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::simple_moves::BBGaussianMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, : pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover) → pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover¶: C++: protocols::simple_moves::BBGaussianMover::operator=(const class protocols::simple_moves::BBGaussianMover &) –> class protocols::simple_moves::BBGaussianMover &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::BBGaussianMover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

factorA(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, fA: float) → None¶: C++: protocols::simple_moves::BBGaussianMover::factorA(const double) –> void

factorB(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, fB: float) → None¶: C++: protocols::simple_moves::BBGaussianMover::factorB(const double) –> void

finalize_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, pose: pyrosetta.rosetta.core.pose.Pose, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover) → None¶

Callback executed after all Monte Carlo trials are completed.

C++: protocols::canonical_sampling::ThermodynamicMover::finalize_simulation(class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover &) –> void

fresh_instance(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶

Generates a new Mover object freshly created with the default ctor.

C++: protocols::moves::Mover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_A(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover) → None¶: C++: protocols::simple_moves::BBGaussianMover::get_A() –> void

get_G(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover) → None¶: C++: protocols::simple_moves::BBGaussianMover::get_G() –> void

get_L_move(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, : pyrosetta.rosetta.core.pose.Pose) → float¶

calculate L matrix and update pose

C++: protocols::simple_moves::BBGaussianMover::get_L_move(class core::pose::Pose &) –> double

get_L_prime(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover) → float¶

calculate L’, update last_proposal_density

C++: protocols::simple_moves::BBGaussianMover::get_L_prime() –> double

get_VdRdPhi(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, : pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::simple_moves::BBGaussianMover::get_VdRdPhi(const class core::pose::Pose &) –> void

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover) → str¶: C++: protocols::simple_moves::BBGaussianMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

init(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover) → None¶: C++: protocols::simple_moves::BBGaussianMover::init() –> void

init_kic_loop(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, looplength: int, mm: pyrosetta.rosetta.core.kinematics.MoveMap) → None¶: C++: protocols::simple_moves::BBGaussianMover::init_kic_loop(unsigned long, class std::shared_ptr<const class core::kinematics::MoveMap>) –> void

initialize_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, pose: pyrosetta.rosetta.core.pose.Pose, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover, cycle: int) → None¶

Callback executed before any Monte Carlo trials are attempted.

C++: protocols::canonical_sampling::ThermodynamicMover::initialize_simulation(class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover &, unsigned long) –> void

is_multi_trial(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → bool¶

Return true if the move performs multiple trials on each apply.

last_inner_score_delta_over_temperature()

metropolis_hastings_mover()

set_metropolis_hastings_mover()

C++: protocols::canonical_sampling::ThermodynamicMover::is_multi_trial() –> bool

last_inner_score_delta_over_temperature(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → float¶

If this is a multi-trial move, return the change in internal

score/temperature caused by the last call to apply().

is_multi_trial()

C++: protocols::canonical_sampling::ThermodynamicMover::last_inner_score_delta_over_temperature() –> double

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover) → float¶

get the ratio of proposal densities for the last move

C++: protocols::simple_moves::BBGaussianMover::last_proposal_density_ratio() –> double

metropolis_hastings_mover(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → pyrosetta.rosetta.std.weak_ptr_protocols_canonical_sampling_MetropolisHastingsMover_t¶

If this is a multi-trial move, return the MetropolisHastingsMover

being used internally.

is_multi_trial()

C++: protocols::canonical_sampling::ThermodynamicMover::metropolis_hastings_mover() –> class std::weak_ptr<class protocols::canonical_sampling::MetropolisHastingsMover>

movemap(*args, **kwargs)¶

Overloaded function.

movemap(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, : pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.core.kinematics.MoveMap

Generates the movemap used by this mover for the given pose

C++: protocols::simple_moves::BBGaussianMover::movemap(const class core::pose::Pose &) const –> class std::shared_ptr<const class core::kinematics::MoveMap>

movemap(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, new_movemap: pyrosetta.rosetta.core.kinematics.MoveMap) -> None

C++: protocols::simple_moves::BBGaussianMover::movemap(class std::shared_ptr<const class core::kinematics::MoveMap>) –> void

movemap_factory(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, new_movemap_factory: pyrosetta.rosetta.core.select.movemap.MoveMapFactory) → None¶

The movemap_factory will be used to generate a movemap, if an explcit one hasn’t already been set.

C++: protocols::simple_moves::BBGaussianMover::movemap_factory(class std::shared_ptr<const class core::select::movemap::MoveMapFactory>) –> void

static mover_name() → str¶: C++: protocols::simple_moves::BBGaussianMover::mover_name() –> std::string

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

observe_after_metropolis(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover) → None¶

Callback executed after the Metropolis criterion is evaluated.

C++: protocols::canonical_sampling::ThermodynamicMover::observe_after_metropolis(const class protocols::canonical_sampling::MetropolisHastingsMover &) –> void

parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.

C++: protocols::moves::Mover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

preserve_detailed_balance(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover) → bool¶

get whether detailed balance is preserved (i.e. no Ramachandran biasing)

C++: protocols::simple_moves::BBGaussianMover::preserve_detailed_balance() const –> bool

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::BBGaussianMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

resize(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, : int, : int, : int) → None¶: C++: protocols::simple_moves::BBGaussianMover::resize(unsigned long, unsigned long, unsigned long) –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_metropolis_hastings_mover(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, metropolis_hastings_mover: pyrosetta.rosetta.std.weak_ptr_protocols_canonical_sampling_MetropolisHastingsMover_t) → None¶

If this is a multi-trial move, set the MetropolisHastingsMover to

be used internally.

is_multi_trial()

C++: protocols::canonical_sampling::ThermodynamicMover::set_metropolis_hastings_mover(class std::weak_ptr<class protocols::canonical_sampling::MetropolisHastingsMover>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_preserve_detailed_balance(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, preserve_detailed_balance: bool) → None¶

set whether detailed balance is preserved (i.e. no Ramachandran biasing)

C++: protocols::simple_moves::BBGaussianMover::set_preserve_detailed_balance(bool) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

torsion_id_ranges(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, : pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_core_id_TorsionID_Range¶

dummy

C++: protocols::simple_moves::BBGaussianMover::torsion_id_ranges(class core::pose::Pose &) –> class utility::vector1<class core::id::TorsionID_Range, class std::allocator<class core::id::TorsionID_Range> >

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

update_counting_last_PDR(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, : float) → None¶: C++: protocols::simple_moves::BBGaussianMover::update_counting_last_PDR(double) –> void

class pyrosetta.rosetta.protocols.simple_moves.BBGaussianMoverCreator¶

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMoverCreator, : pyrosetta.rosetta.protocols.simple_moves.BBGaussianMoverCreator) → pyrosetta.rosetta.protocols.simple_moves.BBGaussianMoverCreator¶: C++: protocols::simple_moves::BBGaussianMoverCreator::operator=(const class protocols::simple_moves::BBGaussianMoverCreator &) –> class protocols::simple_moves::BBGaussianMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::BBGaussianMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMoverCreator) → str¶: C++: protocols::simple_moves::BBGaussianMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMoverCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::BBGaussianMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.simple_moves.BackboneMover¶

Bases: ThermodynamicMover

BackboneMover class has elements of the MC temperature to do repetitions of bb moves (small, shear, wobble, etc.).

angle_max(*args, **kwargs)¶

Overloaded function.

angle_max(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, angle: float) -> None

Set the maximum angle of perturbation, independent of

secondary structure. new_angle = old_angle +/- ( angle_max/2 )

Example:: bbmover.angle_max(25)
See also:: ShearMover SmallMover

C++: protocols::simple_moves::BackboneMover::angle_max(const double) –> void

angle_max(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, type: str, angle: float) -> None

Sets the max angle of perturbation for residues with <type>

secondary structure. (<type> must be ‘H’, ‘E’, or ‘L’.) new_angle = old_angle +/- ( angle_max/2 )

Example:: bbmover.angle_max(‘H’, 25)
See also:: ShearMover SmallMover

C++: protocols::simple_moves::BackboneMover::angle_max(const char, const double) –> void

angle_max(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, angle_max_in: pyrosetta.rosetta.std.map_char_double) -> None

Sets the max angle of perturbation, for secondary structures: ‘H’, ‘E’, and ‘L’. new_angle = old_angle +/- ( angle_max/2 )

C++: protocols::simple_moves::BackboneMover::angle_max(class std::map<char, double, struct std::less<char>, class std::allocator<struct std::pair<const char, double> > >) –> void

apply(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, : pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::simple_moves::BackboneMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, : pyrosetta.rosetta.protocols.simple_moves.BackboneMover) → pyrosetta.rosetta.protocols.simple_moves.BackboneMover¶: C++: protocols::simple_moves::BackboneMover::operator=(const class protocols::simple_moves::BackboneMover &) –> class protocols::simple_moves::BackboneMover &

static backbone_mover_complex_type_namer(tag_name: str) → str¶: C++: protocols::simple_moves::BackboneMover::backbone_mover_complex_type_namer(std::string) –> std::string

check_rama(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover) → bool¶: C++: protocols::simple_moves::BackboneMover::check_rama() –> bool

clear(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover) → None¶: C++: protocols::simple_moves::BackboneMover::clear() –> void

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶

Return a clone of the Mover object.

C++: protocols::moves::Mover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

static complex_type_generator_for_backbone_mover(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → pyrosetta.rosetta.utility.tag.XMLSchemaComplexTypeGenerator¶: C++: protocols::simple_moves::BackboneMover::complex_type_generator_for_backbone_mover(class utility::tag::XMLSchemaDefinition &) –> class std::shared_ptr<class utility::tag::XMLSchemaComplexTypeGenerator>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

finalize_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, pose: pyrosetta.rosetta.core.pose.Pose, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover) → None¶

Callback executed after all Monte Carlo trials are completed.

C++: protocols::canonical_sampling::ThermodynamicMover::finalize_simulation(class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover &) –> void

fresh_instance(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶

Generates a new Mover object freshly created with the default ctor.

C++: protocols::moves::Mover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_angle_max(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, type: str) → float¶

Gets the max angle of perturbation for residues with <type>

secondary structure. (<type> must be ‘H’, ‘E’, or ‘L’.)

Example:: bbmover.angle_max(‘H’)
See also:: ShearMover SmallMover

C++: protocols::simple_moves::BackboneMover::get_angle_max(const char) const –> double

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover) → str¶: C++: protocols::simple_moves::BackboneMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

initialize_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, pose: pyrosetta.rosetta.core.pose.Pose, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover, cycle: int) → None¶

Callback executed before any Monte Carlo trials are attempted.

C++: protocols::canonical_sampling::ThermodynamicMover::initialize_simulation(class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover &, unsigned long) –> void

is_multi_trial(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → bool¶

Return true if the move performs multiple trials on each apply.

last_inner_score_delta_over_temperature()

metropolis_hastings_mover()

set_metropolis_hastings_mover()

C++: protocols::canonical_sampling::ThermodynamicMover::is_multi_trial() –> bool

last_inner_score_delta_over_temperature(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → float¶

If this is a multi-trial move, return the change in internal

score/temperature caused by the last call to apply().

is_multi_trial()

C++: protocols::canonical_sampling::ThermodynamicMover::last_inner_score_delta_over_temperature() –> double

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → float¶

Return the proposal density ratio for last apply method.

C++: protocols::canonical_sampling::ThermodynamicMover::last_proposal_density_ratio() –> double

make_move(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, : pyrosetta.rosetta.core.pose.Pose) → bool¶: C++: protocols::simple_moves::BackboneMover::make_move(class core::pose::Pose &) –> bool

metropolis_hastings_mover(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → pyrosetta.rosetta.std.weak_ptr_protocols_canonical_sampling_MetropolisHastingsMover_t¶

If this is a multi-trial move, return the MetropolisHastingsMover

being used internally.

is_multi_trial()

C++: protocols::canonical_sampling::ThermodynamicMover::metropolis_hastings_mover() –> class std::weak_ptr<class protocols::canonical_sampling::MetropolisHastingsMover>

move_with_rama(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, pose: pyrosetta.rosetta.core.pose.Pose) → bool¶: C++: protocols::simple_moves::BackboneMover::move_with_rama(class core::pose::Pose &) –> bool

move_with_scorefxn(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, pose: pyrosetta.rosetta.core.pose.Pose) → bool¶: C++: protocols::simple_moves::BackboneMover::move_with_scorefxn(class core::pose::Pose &) –> bool

movemap(*args, **kwargs)¶

Overloaded function.

movemap(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, new_movemap: pyrosetta.rosetta.core.kinematics.MoveMap) -> None

C++: protocols::simple_moves::BackboneMover::movemap(class std::shared_ptr<class core::kinematics::MoveMap>) –> void

movemap(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, pose: pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.core.kinematics.MoveMap

Get the movemap for this pose.

C++: protocols::simple_moves::BackboneMover::movemap(const class core::pose::Pose &) –> class std::shared_ptr<const class core::kinematics::MoveMap>

movemap_factory(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, new_movemap_factory: pyrosetta.rosetta.core.select.movemap.MoveMapFactory) → None¶: C++: protocols::simple_moves::BackboneMover::movemap_factory(class std::shared_ptr<const class core::select::movemap::MoveMapFactory>) –> void

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

nmoves(*args, **kwargs)¶

Overloaded function.

nmoves(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, nmoves_in: int) -> None

C++: protocols::simple_moves::BackboneMover::nmoves(const unsigned long) –> void

nmoves(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover) -> int

C++: protocols::simple_moves::BackboneMover::nmoves() const –> unsigned long

observe_after_metropolis(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover) → None¶

Callback executed after the Metropolis criterion is evaluated.

C++: protocols::canonical_sampling::ThermodynamicMover::observe_after_metropolis(const class protocols::canonical_sampling::MetropolisHastingsMover &) –> void

parse_my_tag(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::simple_moves::BackboneMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

preserve_detailed_balance(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover) → bool¶

get whether detailed balance is preserved (i.e. no Ramachandran biasing)

C++: protocols::simple_moves::BackboneMover::preserve_detailed_balance() const –> bool

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

scorefxn(*args, **kwargs)¶

Overloaded function.

scorefxn(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover) -> pyrosetta.rosetta.core.scoring.ScoreFunction

If set, this scorefunction will be used instead of the original rama method (default = not set).

C++: protocols::simple_moves::BackboneMover::scorefxn() const –> class std::shared_ptr<class core::scoring::ScoreFunction>

scorefxn(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None

C++: protocols::simple_moves::BackboneMover::scorefxn(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void

selector(*args, **kwargs)¶

Overloaded function.

selector(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover) -> pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

Return the residue selector that can be used to dynamically select residues to perturb: at runtime.

C++: protocols::simple_moves::BackboneMover::selector() const –> class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>

selector(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) -> None

C++: protocols::simple_moves::BackboneMover::selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

set_angles(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, : float) → None¶: C++: protocols::simple_moves::BackboneMover::set_angles(double) –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_metropolis_hastings_mover(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, metropolis_hastings_mover: pyrosetta.rosetta.std.weak_ptr_protocols_canonical_sampling_MetropolisHastingsMover_t) → None¶

If this is a multi-trial move, set the MetropolisHastingsMover to

be used internally.

is_multi_trial()

C++: protocols::canonical_sampling::ThermodynamicMover::set_metropolis_hastings_mover(class std::weak_ptr<class protocols::canonical_sampling::MetropolisHastingsMover>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_preserve_detailed_balance(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, preserve_detailed_balance: bool) → None¶

set whether detailed balance is preserved (i.e. no Ramachandran biasing)

C++: protocols::simple_moves::BackboneMover::set_preserve_detailed_balance(bool) –> void

set_residue_selector(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) → None¶

Set the ResidueSelector that this mover will use.

Clones the input.

C++: protocols::simple_moves::BackboneMover::set_residue_selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

set_warn_empty_list(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, warn_empty: bool) → None¶

Set to warn of an empty setup list. Default true.

C++: protocols::simple_moves::BackboneMover::set_warn_empty_list(bool) –> void

setup_list(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, : pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::simple_moves::BackboneMover::setup_list(class core::pose::Pose &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover) -> None
show(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, output: pyrosetta.rosetta.std.ostream) -> None

C++: protocols::simple_moves::BackboneMover::show(std::ostream &) const –> void

temperature(*args, **kwargs)¶

Overloaded function.

temperature(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, temperature_in: float) -> None

C++: protocols::simple_moves::BackboneMover::temperature(const double) –> void

temperature(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover) -> float

C++: protocols::simple_moves::BackboneMover::temperature() const –> double

test_move(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, : pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::simple_moves::BackboneMover::test_move(class core::pose::Pose &) –> void

torsion_id_ranges(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_core_id_TorsionID_Range¶

Return a list specifying which torsions may be perturbed by

apply(), and the in what range each perturbation may be.

This method should probably not be pure virtual, and in fact should probably not even exist. I searched most of the codebase, and could only find it being used in one pilot app. It is also a somewhat difficult method to write, which means that most of the implementations are either untested or no-ops. It might be better to remove the method altogether and implement it on a class-by-class basis as necessary.

C++: protocols::canonical_sampling::ThermodynamicMover::torsion_id_ranges(class core::pose::Pose &) –> class utility::vector1<class core::id::TorsionID_Range, class std::allocator<class core::id::TorsionID_Range> >

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover¶

Bases: Mover

ChainSplitMover splits a pose into two chains given a cutpoint. This may be necessary for evaluating a domain interface using classes such as the InterfaceAnalyzerMover

apply(self: pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::simple_moves::ChainSplitMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover, : pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover) → pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover¶: C++: protocols::simple_moves::ChainSplitMover::operator=(const class protocols::simple_moves::ChainSplitMover &) –> class protocols::simple_moves::ChainSplitMover &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::ChainSplitMover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::ChainSplitMover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover) → str¶: C++: protocols::simple_moves::ChainSplitMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.

C++: protocols::moves::Mover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover¶

Bases: MoverApplyingMover

Basic mover used primarily for setting up atomic protocols, especially in generator functions.

As the Topology Broker system includes more claims and is more widely adopted, This should not be used in favor of the Broker system.

Holds the Pose’s original FoldTree

Applies its ChangeFoldTreeMover

Applies its Main mover

Returns the Pose’s original FoldTree

apply(self: pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Holds the Pose’s original FoldTree

Applies the ChangeFoldTreeMover

Applies the Main mover

Returns the Pose’s original FoldTree

C++: protocols::simple_moves::ChangeAndResetFoldTreeMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover, : pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover) → pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover¶: C++: protocols::simple_moves::ChangeAndResetFoldTreeMover::operator=(const class protocols::simple_moves::ChangeAndResetFoldTreeMover &) –> class protocols::simple_moves::ChangeAndResetFoldTreeMover &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::ChangeAndResetFoldTreeMover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::ChangeAndResetFoldTreeMover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

ft_mover(self: pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover) → pyrosetta.rosetta.protocols.moves.ChangeFoldTreeMover¶

Get the ChangeFoldTreeMover

C++: protocols::simple_moves::ChangeAndResetFoldTreeMover::ft_mover() const –> class std::shared_ptr<class protocols::moves::ChangeFoldTreeMover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover) → str¶: C++: protocols::simple_moves::ChangeAndResetFoldTreeMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

mover(self: pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover) → pyrosetta.rosetta.protocols.moves.Mover¶

Get the main mover

C++: protocols::simple_moves::ChangeAndResetFoldTreeMover::mover() const –> class std::shared_ptr<class protocols::moves::Mover>

static mover_name() → str¶: C++: protocols::simple_moves::ChangeAndResetFoldTreeMover::mover_name() –> std::string

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.

C++: protocols::moves::Mover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::ChangeAndResetFoldTreeMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

scorefxn(self: pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover) → pyrosetta.rosetta.core.scoring.ScoreFunction¶

Get the set ScoreFunction

C++: protocols::simple_moves::ChangeAndResetFoldTreeMover::scorefxn() const –> class std::shared_ptr<const class core::scoring::ScoreFunction>

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_ft_mover(self: pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover, ft_mover: pyrosetta.rosetta.protocols.moves.ChangeFoldTreeMover) → None¶

Set the ChangeFoldTreeMover

C++: protocols::simple_moves::ChangeAndResetFoldTreeMover::set_ft_mover(class std::shared_ptr<class protocols::moves::ChangeFoldTreeMover>) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_mover(self: pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover, main_mover: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Set the main mover to apply

C++: protocols::simple_moves::ChangeAndResetFoldTreeMover::set_mover(class std::shared_ptr<class protocols::moves::Mover>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_scorefxn(self: pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) → None¶

Set the ScoreFunction.: Used ONLY for printing score information before and after the move!!

C++: protocols::simple_moves::ChangeAndResetFoldTreeMover::set_scorefxn(class std::shared_ptr<const class core::scoring::ScoreFunction>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMoverCreator¶

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMoverCreator, : pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMoverCreator) → pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMoverCreator¶: C++: protocols::simple_moves::ChangeAndResetFoldTreeMoverCreator::operator=(const class protocols::simple_moves::ChangeAndResetFoldTreeMoverCreator &) –> class protocols::simple_moves::ChangeAndResetFoldTreeMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::ChangeAndResetFoldTreeMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMoverCreator) → str¶: C++: protocols::simple_moves::ChangeAndResetFoldTreeMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMoverCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::ChangeAndResetFoldTreeMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover¶

Bases: FragmentMover

A FragmentMover that applies uniform sampling of fragments

apply(*args, **kwargs)¶

Overloaded function.

apply(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, : pyrosetta.rosetta.core.pose.Pose, pos: int) -> bool
apply(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, : pyrosetta.rosetta.core.pose.Pose) -> None

Applies classic fragment insertion based on a FragSet

example:
mover_3mer.apply(pose)

See also:
ClassicFragmentMover Pose ConstantLengthFragSet

C++: protocols::simple_moves::ClassicFragmentMover::apply(class core::pose::Pose &) –> void

apply_at_all_positions(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover, : pyrosetta.rosetta.core.pose.Pose) → int¶

apply at all movemable positions — honors movemap

C++: protocols::simple_moves::FragmentMover::apply_at_all_positions(class core::pose::Pose &) const –> unsigned long

apply_fragment(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, frame: pyrosetta.rosetta.core.fragment.Frame, frag_num: int, movemap: pyrosetta.rosetta.core.kinematics.MoveMap, pose: pyrosetta.rosetta.core.pose.Pose) → bool¶

apply the chosen fragment,

this can be overloaded to change action, e.,g., WobbleMover introduces chain-break before fragment insertion and does ccd-loop closure afterwards

C++: protocols::simple_moves::ClassicFragmentMover::apply_fragment(const class core::fragment::Frame &, unsigned long, const class core::kinematics::MoveMap &, class core::pose::Pose &) const –> bool

assign(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, : pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover) → pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover¶: C++: protocols::simple_moves::ClassicFragmentMover::operator=(const class protocols::simple_moves::ClassicFragmentMover &) –> class protocols::simple_moves::ClassicFragmentMover &

check_ss(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover) → bool¶

accessor

C++: protocols::simple_moves::ClassicFragmentMover::check_ss() const –> bool

choose_fragment(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, : pyrosetta.rosetta.core.fragment.FrameList, : pyrosetta.rosetta.core.pose.Pose, frame_num: int, frag_num: int) → bool¶

given FrameList and pose, this method yields a fragment ( frame_num/ frag_num);: return false if nothing suitable is found

C++: protocols::simple_moves::ClassicFragmentMover::choose_fragment(const class core::fragment::FrameList &, const class core::pose::Pose &, unsigned long &, unsigned long &) const –> bool

choose_window_length(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, : pyrosetta.rosetta.core.pose.Pose, window_length: int) → bool¶

yields a length (window_length) of the fragment window to sample from: ( return false, if no suitable length is found )

C++: protocols::simple_moves::ClassicFragmentMover::choose_window_length(const class core::pose::Pose &, unsigned long &) const –> bool

choose_window_start(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, : pyrosetta.rosetta.core.pose.Pose, window_length: int, window_start: int) → bool¶

yields a start position (window_start) for fragment window to sample from: ( return false, if nothing suitable is found )

C++: protocols::simple_moves::ClassicFragmentMover::choose_window_start(const class core::pose::Pose &, unsigned long, unsigned long &) const –> bool

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::ClassicFragmentMover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

define_start_window(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, window_start: int) → None¶

apply fragment at predefined position

C++: protocols::simple_moves::ClassicFragmentMover::define_start_window(unsigned long) –> void

enable_end_bias_check(*args, **kwargs)¶

Overloaded function.

enable_end_bias_check(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover) -> None
enable_end_bias_check(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, setting: bool) -> None

C++: protocols::simple_moves::ClassicFragmentMover::enable_end_bias_check(bool) –> void

end_bias(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover) → float¶: C++: protocols::simple_moves::ClassicFragmentMover::end_bias() const –> double

end_bias_check(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, : pyrosetta.rosetta.core.pose.Pose, window_start: int) → bool¶: C++: protocols::simple_moves::ClassicFragmentMover::end_bias_check(const class core::pose::Pose &, unsigned long) const –> bool

end_bias_check_enabled(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover) → bool¶: C++: protocols::simple_moves::ClassicFragmentMover::end_bias_check_enabled() const –> bool

fragments(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover) → pyrosetta.rosetta.core.fragment.FragSet¶

accessor to the fragment set

C++: protocols::simple_moves::FragmentMover::fragments() const –> class std::shared_ptr<const class core::fragment::FragSet>

fresh_instance(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::ClassicFragmentMover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover) → str¶: C++: protocols::simple_moves::ClassicFragmentMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

initialize(self: pyrosetta.rosetta.protocols.moves.MoveMapMover, : pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::moves::MoveMapMover::initialize(class core::pose::Pose &) –> void

insert_map(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover) → pyrosetta.rosetta.utility.vector1_unsigned_long¶: C++: protocols::simple_moves::FragmentMover::insert_map() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

insert_size(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover) → pyrosetta.rosetta.utility.vector1_unsigned_long¶: C++: protocols::simple_moves::FragmentMover::insert_size() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

movemap(*args, **kwargs)¶

Overloaded function.

movemap(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover, : pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.core.kinematics.MoveMap

C++: protocols::simple_moves::FragmentMover::movemap(const class core::pose::Pose &) const –> class std::shared_ptr<const class core::kinematics::MoveMap>

movemap(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover) -> pyrosetta.rosetta.core.kinematics.MoveMap

C++: protocols::simple_moves::FragmentMover::movemap() const –> class std::shared_ptr<const class core::kinematics::MoveMap>

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

on_new_fragments(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover) → None¶

is called from set_fragments()

C++: protocols::simple_moves::ClassicFragmentMover::on_new_fragments() –> void

parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.

C++: protocols::moves::Mover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_check_ss(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, setting: bool) → None¶

check_ss controls whether fragment insertions are rejected that create short helices (<3) or strands (<2)

C++: protocols::simple_moves::ClassicFragmentMover::set_check_ss(bool) –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_end_bias(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, setting: float) → None¶: C++: protocols::simple_moves::ClassicFragmentMover::set_end_bias(double) –> void

set_fragments(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover, new_frags_: pyrosetta.rosetta.core.fragment.FragSet) → None¶

setter for the fragment set

C++: protocols::simple_moves::FragmentMover::set_fragments(class std::shared_ptr<const class core::fragment::FragSet>) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_min_frag_length(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, setting: int) → None¶

min_frag_length controls the behaviour fragset->region()

C++: protocols::simple_moves::ClassicFragmentMover::set_min_frag_length(unsigned long) –> void

set_min_overlap(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, setting: int) → None¶

min_overlap controls the behaviour fragset->region()

C++: protocols::simple_moves::ClassicFragmentMover::set_min_overlap(unsigned long) –> void

set_movemap(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover, movemap: pyrosetta.rosetta.core.kinematics.MoveMap) → None¶

setter for the movemap

C++: protocols::simple_moves::FragmentMover::set_movemap(class std::shared_ptr<const class core::kinematics::MoveMap>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover) -> None
show(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, output: pyrosetta.rosetta.std.ostream) -> None

C++: protocols::simple_moves::ClassicFragmentMover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

valid_ss(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, new_ss: str) → bool¶

returns true if the ss string is acceptable

C++: protocols::simple_moves::ClassicFragmentMover::valid_ss(const std::string &) const –> bool

class pyrosetta.rosetta.protocols.simple_moves.CombinePoseMover¶

Bases: Mover

append_combine_history(self: pyrosetta.rosetta.protocols.simple_moves.CombinePoseMover, v: pyrosetta.rosetta.std.vector_unsigned_long) → None¶: C++: protocols::simple_moves::CombinePoseMover::append_combine_history(const class std::vector<unsigned long, class std::allocator<unsigned long> >) –> void

apply(self: pyrosetta.rosetta.protocols.simple_moves.CombinePoseMover, pose2: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::simple_moves::CombinePoseMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.CombinePoseMover, : pyrosetta.rosetta.protocols.simple_moves.CombinePoseMover) → pyrosetta.rosetta.protocols.simple_moves.CombinePoseMover¶: C++: protocols::simple_moves::CombinePoseMover::operator=(const class protocols::simple_moves::CombinePoseMover &) –> class protocols::simple_moves::CombinePoseMover &

clear_combine_history(self: pyrosetta.rosetta.protocols.simple_moves.CombinePoseMover) → None¶: C++: protocols::simple_moves::CombinePoseMover::clear_combine_history() –> void

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶

Return a clone of the Mover object.

C++: protocols::moves::Mover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶

Generates a new Mover object freshly created with the default ctor.

C++: protocols::moves::Mover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.simple_moves.CombinePoseMover) → str¶: C++: protocols::simple_moves::CombinePoseMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

max_struct(self: pyrosetta.rosetta.protocols.simple_moves.CombinePoseMover) → int¶: C++: protocols::simple_moves::CombinePoseMover::max_struct() const –> unsigned long

max_struct_try(self: pyrosetta.rosetta.protocols.simple_moves.CombinePoseMover) → int¶: C++: protocols::simple_moves::CombinePoseMover::max_struct_try() const –> unsigned long

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.

C++: protocols::moves::Mover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

pose_ref(self: pyrosetta.rosetta.protocols.simple_moves.CombinePoseMover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::simple_moves::CombinePoseMover::pose_ref() const –> const class core::pose::Pose

pose_tag(self: pyrosetta.rosetta.protocols.simple_moves.CombinePoseMover) → str¶: C++: protocols::simple_moves::CombinePoseMover::pose_tag() const –> std::string

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

return_combine_history(self: pyrosetta.rosetta.protocols.simple_moves.CombinePoseMover) → pyrosetta.rosetta.std.vector_std_vector_unsigned_long_t¶: C++: protocols::simple_moves::CombinePoseMover::return_combine_history() const –> class std::vector<class std::vector<unsigned long, class std::allocator<unsigned long> >, class std::allocator<class std::vector<unsigned long, class std::allocator<unsigned long> > > >

return_silent(self: pyrosetta.rosetta.protocols.simple_moves.CombinePoseMover) → pyrosetta.rosetta.std.vector_std_shared_ptr_core_io_silent_SilentStruct_t¶: C++: protocols::simple_moves::CombinePoseMover::return_silent() const –> class std::vector<class std::shared_ptr<class core::io::silent::SilentStruct>, class std::allocator<class std::shared_ptr<class core::io::silent::SilentStruct> > >

set_cartesian(self: pyrosetta.rosetta.protocols.simple_moves.CombinePoseMover, setting: bool) → None¶: C++: protocols::simple_moves::CombinePoseMover::set_cartesian(const bool) –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_default(self: pyrosetta.rosetta.protocols.simple_moves.CombinePoseMover) → None¶: C++: protocols::simple_moves::CombinePoseMover::set_default() –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_max_struct(self: pyrosetta.rosetta.protocols.simple_moves.CombinePoseMover, n: int) → None¶: C++: protocols::simple_moves::CombinePoseMover::set_max_struct(const unsigned long) –> void

set_max_try(self: pyrosetta.rosetta.protocols.simple_moves.CombinePoseMover, n: int) → None¶: C++: protocols::simple_moves::CombinePoseMover::set_max_try(const unsigned long) –> void

set_maxfrac_crossover(self: pyrosetta.rosetta.protocols.simple_moves.CombinePoseMover, value: float) → None¶: C++: protocols::simple_moves::CombinePoseMover::set_maxfrac_crossover(const double) –> void

set_minfrac_crossover(self: pyrosetta.rosetta.protocols.simple_moves.CombinePoseMover, value: float) → None¶: C++: protocols::simple_moves::CombinePoseMover::set_minfrac_crossover(const double) –> void

set_minimize(self: pyrosetta.rosetta.protocols.simple_moves.CombinePoseMover, setting: bool) → None¶: C++: protocols::simple_moves::CombinePoseMover::set_minimize(const bool) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_nonideal(self: pyrosetta.rosetta.protocols.simple_moves.CombinePoseMover, setting: bool) → None¶: C++: protocols::simple_moves::CombinePoseMover::set_nonideal(const bool) –> void

set_pose_tag(self: pyrosetta.rosetta.protocols.simple_moves.CombinePoseMover, value: str) → None¶: C++: protocols::simple_moves::CombinePoseMover::set_pose_tag(const std::string) –> void

set_rmsdcut(self: pyrosetta.rosetta.protocols.simple_moves.CombinePoseMover, setting: float) → None¶: C++: protocols::simple_moves::CombinePoseMover::set_rmsdcut(const double) –> void

set_store_silents(self: pyrosetta.rosetta.protocols.simple_moves.CombinePoseMover, value: bool) → None¶: C++: protocols::simple_moves::CombinePoseMover::set_store_silents(const bool) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.simple_moves.ConcatenatePosesMover¶

Bases: Mover

links supplied Poses by their termini

apply(self: pyrosetta.rosetta.protocols.simple_moves.ConcatenatePosesMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Apply the mover

C++: protocols::simple_moves::ConcatenatePosesMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.ConcatenatePosesMover, : pyrosetta.rosetta.protocols.simple_moves.ConcatenatePosesMover) → pyrosetta.rosetta.protocols.simple_moves.ConcatenatePosesMover¶: C++: protocols::simple_moves::ConcatenatePosesMover::operator=(const class protocols::simple_moves::ConcatenatePosesMover &) –> class protocols::simple_moves::ConcatenatePosesMover &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.simple_moves.ConcatenatePosesMover) → pyrosetta.rosetta.protocols.moves.Mover¶

required in the context of the parser/scripting scheme

C++: protocols::simple_moves::ConcatenatePosesMover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

concatenate_poses(self: pyrosetta.rosetta.protocols.simple_moves.ConcatenatePosesMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::simple_moves::ConcatenatePosesMover::concatenate_poses(class core::pose::Pose &) –> void

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.simple_moves.ConcatenatePosesMover) → pyrosetta.rosetta.protocols.moves.Mover¶

required in the context of the parser/scripting scheme

C++: protocols::simple_moves::ConcatenatePosesMover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_component_file(self: pyrosetta.rosetta.protocols.simple_moves.ConcatenatePosesMover) → str¶: C++: protocols::simple_moves::ConcatenatePosesMover::get_component_file() const –> std::string

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.simple_moves.ConcatenatePosesMover) → str¶: C++: protocols::simple_moves::ConcatenatePosesMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static mover_name() → str¶: C++: protocols::simple_moves::ConcatenatePosesMover::mover_name() –> std::string

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.simple_moves.ConcatenatePosesMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

parse XML tag (to use this Mover in Rosetta Scripts)

C++: protocols::simple_moves::ConcatenatePosesMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::ConcatenatePosesMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_component_file(self: pyrosetta.rosetta.protocols.simple_moves.ConcatenatePosesMover, : str) → None¶: C++: protocols::simple_moves::ConcatenatePosesMover::set_component_file(const std::string &) –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.simple_moves.ConcatenatePosesMover) -> None
show(self: pyrosetta.rosetta.protocols.simple_moves.ConcatenatePosesMover, output: pyrosetta.rosetta.std.ostream) -> None

C++: protocols::simple_moves::ConcatenatePosesMover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.simple_moves.ConcatenatePosesMoverCreator¶

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.simple_moves.ConcatenatePosesMoverCreator, : pyrosetta.rosetta.protocols.simple_moves.ConcatenatePosesMoverCreator) → pyrosetta.rosetta.protocols.simple_moves.ConcatenatePosesMoverCreator¶: C++: protocols::simple_moves::ConcatenatePosesMoverCreator::operator=(const class protocols::simple_moves::ConcatenatePosesMoverCreator &) –> class protocols::simple_moves::ConcatenatePosesMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.simple_moves.ConcatenatePosesMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::ConcatenatePosesMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.simple_moves.ConcatenatePosesMoverCreator) → str¶: C++: protocols::simple_moves::ConcatenatePosesMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.simple_moves.ConcatenatePosesMoverCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::ConcatenatePosesMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover¶

Bases: Mover

Idealization is generally performed by adding constraints to the Pose that keep bond lengths and angles within the appropriate ranges; then freeing those DOFs and performing minimization or sampling. This protocols::moves::Mover creates bond and angle constraints compatible with idealization; it does not modify the input Pose other than by adding constraints. If your pose is already ideal, this is likely to unidealize it. Also, it will add a LOT of degrees of freedom to your minimization, which may lead to significant slowdowns!

apply(*args, **kwargs)¶

Overloaded function.

apply(self: pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover, pose: pyrosetta.rosetta.core.pose.Pose) -> None

C++: protocols::simple_moves::ConstrainToIdealMover::apply(class core::pose::Pose &) –> void

apply(self: pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover, pose: pyrosetta.rosetta.core.pose.Pose, mm: pyrosetta.rosetta.core.kinematics.MoveMap) -> None

C++: protocols::simple_moves::ConstrainToIdealMover::apply(class core::pose::Pose &, class core::kinematics::MoveMap &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover, rhs: pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover) → pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover¶: C++: protocols::simple_moves::ConstrainToIdealMover::operator=(const class protocols::simple_moves::ConstrainToIdealMover &) –> class protocols::simple_moves::ConstrainToIdealMover &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::ConstrainToIdealMover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::ConstrainToIdealMover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_atom_level_domain_map(self: pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover) → pyrosetta.rosetta.core.pose.toolbox.AtomLevelDomainMap¶

getter for AtomLevelDomainMap

C++: protocols::simple_moves::ConstrainToIdealMover::get_atom_level_domain_map() const –> class std::shared_ptr<const class core::pose::toolbox::AtomLevelDomainMap>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover) → str¶: C++: protocols::simple_moves::ConstrainToIdealMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.

C++: protocols::moves::Mover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_atom_level_domain_map(self: pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover, atom_level_domain_map: pyrosetta.rosetta.core.pose.toolbox.AtomLevelDomainMap) → None¶

setter for AtomLevelDomainMap; makes a shallow copy

C++: protocols::simple_moves::ConstrainToIdealMover::set_atom_level_domain_map(class std::shared_ptr<const class core::pose::toolbox::AtomLevelDomainMap>) –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_fix_angles(self: pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover, setting: bool) → None¶: C++: protocols::simple_moves::ConstrainToIdealMover::set_fix_angles(const bool &) –> void

set_fix_lengths(self: pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover, setting: bool) → None¶: C++: protocols::simple_moves::ConstrainToIdealMover::set_fix_lengths(const bool &) –> void

set_fix_torsions(self: pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover, setting: bool) → None¶: C++: protocols::simple_moves::ConstrainToIdealMover::set_fix_torsions(const bool &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_just_polar_hydrogens(self: pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover, setting: bool) → None¶: C++: protocols::simple_moves::ConstrainToIdealMover::set_just_polar_hydrogens(const bool) –> void

set_just_rna_backbone(self: pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover, setting: bool) → None¶: C++: protocols::simple_moves::ConstrainToIdealMover::set_just_rna_backbone(const bool) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_score_type(self: pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover, setting: pyrosetta.rosetta.core.scoring.ScoreType) → None¶: C++: protocols::simple_moves::ConstrainToIdealMover::set_score_type(const enum core::scoring::ScoreType) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.simple_moves.ContingentAcceptMover¶

Bases: Mover

apply(self: pyrosetta.rosetta.protocols.simple_moves.ContingentAcceptMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::simple_moves::ContingentAcceptMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.ContingentAcceptMover, : pyrosetta.rosetta.protocols.simple_moves.ContingentAcceptMover) → pyrosetta.rosetta.protocols.simple_moves.ContingentAcceptMover¶: C++: protocols::simple_moves::ContingentAcceptMover::operator=(const class protocols::simple_moves::ContingentAcceptMover &) –> class protocols::simple_moves::ContingentAcceptMover &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.simple_moves.ContingentAcceptMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::ContingentAcceptMover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

delta(*args, **kwargs)¶

Overloaded function.

delta(self: pyrosetta.rosetta.protocols.simple_moves.ContingentAcceptMover) -> float

C++: protocols::simple_moves::ContingentAcceptMover::delta() const –> double

delta(self: pyrosetta.rosetta.protocols.simple_moves.ContingentAcceptMover, s: float) -> None

C++: protocols::simple_moves::ContingentAcceptMover::delta(const double) –> void

filter(*args, **kwargs)¶

Overloaded function.

filter(self: pyrosetta.rosetta.protocols.simple_moves.ContingentAcceptMover) -> pyrosetta.rosetta.protocols.filters.Filter

C++: protocols::simple_moves::ContingentAcceptMover::filter() const –> class std::shared_ptr<class protocols::filters::Filter>

filter(self: pyrosetta.rosetta.protocols.simple_moves.ContingentAcceptMover, f: pyrosetta.rosetta.protocols.filters.Filter) -> None

C++: protocols::simple_moves::ContingentAcceptMover::filter(class std::shared_ptr<class protocols::filters::Filter>) –> void

fresh_instance(self: pyrosetta.rosetta.protocols.simple_moves.ContingentAcceptMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::ContingentAcceptMover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.simple_moves.ContingentAcceptMover) → str¶: C++: protocols::simple_moves::ContingentAcceptMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

mover(*args, **kwargs)¶

Overloaded function.

mover(self: pyrosetta.rosetta.protocols.simple_moves.ContingentAcceptMover) -> pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::simple_moves::ContingentAcceptMover::mover() const –> class std::shared_ptr<class protocols::moves::Mover>

mover(self: pyrosetta.rosetta.protocols.simple_moves.ContingentAcceptMover, m: pyrosetta.rosetta.protocols.moves.Mover) -> None

C++: protocols::simple_moves::ContingentAcceptMover::mover(class std::shared_ptr<class protocols::moves::Mover>) –> void

static mover_name() → str¶: C++: protocols::simple_moves::ContingentAcceptMover::mover_name() –> std::string

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.simple_moves.ContingentAcceptMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::simple_moves::ContingentAcceptMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::ContingentAcceptMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.simple_moves.ContingentAcceptMoverCreator¶

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.simple_moves.ContingentAcceptMoverCreator, : pyrosetta.rosetta.protocols.simple_moves.ContingentAcceptMoverCreator) → pyrosetta.rosetta.protocols.simple_moves.ContingentAcceptMoverCreator¶: C++: protocols::simple_moves::ContingentAcceptMoverCreator::operator=(const class protocols::simple_moves::ContingentAcceptMoverCreator &) –> class protocols::simple_moves::ContingentAcceptMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.simple_moves.ContingentAcceptMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::ContingentAcceptMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.simple_moves.ContingentAcceptMoverCreator) → str¶: C++: protocols::simple_moves::ContingentAcceptMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.simple_moves.ContingentAcceptMoverCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::ContingentAcceptMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover¶

Bases: Mover

Mover for switching a residue type to all VIRTUAL.: A VIRTUAL Residue is one that is not scored or output.

If no residue_selector is set, will work on ALL residues

See also:

FAToVirtualMover

apply(self: pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::simple_moves::ConvertVirtualToRealMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover, : pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover) → pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover¶: C++: protocols::simple_moves::ConvertVirtualToRealMover::operator=(const class protocols::simple_moves::ConvertVirtualToRealMover &) –> class protocols::simple_moves::ConvertVirtualToRealMover &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover) → pyrosetta.rosetta.protocols.moves.Mover¶

required in the context of the parser/scripting scheme

C++: protocols::simple_moves::ConvertVirtualToRealMover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover) → pyrosetta.rosetta.protocols.moves.Mover¶

required in the context of the parser/scripting scheme

C++: protocols::simple_moves::ConvertVirtualToRealMover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover) → str¶: C++: protocols::simple_moves::ConvertVirtualToRealMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static mover_name() → str¶: C++: protocols::simple_moves::ConvertVirtualToRealMover::mover_name() –> std::string

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

parse XML tag (to use this Mover in Rosetta Scripts)

C++: protocols::simple_moves::ConvertVirtualToRealMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide the citation.

C++: protocols::simple_moves::ConvertVirtualToRealMover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::ConvertVirtualToRealMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_residue_selector(self: pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) → None¶

Set the residue selector. If you need a particular set of residues,: use the ReturnSubsetResidueSelector.

C++: protocols::simple_moves::ConvertVirtualToRealMover::set_residue_selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover) -> None
show(self: pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover, output: pyrosetta.rosetta.std.ostream) -> None

C++: protocols::simple_moves::ConvertVirtualToRealMover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMoverCreator¶

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMoverCreator, : pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMoverCreator) → pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMoverCreator¶: C++: protocols::simple_moves::ConvertVirtualToRealMoverCreator::operator=(const class protocols::simple_moves::ConvertVirtualToRealMoverCreator &) –> class protocols::simple_moves::ConvertVirtualToRealMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::ConvertVirtualToRealMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMoverCreator) → str¶: C++: protocols::simple_moves::ConvertVirtualToRealMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMoverCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::ConvertVirtualToRealMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.simple_moves.CopyDofMover¶

Bases: Mover

apply(self: pyrosetta.rosetta.protocols.simple_moves.CopyDofMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::simple_moves::CopyDofMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::operator=(const class protocols::moves::Mover &) –> class protocols::moves::Mover &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶

Return a clone of the Mover object.

C++: protocols::moves::Mover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

copy_dofs_info(self: pyrosetta.rosetta.protocols.simple_moves.CopyDofMover, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.core.pose.copydofs.CopyDofsInfo¶: C++: protocols::simple_moves::CopyDofMover::copy_dofs_info(const class core::pose::Pose &) const –> const class core::pose::copydofs::CopyDofsInfo &

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶

Generates a new Mover object freshly created with the default ctor.

C++: protocols::moves::Mover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.simple_moves.CopyDofMover) → str¶: C++: protocols::simple_moves::CopyDofMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.

C++: protocols::moves::Mover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_copy_dofs_info(self: pyrosetta.rosetta.protocols.simple_moves.CopyDofMover, pose: pyrosetta.rosetta.core.pose.Pose, copy_dofs_info: pyrosetta.rosetta.core.pose.copydofs.CopyDofsInfo) → None¶: C++: protocols::simple_moves::CopyDofMover::set_copy_dofs_info(const class core::pose::Pose &, const class core::pose::copydofs::CopyDofsInfo &) –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover¶

Bases: Mover

A mover to copy a rotamer (residue identity and conformation) from one position in a pose to another.

apply(self: pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Apply the mover

C++: protocols::simple_moves::CopyRotamerMover::apply(class core::pose::Pose &) –> void

apply_from_template_pose(self: pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover, target_pose: pyrosetta.rosetta.core.pose.Pose, template_pose: pyrosetta.rosetta.core.pose.Pose, target_res_index: int, template_res_index: int) → None¶

Apply the mover on another pose, not accessible from rosetta_scripts

C++: protocols::simple_moves::CopyRotamerMover::apply_from_template_pose(class core::pose::Pose &, const class core::pose::Pose &, unsigned long, unsigned long) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover, : pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover) → pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover¶: C++: protocols::simple_moves::CopyRotamerMover::operator=(const class protocols::simple_moves::CopyRotamerMover &) –> class protocols::simple_moves::CopyRotamerMover &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover) → pyrosetta.rosetta.protocols.moves.Mover¶

required in the context of the parser/scripting scheme

C++: protocols::simple_moves::CopyRotamerMover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover) → pyrosetta.rosetta.protocols.moves.Mover¶

required in the context of the parser/scripting scheme

C++: protocols::simple_moves::CopyRotamerMover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover) → str¶: C++: protocols::simple_moves::CopyRotamerMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static mover_name() → str¶: C++: protocols::simple_moves::CopyRotamerMover::mover_name() –> std::string

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

parse XML tag (to use this Mover in Rosetta Scripts)

C++: protocols::simple_moves::CopyRotamerMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::CopyRotamerMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_copy_identity(self: pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover, setting_in: bool) → None¶

Set whether we’re copying the residue identity.

C++: protocols::simple_moves::CopyRotamerMover::set_copy_identity(const bool) –> void

set_copy_torsions(self: pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover, setting_in: bool) → None¶

Set whether we’re copying the residue side-chain torsions.

C++: protocols::simple_moves::CopyRotamerMover::set_copy_torsions(const bool) –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_target_res_index(self: pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover, index_in: int) → None¶

Set pose index of the residue TO which we’re copying.

C++: protocols::simple_moves::CopyRotamerMover::set_target_res_index(const unsigned long) –> void

set_template_res_index(self: pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover, index_in: int) → None¶

Set pose index of the residue FROM which we’re copying.

C++: protocols::simple_moves::CopyRotamerMover::set_template_res_index(const unsigned long) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover) -> None
show(self: pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover, output: pyrosetta.rosetta.std.ostream) -> None

Show the contents of the Mover

C++: protocols::simple_moves::CopyRotamerMover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMoverCreator¶

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMoverCreator, : pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMoverCreator) → pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMoverCreator¶: C++: protocols::simple_moves::CopyRotamerMoverCreator::operator=(const class protocols::simple_moves::CopyRotamerMoverCreator &) –> class protocols::simple_moves::CopyRotamerMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::CopyRotamerMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMoverCreator) → str¶: C++: protocols::simple_moves::CopyRotamerMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMoverCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::CopyRotamerMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.simple_moves.CoupledMover¶

Bases: Mover

This mover is called by CoupledMovesProtocol to make a single coupled move.

The CoupledMover apply function makes a single coupled move as follows: (1) Backbone move – As of March 2018, there are three options: backrub, kinematic closure with walking perturber, or kinematic closure with fragment perturber. (2) Side chain move – The three residues at the center of the perturbed backbone are sampled by BoltzmannRotamerMover. (3) Repack – 10A shell around the residues from step 2 is repacked.

apply(self: pyrosetta.rosetta.protocols.simple_moves.CoupledMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::simple_moves::CoupledMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.CoupledMover, : pyrosetta.rosetta.protocols.simple_moves.CoupledMover) → pyrosetta.rosetta.protocols.simple_moves.CoupledMover¶: C++: protocols::simple_moves::CoupledMover::operator=(const class protocols::simple_moves::CoupledMover &) –> class protocols::simple_moves::CoupledMover &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.simple_moves.CoupledMover) → pyrosetta.rosetta.protocols.moves.Mover¶

clone this object

C++: protocols::simple_moves::CoupledMover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.simple_moves.CoupledMover) → pyrosetta.rosetta.protocols.moves.Mover¶

create this type of object

C++: protocols::simple_moves::CoupledMover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_backbone_mover(self: pyrosetta.rosetta.protocols.simple_moves.CoupledMover) → str¶: C++: protocols::simple_moves::CoupledMover::get_backbone_mover() const –> const std::string &

get_bias_sampling(self: pyrosetta.rosetta.protocols.simple_moves.CoupledMover) → bool¶: C++: protocols::simple_moves::CoupledMover::get_bias_sampling() const –> bool

get_boltzmann_rotamer_mover(self: pyrosetta.rosetta.protocols.simple_moves.CoupledMover) → pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMover¶: C++: protocols::simple_moves::CoupledMover::get_boltzmann_rotamer_mover() const –> class std::shared_ptr<class protocols::minimization_packing::BoltzmannRotamerMover>

get_bump_check(self: pyrosetta.rosetta.protocols.simple_moves.CoupledMover) → bool¶: C++: protocols::simple_moves::CoupledMover::get_bump_check() const –> bool

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_fix_backbone(self: pyrosetta.rosetta.protocols.simple_moves.CoupledMover) → bool¶: C++: protocols::simple_moves::CoupledMover::get_fix_backbone() const –> bool

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_ligand_jump_id(self: pyrosetta.rosetta.protocols.simple_moves.CoupledMover) → int¶: C++: protocols::simple_moves::CoupledMover::get_ligand_jump_id() const –> unsigned long

get_ligand_resnum(self: pyrosetta.rosetta.protocols.simple_moves.CoupledMover) → int¶: C++: protocols::simple_moves::CoupledMover::get_ligand_resnum() const –> unsigned long

get_ligand_weight(self: pyrosetta.rosetta.protocols.simple_moves.CoupledMover) → float¶: C++: protocols::simple_moves::CoupledMover::get_ligand_weight() const –> double

get_loop_size(self: pyrosetta.rosetta.protocols.simple_moves.CoupledMover) → int¶: C++: protocols::simple_moves::CoupledMover::get_loop_size() const –> unsigned long

get_name(self: pyrosetta.rosetta.protocols.simple_moves.CoupledMover) → str¶: C++: protocols::simple_moves::CoupledMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_packer_task(self: pyrosetta.rosetta.protocols.simple_moves.CoupledMover) → pyrosetta.rosetta.core.pack.task.PackerTask¶: C++: protocols::simple_moves::CoupledMover::get_packer_task() const –> class std::shared_ptr<class core::pack::task::PackerTask>

get_perturber(self: pyrosetta.rosetta.protocols.simple_moves.CoupledMover) → pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Perturber¶: C++: protocols::simple_moves::CoupledMover::get_perturber() const –> class std::shared_ptr<class protocols::kinematic_closure::perturbers::Perturber>

get_randomize_resnum(self: pyrosetta.rosetta.protocols.simple_moves.CoupledMover) → bool¶: C++: protocols::simple_moves::CoupledMover::get_randomize_resnum() const –> bool

get_repack_neighborhood(self: pyrosetta.rosetta.protocols.simple_moves.CoupledMover) → bool¶: C++: protocols::simple_moves::CoupledMover::get_repack_neighborhood() const –> const bool &

get_resnum(self: pyrosetta.rosetta.protocols.simple_moves.CoupledMover) → int¶: C++: protocols::simple_moves::CoupledMover::get_resnum() const –> unsigned long

get_rigid_body_mover(self: pyrosetta.rosetta.protocols.simple_moves.CoupledMover) → pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover¶: C++: protocols::simple_moves::CoupledMover::get_rigid_body_mover() const –> class std::shared_ptr<class protocols::rigid::RigidBodyPerturbMover>

get_rotation_magnitude(self: pyrosetta.rosetta.protocols.simple_moves.CoupledMover) → float¶: C++: protocols::simple_moves::CoupledMover::get_rotation_magnitude() const –> double

get_rotation_std_dev(self: pyrosetta.rosetta.protocols.simple_moves.CoupledMover) → float¶: C++: protocols::simple_moves::CoupledMover::get_rotation_std_dev() const –> double

get_score_fxn(self: pyrosetta.rosetta.protocols.simple_moves.CoupledMover) → pyrosetta.rosetta.core.scoring.ScoreFunction¶: C++: protocols::simple_moves::CoupledMover::get_score_fxn() const –> class std::shared_ptr<class core::scoring::ScoreFunction>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_short_backrub_mover(self: pyrosetta.rosetta.protocols.simple_moves.CoupledMover) → protocols::simple_moves::ShortBackrubMover¶: C++: protocols::simple_moves::CoupledMover::get_short_backrub_mover() const –> class std::shared_ptr<class protocols::simple_moves::ShortBackrubMover>

get_temperature(self: pyrosetta.rosetta.protocols.simple_moves.CoupledMover) → float¶: C++: protocols::simple_moves::CoupledMover::get_temperature() const –> double

get_translation_magnitude(self: pyrosetta.rosetta.protocols.simple_moves.CoupledMover) → float¶: C++: protocols::simple_moves::CoupledMover::get_translation_magnitude() const –> double

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

get_uniform_backrub(self: pyrosetta.rosetta.protocols.simple_moves.CoupledMover) → bool¶: C++: protocols::simple_moves::CoupledMover::get_uniform_backrub() const –> bool

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static mover_name() → str¶: C++: protocols::simple_moves::CoupledMover::mover_name() –> std::string

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.

C++: protocols::moves::Mover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::CoupledMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_backbone_mover(self: pyrosetta.rosetta.protocols.simple_moves.CoupledMover, backbone_mover: str) → None¶: C++: protocols::simple_moves::CoupledMover::set_backbone_mover(const std::string &) –> void

set_bias_sampling(self: pyrosetta.rosetta.protocols.simple_moves.CoupledMover, bias_sampling: bool) → None¶: C++: protocols::simple_moves::CoupledMover::set_bias_sampling(bool) –> void

set_boltzmann_rotamer_mover(self: pyrosetta.rosetta.protocols.simple_moves.CoupledMover, boltzmann_rotamer_mover: pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMover) → None¶: C++: protocols::simple_moves::CoupledMover::set_boltzmann_rotamer_mover(class std::shared_ptr<class protocols::minimization_packing::BoltzmannRotamerMover>) –> void

set_bump_check(self: pyrosetta.rosetta.protocols.simple_moves.CoupledMover, bump_check: bool) → None¶: C++: protocols::simple_moves::CoupledMover::set_bump_check(bool) –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_fix_backbone(self: pyrosetta.rosetta.protocols.simple_moves.CoupledMover, fix_backbone: bool) → None¶: C++: protocols::simple_moves::CoupledMover::set_fix_backbone(bool) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.simple_moves.CoupledMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::simple_moves::CoupledMover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_ligand_jump_id(self: pyrosetta.rosetta.protocols.simple_moves.CoupledMover, ligand_jump_id: int) → None¶: C++: protocols::simple_moves::CoupledMover::set_ligand_jump_id(unsigned long) –> void

set_ligand_resnum(self: pyrosetta.rosetta.protocols.simple_moves.CoupledMover, ligand_resnum: int, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::simple_moves::CoupledMover::set_ligand_resnum(unsigned long, class std::shared_ptr<const class core::pose::Pose>) –> void

set_ligand_weight(self: pyrosetta.rosetta.protocols.simple_moves.CoupledMover, ligand_weight: float) → None¶: C++: protocols::simple_moves::CoupledMover::set_ligand_weight(double) –> void

set_loop_size(self: pyrosetta.rosetta.protocols.simple_moves.CoupledMover, loop_size: int) → None¶: C++: protocols::simple_moves::CoupledMover::set_loop_size(unsigned long) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_packer_task(self: pyrosetta.rosetta.protocols.simple_moves.CoupledMover, packer_task: pyrosetta.rosetta.core.pack.task.PackerTask) → None¶: C++: protocols::simple_moves::CoupledMover::set_packer_task(class std::shared_ptr<class core::pack::task::PackerTask>) –> void

set_perturber(self: pyrosetta.rosetta.protocols.simple_moves.CoupledMover, perturber: pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Perturber) → None¶: C++: protocols::simple_moves::CoupledMover::set_perturber(class std::shared_ptr<class protocols::kinematic_closure::perturbers::Perturber>) –> void

set_randomize_resnum(self: pyrosetta.rosetta.protocols.simple_moves.CoupledMover, randomize_resnum: bool) → None¶: C++: protocols::simple_moves::CoupledMover::set_randomize_resnum(bool) –> void

set_repack_neighborhood(self: pyrosetta.rosetta.protocols.simple_moves.CoupledMover, repack_neighborhood: bool) → None¶: C++: protocols::simple_moves::CoupledMover::set_repack_neighborhood(bool) –> void

set_resnum(self: pyrosetta.rosetta.protocols.simple_moves.CoupledMover, resnum: int) → None¶: C++: protocols::simple_moves::CoupledMover::set_resnum(unsigned long) –> void

set_rigid_body_mover(self: pyrosetta.rosetta.protocols.simple_moves.CoupledMover, rigid_body_mover: pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover) → None¶: C++: protocols::simple_moves::CoupledMover::set_rigid_body_mover(class std::shared_ptr<class protocols::rigid::RigidBodyPerturbMover>) –> void

set_rotation_magnitude(self: pyrosetta.rosetta.protocols.simple_moves.CoupledMover, rotation_magnitude: float) → None¶: C++: protocols::simple_moves::CoupledMover::set_rotation_magnitude(double) –> void

set_rotation_std_dev(self: pyrosetta.rosetta.protocols.simple_moves.CoupledMover, rotation_std_dev: float) → None¶: C++: protocols::simple_moves::CoupledMover::set_rotation_std_dev(double) –> void

set_score_fxn(self: pyrosetta.rosetta.protocols.simple_moves.CoupledMover, score_fxn: pyrosetta.rosetta.core.scoring.ScoreFunction) → None¶: C++: protocols::simple_moves::CoupledMover::set_score_fxn(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void

set_short_backrub_mover(self: pyrosetta.rosetta.protocols.simple_moves.CoupledMover, short_backrub_mover: protocols::simple_moves::ShortBackrubMover) → None¶: C++: protocols::simple_moves::CoupledMover::set_short_backrub_mover(class std::shared_ptr<class protocols::simple_moves::ShortBackrubMover>) –> void

set_temperature(self: pyrosetta.rosetta.protocols.simple_moves.CoupledMover, temperature: float) → None¶: C++: protocols::simple_moves::CoupledMover::set_temperature(double) –> void

set_translation_magnitude(self: pyrosetta.rosetta.protocols.simple_moves.CoupledMover, translation_magnitude: float) → None¶: C++: protocols::simple_moves::CoupledMover::set_translation_magnitude(double) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

set_uniform_backrub(self: pyrosetta.rosetta.protocols.simple_moves.CoupledMover, uniform_backrub: bool) → None¶: C++: protocols::simple_moves::CoupledMover::set_uniform_backrub(bool) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.simple_moves.CoupledMoverCreator¶

Bases: MoverCreator

This is used by CoupledMover.cc.

assign(self: pyrosetta.rosetta.protocols.simple_moves.CoupledMoverCreator, : pyrosetta.rosetta.protocols.simple_moves.CoupledMoverCreator) → pyrosetta.rosetta.protocols.simple_moves.CoupledMoverCreator¶: C++: protocols::simple_moves::CoupledMoverCreator::operator=(const class protocols::simple_moves::CoupledMoverCreator &) –> class protocols::simple_moves::CoupledMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.simple_moves.CoupledMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::CoupledMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.simple_moves.CoupledMoverCreator) → str¶: C++: protocols::simple_moves::CoupledMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.simple_moves.CoupledMoverCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::CoupledMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.simple_moves.CutChainMover¶

Bases: Mover

simple mover that sperates Fv from Fl into two seperate chains

apply(self: pyrosetta.rosetta.protocols.simple_moves.CutChainMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::simple_moves::CutChainMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.CutChainMover, : pyrosetta.rosetta.protocols.simple_moves.CutChainMover) → pyrosetta.rosetta.protocols.simple_moves.CutChainMover¶: C++: protocols::simple_moves::CutChainMover::operator=(const class protocols::simple_moves::CutChainMover &) –> class protocols::simple_moves::CutChainMover &

bond_length(*args, **kwargs)¶

Overloaded function.

bond_length(self: pyrosetta.rosetta.protocols.simple_moves.CutChainMover) -> float

C++: protocols::simple_moves::CutChainMover::bond_length() const –> double

bond_length(self: pyrosetta.rosetta.protocols.simple_moves.CutChainMover, : float) -> None

C++: protocols::simple_moves::CutChainMover::bond_length(const double) –> void

chain_cut(*args, **kwargs)¶

Overloaded function.

chain_cut(self: pyrosetta.rosetta.protocols.simple_moves.CutChainMover, pose: pyrosetta.rosetta.core.pose.Pose) -> int

C++: protocols::simple_moves::CutChainMover::chain_cut(class core::pose::Pose &) –> unsigned long

chain_cut(self: pyrosetta.rosetta.protocols.simple_moves.CutChainMover, pose: pyrosetta.rosetta.core.pose.Pose, start_res: int, end_res: int) -> int

C++: protocols::simple_moves::CutChainMover::chain_cut(class core::pose::Pose &, unsigned long, unsigned long) –> unsigned long

chain_id(*args, **kwargs)¶

Overloaded function.

chain_id(self: pyrosetta.rosetta.protocols.simple_moves.CutChainMover) -> int

C++: protocols::simple_moves::CutChainMover::chain_id() const –> unsigned long

chain_id(self: pyrosetta.rosetta.protocols.simple_moves.CutChainMover, : int) -> None

C++: protocols::simple_moves::CutChainMover::chain_id(const unsigned long) –> void

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.simple_moves.CutChainMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::CutChainMover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

create_subpose(self: pyrosetta.rosetta.protocols.simple_moves.CutChainMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::simple_moves::CutChainMover::create_subpose(class core::pose::Pose &) –> void

foldTree(self: pyrosetta.rosetta.protocols.simple_moves.CutChainMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::simple_moves::CutChainMover::foldTree(class core::pose::Pose &) –> void

fresh_instance(self: pyrosetta.rosetta.protocols.simple_moves.CutChainMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::CutChainMover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.simple_moves.CutChainMover) → str¶: C++: protocols::simple_moves::CutChainMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.simple_moves.CutChainMover, tag: pyrosetta.rosetta.utility.tag.Tag, data_map: pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::simple_moves::CutChainMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.simple_moves.CutChainMoverCreator¶

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.simple_moves.CutChainMoverCreator, : pyrosetta.rosetta.protocols.simple_moves.CutChainMoverCreator) → pyrosetta.rosetta.protocols.simple_moves.CutChainMoverCreator¶: C++: protocols::simple_moves::CutChainMoverCreator::operator=(const class protocols::simple_moves::CutChainMoverCreator &) –> class protocols::simple_moves::CutChainMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.simple_moves.CutChainMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::CutChainMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.simple_moves.CutChainMoverCreator) → str¶: C++: protocols::simple_moves::CutChainMoverCreator::keyname() const –> std::string

static mover_name() → str¶: C++: protocols::simple_moves::CutChainMoverCreator::mover_name() –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.moves.MoverCreator, xsd: utility::tag::XMLSchemaDefinition) → None¶

Describe the schema for the Mover that this Creator is responsible for

C++: protocols::moves::MoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.simple_moves.CyclizationMover¶

Bases: Mover

This mover performas a variaty of functions related to cyclizing a chain in a pose.

apply(self: pyrosetta.rosetta.protocols.simple_moves.CyclizationMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::simple_moves::CyclizationMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::operator=(const class protocols::moves::Mover &) –> class protocols::moves::Mover &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶

Return a clone of the Mover object.

C++: protocols::moves::Mover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶

Generates a new Mover object freshly created with the default ctor.

C++: protocols::moves::Mover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.simple_moves.CyclizationMover) → str¶: C++: protocols::simple_moves::CyclizationMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.

C++: protocols::moves::Mover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.simple_moves.DEEROptimizeCoordsMover¶

Bases: Mover

apply(self: pyrosetta.rosetta.protocols.simple_moves.DEEROptimizeCoordsMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::simple_moves::DEEROptimizeCoordsMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.DEEROptimizeCoordsMover, : pyrosetta.rosetta.protocols.simple_moves.DEEROptimizeCoordsMover) → pyrosetta.rosetta.protocols.simple_moves.DEEROptimizeCoordsMover¶: C++: protocols::simple_moves::DEEROptimizeCoordsMover::operator=(const class protocols::simple_moves::DEEROptimizeCoordsMover &) –> class protocols::simple_moves::DEEROptimizeCoordsMover &

boltzmann(*args, **kwargs)¶

Overloaded function.

boltzmann(self: pyrosetta.rosetta.protocols.simple_moves.DEEROptimizeCoordsMover, diff: float) -> bool
boltzmann(self: pyrosetta.rosetta.protocols.simple_moves.DEEROptimizeCoordsMover, diff: float, temp: float) -> bool

C++: protocols::simple_moves::DEEROptimizeCoordsMover::boltzmann(const double &, const double &) const –> bool

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.simple_moves.DEEROptimizeCoordsMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::DEEROptimizeCoordsMover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

create_mover(self: pyrosetta.rosetta.protocols.simple_moves.DEEROptimizeCoordsMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::DEEROptimizeCoordsMover::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶

Generates a new Mover object freshly created with the default ctor.

C++: protocols::moves::Mover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.simple_moves.DEEROptimizeCoordsMover) → str¶: C++: protocols::simple_moves::DEEROptimizeCoordsMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

init_coords(self: pyrosetta.rosetta.protocols.simple_moves.DEEROptimizeCoordsMover, pose: pyrosetta.rosetta.core.pose.Pose, datacache: pyrosetta.rosetta.core.scoring.epr_deer.DEERDataCache) → pyrosetta.rosetta.std.map_std_pair_unsigned_long_std_string_t_utility_vector1_std_pair_numeric_xyzVector_double_double_std_allocator_std_pair_numeric_xyzVector_double_double_t_std_less_std_pair_unsigned_long_std_string_t_std_allocator_std_pair_const_std_pair_unsigned_long_std_string_utility_vector1_std_pair_numeric_xyzVector_double_double_std_allocator_std_pair_numeric_xyzVector_double_double_t¶

Initializes coords used throughout method

Pose being labeled

Coords that pass clash evaluation

C++: protocols::simple_moves::DEEROptimizeCoordsMover::init_coords(class core::pose::Pose &, const class core::scoring::epr_deer::DEERDataCache &) –> class std::map<struct std::pair<unsigned long, std::string >, class utility::vector1<struct std::pair<class numeric::xyzVector<double>, double>, class std::allocator<struct std::pair<class numeric::xyzVector<double>, double> > >, struct std::less<struct std::pair<unsigned long, std::string > >, class std::allocator<struct std::pair<const struct std::pair<unsigned long, std::string >, class utility::vector1<struct std::pair<class numeric::xyzVector<double>, double>, class std::allocator<struct std::pair<class numeric::xyzVector<double>, double> > > > > >

keyname(self: pyrosetta.rosetta.protocols.simple_moves.DEEROptimizeCoordsMover) → str¶: C++: protocols::simple_moves::DEEROptimizeCoordsMover::keyname() const –> std::string

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

mover_name(self: pyrosetta.rosetta.protocols.simple_moves.DEEROptimizeCoordsMover) → str¶: C++: protocols::simple_moves::DEEROptimizeCoordsMover::mover_name() const –> std::string

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.simple_moves.DEEROptimizeCoordsMover, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::simple_moves::DEEROptimizeCoordsMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

provide_xml_schema(self: pyrosetta.rosetta.protocols.simple_moves.DEEROptimizeCoordsMover, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::DEEROptimizeCoordsMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.simple_moves.DEEROptimizeCoordsMoverCreator¶

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.simple_moves.DEEROptimizeCoordsMoverCreator, : pyrosetta.rosetta.protocols.simple_moves.DEEROptimizeCoordsMoverCreator) → pyrosetta.rosetta.protocols.simple_moves.DEEROptimizeCoordsMoverCreator¶: C++: protocols::simple_moves::DEEROptimizeCoordsMoverCreator::operator=(const class protocols::simple_moves::DEEROptimizeCoordsMoverCreator &) –> class protocols::simple_moves::DEEROptimizeCoordsMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.simple_moves.DEEROptimizeCoordsMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::DEEROptimizeCoordsMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.simple_moves.DEEROptimizeCoordsMoverCreator) → str¶: C++: protocols::simple_moves::DEEROptimizeCoordsMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.simple_moves.DEEROptimizeCoordsMoverCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::DEEROptimizeCoordsMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.simple_moves.DME_FilterMover¶

Bases: Mover

apply(self: pyrosetta.rosetta.protocols.simple_moves.DME_FilterMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::simple_moves::DME_FilterMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::operator=(const class protocols::moves::Mover &) –> class protocols::moves::Mover &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶

Return a clone of the Mover object.

C++: protocols::moves::Mover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶

Generates a new Mover object freshly created with the default ctor.

C++: protocols::moves::Mover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.simple_moves.DME_FilterMover) → str¶: C++: protocols::simple_moves::DME_FilterMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.

C++: protocols::moves::Mover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.simple_moves.DOFHistogramRecorder¶

Bases: pybind11_object

dofs(self: pyrosetta.rosetta.protocols.simple_moves.DOFHistogramRecorder) → pyrosetta.rosetta.utility.vector1_utility_vector1_core_id_DOF_ID_std_allocator_core_id_DOF_ID_t¶: C++: protocols::simple_moves::DOFHistogramRecorder::dofs() const –> const class utility::vector1<class utility::vector1<class core::id::DOF_ID, class std::allocator<class core::id::DOF_ID> >, class std::allocator<class utility::vector1<class core::id::DOF_ID, class std::allocator<class core::id::DOF_ID> > > > &

histograms(self: pyrosetta.rosetta.protocols.simple_moves.DOFHistogramRecorder) → pyrosetta.rosetta.utility.vector1_numeric_MultiDimensionalHistogram¶: C++: protocols::simple_moves::DOFHistogramRecorder::histograms() const –> const class utility::vector1<class numeric::MultiDimensionalHistogram, class std::allocator<class numeric::MultiDimensionalHistogram> > &

num_bins(*args, **kwargs)¶

Overloaded function.

num_bins(self: pyrosetta.rosetta.protocols.simple_moves.DOFHistogramRecorder) -> int

C++: protocols::simple_moves::DOFHistogramRecorder::num_bins() const –> unsigned long

num_bins(self: pyrosetta.rosetta.protocols.simple_moves.DOFHistogramRecorder, num_bins: int) -> None

C++: protocols::simple_moves::DOFHistogramRecorder::num_bins(unsigned long) –> void

update_after_boltzmann(self: pyrosetta.rosetta.protocols.simple_moves.DOFHistogramRecorder, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::simple_moves::DOFHistogramRecorder::update_after_boltzmann(const class core::pose::Pose &) –> void

write_mse_summary(self: pyrosetta.rosetta.protocols.simple_moves.DOFHistogramRecorder, os: pyrosetta.rosetta.std.ostream) → None¶: C++: protocols::simple_moves::DOFHistogramRecorder::write_mse_summary(std::ostream &) const –> void

class pyrosetta.rosetta.protocols.simple_moves.DeclareBond¶

Bases: Mover

apply(self: pyrosetta.rosetta.protocols.simple_moves.DeclareBond, : pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::simple_moves::DeclareBond::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.DeclareBond, : pyrosetta.rosetta.protocols.simple_moves.DeclareBond) → pyrosetta.rosetta.protocols.simple_moves.DeclareBond¶: C++: protocols::simple_moves::DeclareBond::operator=(const class protocols::simple_moves::DeclareBond &) –> class protocols::simple_moves::DeclareBond &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.simple_moves.DeclareBond) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::DeclareBond::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.simple_moves.DeclareBond) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::DeclareBond::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.simple_moves.DeclareBond) → str¶: C++: protocols::simple_moves::DeclareBond::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static mover_name() → str¶: C++: protocols::simple_moves::DeclareBond::mover_name() –> std::string

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.simple_moves.DeclareBond, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::simple_moves::DeclareBond::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::DeclareBond::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set(*args, **kwargs)¶

Overloaded function.

set(self: pyrosetta.rosetta.protocols.simple_moves.DeclareBond, res1: int, atom1: str, res2: int, atom2: str, add_termini: bool) -> None
set(self: pyrosetta.rosetta.protocols.simple_moves.DeclareBond, res1: int, atom1: str, res2: int, atom2: str, add_termini: bool, run_kic: bool) -> None
set(self: pyrosetta.rosetta.protocols.simple_moves.DeclareBond, res1: int, atom1: str, res2: int, atom2: str, add_termini: bool, run_kic: bool, kic_res1: int) -> None
set(self: pyrosetta.rosetta.protocols.simple_moves.DeclareBond, res1: int, atom1: str, res2: int, atom2: str, add_termini: bool, run_kic: bool, kic_res1: int, kic_res2: int) -> None
set(self: pyrosetta.rosetta.protocols.simple_moves.DeclareBond, res1: int, atom1: str, res2: int, atom2: str, add_termini: bool, run_kic: bool, kic_res1: int, kic_res2: int, rebuild_fold_tree: bool) -> None

C++: protocols::simple_moves::DeclareBond::set(const unsigned long, const std::string &, const unsigned long, const std::string &, const bool, const bool, const unsigned long, const unsigned long, const bool) –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_selector_for_res1(self: pyrosetta.rosetta.protocols.simple_moves.DeclareBond, selector1: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) → None¶: C++: protocols::simple_moves::DeclareBond::set_selector_for_res1(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

set_selector_for_res2(self: pyrosetta.rosetta.protocols.simple_moves.DeclareBond, selector2: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) → None¶: C++: protocols::simple_moves::DeclareBond::set_selector_for_res2(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.simple_moves.DeclareBondCreator¶

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.simple_moves.DeclareBondCreator, : pyrosetta.rosetta.protocols.simple_moves.DeclareBondCreator) → pyrosetta.rosetta.protocols.simple_moves.DeclareBondCreator¶: C++: protocols::simple_moves::DeclareBondCreator::operator=(const class protocols::simple_moves::DeclareBondCreator &) –> class protocols::simple_moves::DeclareBondCreator &

create_mover(self: pyrosetta.rosetta.protocols.simple_moves.DeclareBondCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::DeclareBondCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.simple_moves.DeclareBondCreator) → str¶: C++: protocols::simple_moves::DeclareBondCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.simple_moves.DeclareBondCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::DeclareBondCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.simple_moves.DeleteChainMover¶

Bases: Mover

apply(self: pyrosetta.rosetta.protocols.simple_moves.DeleteChainMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::simple_moves::DeleteChainMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.DeleteChainMover, : pyrosetta.rosetta.protocols.simple_moves.DeleteChainMover) → pyrosetta.rosetta.protocols.simple_moves.DeleteChainMover¶: C++: protocols::simple_moves::DeleteChainMover::operator=(const class protocols::simple_moves::DeleteChainMover &) –> class protocols::simple_moves::DeleteChainMover &

chain_num(*args, **kwargs)¶

Overloaded function.

chain_num(self: pyrosetta.rosetta.protocols.simple_moves.DeleteChainMover, chain_num: int) -> None

C++: protocols::simple_moves::DeleteChainMover::chain_num(unsigned long) –> void

chain_num(self: pyrosetta.rosetta.protocols.simple_moves.DeleteChainMover) -> int

C++: protocols::simple_moves::DeleteChainMover::chain_num() –> unsigned long

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.simple_moves.DeleteChainMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::DeleteChainMover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.simple_moves.DeleteChainMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::DeleteChainMover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.simple_moves.DeleteChainMover) → str¶: C++: protocols::simple_moves::DeleteChainMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static mover_name() → str¶: C++: protocols::simple_moves::DeleteChainMover::mover_name() –> std::string

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.simple_moves.DeleteChainMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::simple_moves::DeleteChainMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::DeleteChainMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.simple_moves.DeleteChainMoverCreator¶

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.simple_moves.DeleteChainMoverCreator, : pyrosetta.rosetta.protocols.simple_moves.DeleteChainMoverCreator) → pyrosetta.rosetta.protocols.simple_moves.DeleteChainMoverCreator¶: C++: protocols::simple_moves::DeleteChainMoverCreator::operator=(const class protocols::simple_moves::DeleteChainMoverCreator &) –> class protocols::simple_moves::DeleteChainMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.simple_moves.DeleteChainMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::DeleteChainMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.simple_moves.DeleteChainMoverCreator) → str¶: C++: protocols::simple_moves::DeleteChainMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.simple_moves.DeleteChainMoverCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::DeleteChainMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover¶

Bases: Mover

Delete a chain from a Pose, or a set of chains.

Deletes Each chain using conformation.delete_residue_range_slow
1. Calls detect bonds, pseudobonds, and disulfides
2. Makes sure PDBInfo is still intact
3. Sets a new reasonable FoldTree

apply(self: pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::simple_moves::DeleteChainsMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover, : pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover) → pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover¶: C++: protocols::simple_moves::DeleteChainsMover::operator=(const class protocols::simple_moves::DeleteChainsMover &) –> class protocols::simple_moves::DeleteChainsMover &

chains(self: pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover) → str¶

Get the chain

C++: protocols::simple_moves::DeleteChainsMover::chains() const –> std::string

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover) → pyrosetta.rosetta.protocols.moves.Mover¶

///////////// Mover Methods /////////////////////////////////////////////

C++: protocols::simple_moves::DeleteChainsMover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

detect_bonds(self: pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover) → bool¶: C++: protocols::simple_moves::DeleteChainsMover::detect_bonds() const –> bool

detect_pseudobonds(self: pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover) → bool¶: C++: protocols::simple_moves::DeleteChainsMover::detect_pseudobonds() const –> bool

fresh_instance(self: pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::DeleteChainsMover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover) → str¶: C++: protocols::simple_moves::DeleteChainsMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static mover_name() → str¶: C++: protocols::simple_moves::DeleteChainsMover::mover_name() –> std::string

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::simple_moves::DeleteChainsMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide the citation.

C++: protocols::simple_moves::DeleteChainsMover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::DeleteChainsMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_chains(self: pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover, chains: str) → None¶

Set the chain: Will figure out the chainIDs at apply time.

C++: protocols::simple_moves::DeleteChainsMover::set_chains(const std::string &) –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_defaults(self: pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover) → None¶: C++: protocols::simple_moves::DeleteChainsMover::set_defaults() –> void

set_detect_bonds(self: pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover, detect_bonds: bool) → None¶

Set the class to detect bonds after full deletion of chains?: Default True. Override for speed and if you know there are no bonds between chains other than possible disulfides.

C++: protocols::simple_moves::DeleteChainsMover::set_detect_bonds(bool) –> void

set_detect_pseudobonds(self: pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover, detect_pseudobonds: bool) → None¶

Set the class to detect psuedobonds after full deletion of chains?: Default True. Override for speed and if you know there are no pseudobonds between chains other than possible disulfides.

C++: protocols::simple_moves::DeleteChainsMover::set_detect_pseudobonds(bool) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMoverCreator¶

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMoverCreator, : pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMoverCreator) → pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMoverCreator¶: C++: protocols::simple_moves::DeleteChainsMoverCreator::operator=(const class protocols::simple_moves::DeleteChainsMoverCreator &) –> class protocols::simple_moves::DeleteChainsMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::DeleteChainsMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMoverCreator) → str¶: C++: protocols::simple_moves::DeleteChainsMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMoverCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::DeleteChainsMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.simple_moves.DisulfideCyclizationViability¶

Bases: pybind11_object

Members:

DCV_NOT_CYCLIZABLE

DCV_CYCLIZABLE

DCV_ALREADY_CYCLIZED

DCV_ALREADY_CYCLIZED = <DisulfideCyclizationViability.DCV_ALREADY_CYCLIZED: 2>¶

DCV_CYCLIZABLE = <DisulfideCyclizationViability.DCV_CYCLIZABLE: 1>¶

DCV_NOT_CYCLIZABLE = <DisulfideCyclizationViability.DCV_NOT_CYCLIZABLE: 0>¶

property name¶

property value¶

class pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover¶

Bases: Mover

a mover that given a receptor peptide pose mutates the peptides edge residues to cysteins, if needed, and enforces disulfide bonding by constrained minimization of the bond and the interaction

apply(self: pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::simple_moves::DisulfideInsertionMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover, : pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover) → pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover¶: C++: protocols::simple_moves::DisulfideInsertionMover::operator=(const class protocols::simple_moves::DisulfideInsertionMover &) –> class protocols::simple_moves::DisulfideInsertionMover &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::DisulfideInsertionMover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

determine_cyclization_viability(self: pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover, partner_pose: pyrosetta.rosetta.core.pose.Pose, n_cyd_position: int, c_cyd_position: int) → pyrosetta.rosetta.protocols.simple_moves.DisulfideCyclizationViability¶

checks if two residues in a pose are near enough in space: and geometrically similar enough to existing disulfide forming cys

C++: protocols::simple_moves::DisulfideInsertionMover::determine_cyclization_viability(const class core::pose::Pose &, const unsigned long, unsigned long) –> enum protocols::simple_moves::DisulfideCyclizationViability

fresh_instance(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶

Generates a new Mover object freshly created with the default ctor.

C++: protocols::moves::Mover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_c_cyd_seqpos(self: pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover) → int¶: C++: protocols::simple_moves::DisulfideInsertionMover::get_c_cyd_seqpos() const –> unsigned long

get_constraint_weight(self: pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover) → float¶: C++: protocols::simple_moves::DisulfideInsertionMover::get_constraint_weight() const –> double

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_max_dslf_energy(self: pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover) → float¶: C++: protocols::simple_moves::DisulfideInsertionMover::get_max_dslf_energy() –> double

get_max_dslf_pot(self: pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover) → float¶: C++: protocols::simple_moves::DisulfideInsertionMover::get_max_dslf_pot() –> double

get_movemap_factory(self: pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover) → pyrosetta.rosetta.core.select.movemap.MoveMapFactory¶: C++: protocols::simple_moves::DisulfideInsertionMover::get_movemap_factory() const –> class std::shared_ptr<const class core::select::movemap::MoveMapFactory>

get_n_cyd_seqpos(self: pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover) → int¶: C++: protocols::simple_moves::DisulfideInsertionMover::get_n_cyd_seqpos() const –> unsigned long

get_name(self: pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover) → str¶: C++: protocols::simple_moves::DisulfideInsertionMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_peptide_chain(self: pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover) → int¶: C++: protocols::simple_moves::DisulfideInsertionMover::get_peptide_chain() const –> unsigned long

get_scorefxn(self: pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover) → pyrosetta.rosetta.core.scoring.ScoreFunction¶: C++: protocols::simple_moves::DisulfideInsertionMover::get_scorefxn() const –> class std::shared_ptr<class core::scoring::ScoreFunction>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static mover_name() → str¶: C++: protocols::simple_moves::DisulfideInsertionMover::mover_name() –> std::string

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::simple_moves::DisulfideInsertionMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::DisulfideInsertionMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_c_cyd_seqpos(self: pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover, c_cyd_seqpos: int) → None¶: C++: protocols::simple_moves::DisulfideInsertionMover::set_c_cyd_seqpos(const unsigned long) –> void

set_constraint_weight(self: pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover, value: float) → None¶: C++: protocols::simple_moves::DisulfideInsertionMover::set_constraint_weight(const double) –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_max_dslf_energy(self: pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover, value: float) → None¶: C++: protocols::simple_moves::DisulfideInsertionMover::set_max_dslf_energy(const double) –> void

set_max_dslf_pot(self: pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover, value: float) → None¶: C++: protocols::simple_moves::DisulfideInsertionMover::set_max_dslf_pot(const double) –> void

set_movemap_factory(self: pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover, mm: pyrosetta.rosetta.core.select.movemap.MoveMapFactory) → None¶: C++: protocols::simple_moves::DisulfideInsertionMover::set_movemap_factory(const class std::shared_ptr<const class core::select::movemap::MoveMapFactory>) –> void

set_n_cyd_seqpos(self: pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover, n_cyd_seqpos: int) → None¶: C++: protocols::simple_moves::DisulfideInsertionMover::set_n_cyd_seqpos(const unsigned long) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_peptide_chain(self: pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover, value: int) → None¶: C++: protocols::simple_moves::DisulfideInsertionMover::set_peptide_chain(const unsigned long) –> void

set_scorefxn(self: pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover, score_function: pyrosetta.rosetta.core.scoring.ScoreFunction) → None¶: C++: protocols::simple_moves::DisulfideInsertionMover::set_scorefxn(const class std::shared_ptr<class core::scoring::ScoreFunction>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMoverCreator¶

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMoverCreator, : pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMoverCreator) → pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMoverCreator¶: C++: protocols::simple_moves::DisulfideInsertionMoverCreator::operator=(const class protocols::simple_moves::DisulfideInsertionMoverCreator &) –> class protocols::simple_moves::DisulfideInsertionMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::DisulfideInsertionMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMoverCreator) → str¶: C++: protocols::simple_moves::DisulfideInsertionMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMoverCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::DisulfideInsertionMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.simple_moves.DumpPdb¶

Bases: Mover

what you think this can now be assimilated into DumpPdbMover

apply(self: pyrosetta.rosetta.protocols.simple_moves.DumpPdb, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::simple_moves::DumpPdb::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.DumpPdb, : pyrosetta.rosetta.protocols.simple_moves.DumpPdb) → pyrosetta.rosetta.protocols.simple_moves.DumpPdb¶: C++: protocols::simple_moves::DumpPdb::operator=(const class protocols::simple_moves::DumpPdb &) –> class protocols::simple_moves::DumpPdb &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.simple_moves.DumpPdb) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::DumpPdb::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.simple_moves.DumpPdb) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::DumpPdb::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.simple_moves.DumpPdb) → str¶: C++: protocols::simple_moves::DumpPdb::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static mover_name() → str¶: C++: protocols::simple_moves::DumpPdb::mover_name() –> std::string

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.simple_moves.DumpPdb, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::simple_moves::DumpPdb::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::DumpPdb::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_filename(self: pyrosetta.rosetta.protocols.simple_moves.DumpPdb, filename_in: str) → None¶

Set the filename for writing.

Vikram K. Mulligan (vmullig.edu).

C++: protocols::simple_moves::DumpPdb::set_filename(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_scorefxn(self: pyrosetta.rosetta.protocols.simple_moves.DumpPdb, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) → None¶: C++: protocols::simple_moves::DumpPdb::set_scorefxn(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

set_use_pose_name(self: pyrosetta.rosetta.protocols.simple_moves.DumpPdb, use_pose_name: bool) → None¶

If set, will use the original pose name in the name. Useful if running xml in parallel.

C++: protocols::simple_moves::DumpPdb::set_use_pose_name(bool) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

tag_time(*args, **kwargs)¶

Overloaded function.

tag_time(self: pyrosetta.rosetta.protocols.simple_moves.DumpPdb, setting: bool) -> None

C++: protocols::simple_moves::DumpPdb::tag_time(bool) –> void

tag_time(self: pyrosetta.rosetta.protocols.simple_moves.DumpPdb) -> bool

C++: protocols::simple_moves::DumpPdb::tag_time() const –> bool

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.simple_moves.DumpPdbCreator¶

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.simple_moves.DumpPdbCreator, : pyrosetta.rosetta.protocols.simple_moves.DumpPdbCreator) → pyrosetta.rosetta.protocols.simple_moves.DumpPdbCreator¶: C++: protocols::simple_moves::DumpPdbCreator::operator=(const class protocols::simple_moves::DumpPdbCreator &) –> class protocols::simple_moves::DumpPdbCreator &

create_mover(self: pyrosetta.rosetta.protocols.simple_moves.DumpPdbCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::DumpPdbCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.simple_moves.DumpPdbCreator) → str¶: C++: protocols::simple_moves::DumpPdbCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.simple_moves.DumpPdbCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::DumpPdbCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers¶

Bases: Mover

Given a residue index, dump all of the rotamers to individual PDB files within 0-1 sd of the mean

apply(self: pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Apply the mover

C++: protocols::simple_moves::DumpSingleResidueRotamers::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers, : pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers) → pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers¶: C++: protocols::simple_moves::DumpSingleResidueRotamers::operator=(const class protocols::simple_moves::DumpSingleResidueRotamers &) –> class protocols::simple_moves::DumpSingleResidueRotamers &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers) → pyrosetta.rosetta.protocols.moves.Mover¶

required in the context of the parser/scripting scheme

C++: protocols::simple_moves::DumpSingleResidueRotamers::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers) → pyrosetta.rosetta.protocols.moves.Mover¶

required in the context of the parser/scripting scheme

C++: protocols::simple_moves::DumpSingleResidueRotamers::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers) → str¶: C++: protocols::simple_moves::DumpSingleResidueRotamers::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static mover_name() → str¶: C++: protocols::simple_moves::DumpSingleResidueRotamers::mover_name() –> std::string

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

parse XML tag (to use this Mover in Rosetta Scripts)

C++: protocols::simple_moves::DumpSingleResidueRotamers::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::DumpSingleResidueRotamers::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers) -> None
show(self: pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers, output: pyrosetta.rosetta.std.ostream) -> None

C++: protocols::simple_moves::DumpSingleResidueRotamers::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamersCreator¶

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamersCreator, : pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamersCreator) → pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamersCreator¶: C++: protocols::simple_moves::DumpSingleResidueRotamersCreator::operator=(const class protocols::simple_moves::DumpSingleResidueRotamersCreator &) –> class protocols::simple_moves::DumpSingleResidueRotamersCreator &

create_mover(self: pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamersCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::DumpSingleResidueRotamersCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamersCreator) → str¶: C++: protocols::simple_moves::DumpSingleResidueRotamersCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamersCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::DumpSingleResidueRotamersCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.simple_moves.ExplicitWaterMover¶

Bases: Mover

apply(self: pyrosetta.rosetta.protocols.simple_moves.ExplicitWaterMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::simple_moves::ExplicitWaterMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.ExplicitWaterMover, : pyrosetta.rosetta.protocols.simple_moves.ExplicitWaterMover) → pyrosetta.rosetta.protocols.simple_moves.ExplicitWaterMover¶: C++: protocols::simple_moves::ExplicitWaterMover::operator=(const class protocols::simple_moves::ExplicitWaterMover &) –> class protocols::simple_moves::ExplicitWaterMover &

attach_rotamer_clouds_to_pose_and_rotset(self: pyrosetta.rosetta.protocols.simple_moves.ExplicitWaterMover, pose: pyrosetta.rosetta.core.pose.Pose, watercloud: pyrosetta.rosetta.utility.vector1_utility_vector1_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t) → None¶: C++: protocols::simple_moves::ExplicitWaterMover::attach_rotamer_clouds_to_pose_and_rotset(class core::pose::Pose &, class utility::vector1<class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > >, class std::allocator<class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > > > > &) –> void

build_backbone_rotamer_clouds(self: pyrosetta.rosetta.protocols.simple_moves.ExplicitWaterMover, pose: pyrosetta.rosetta.core.pose.Pose, new_rotamers: pyrosetta.rosetta.utility.vector1_utility_vector1_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t) → None¶: C++: protocols::simple_moves::ExplicitWaterMover::build_backbone_rotamer_clouds(const class core::pose::Pose &, class utility::vector1<class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > >, class std::allocator<class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > > > > &) –> void

build_lkboverlap_rotamer_clouds(self: pyrosetta.rosetta.protocols.simple_moves.ExplicitWaterMover, pose: pyrosetta.rosetta.core.pose.Pose, new_rotamers: pyrosetta.rosetta.utility.vector1_utility_vector1_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t) → None¶: C++: protocols::simple_moves::ExplicitWaterMover::build_lkboverlap_rotamer_clouds(const class core::pose::Pose &, class utility::vector1<class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > >, class std::allocator<class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > > > > &) –> void

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.simple_moves.ExplicitWaterMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::ExplicitWaterMover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

cluster_rotset(self: pyrosetta.rosetta.protocols.simple_moves.ExplicitWaterMover, rotset: pyrosetta.rosetta.utility.vector1_core_pack_annealer_PointDwell) → None¶

cluster water clouds

C++: protocols::simple_moves::ExplicitWaterMover::cluster_rotset(class utility::vector1<struct core::pack::annealer::PointDwell, class std::allocator<struct core::pack::annealer::PointDwell> > &) –> void

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

static define_explicit_water_mover_schema() → pyrosetta.rosetta.utility.tag.XMLSchemaComplexTypeGenerator¶: C++: protocols::simple_moves::ExplicitWaterMover::define_explicit_water_mover_schema() –> class std::shared_ptr<class utility::tag::XMLSchemaComplexTypeGenerator>

delete_waters(self: pyrosetta.rosetta.protocols.simple_moves.ExplicitWaterMover, pose: pyrosetta.rosetta.core.pose.Pose, virt_only: bool) → None¶: C++: protocols::simple_moves::ExplicitWaterMover::delete_waters(class core::pose::Pose &, bool) –> void

find_closest(self: pyrosetta.rosetta.protocols.simple_moves.ExplicitWaterMover, pose: pyrosetta.rosetta.core.pose.Pose, Ocoord: pyrosetta.rosetta.numeric.xyzVector_double_t) → int¶

find closest protein residue

C++: protocols::simple_moves::ExplicitWaterMover::find_closest(const class core::pose::Pose &, class numeric::xyzVector<double>) –> unsigned long

fresh_instance(self: pyrosetta.rosetta.protocols.simple_moves.ExplicitWaterMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::ExplicitWaterMover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.simple_moves.ExplicitWaterMover) → str¶: C++: protocols::simple_moves::ExplicitWaterMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

init(self: pyrosetta.rosetta.protocols.simple_moves.ExplicitWaterMover) → None¶: C++: protocols::simple_moves::ExplicitWaterMover::init() –> void

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static mover_name() → str¶: C++: protocols::simple_moves::ExplicitWaterMover::mover_name() –> std::string

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.simple_moves.ExplicitWaterMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::simple_moves::ExplicitWaterMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::ExplicitWaterMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

run_pack(self: pyrosetta.rosetta.protocols.simple_moves.ExplicitWaterMover, pose: pyrosetta.rosetta.core.pose.Pose, rot_to_pack: pyrosetta.rosetta.utility.vector0_int, all_rot: pyrosetta.rosetta.utility.vector1_core_pack_annealer_PointDwell) → None¶: C++: protocols::simple_moves::ExplicitWaterMover::run_pack(class core::pose::Pose &, class utility::vector0<int, class std::allocator<int> >, class utility::vector1<struct core::pack::annealer::PointDwell, class std::allocator<struct core::pack::annealer::PointDwell> > &) –> void

set_clust_cutoff(self: pyrosetta.rosetta.protocols.simple_moves.ExplicitWaterMover, val: float) → None¶: C++: protocols::simple_moves::ExplicitWaterMover::set_clust_cutoff(double) –> void

set_clust_radius(self: pyrosetta.rosetta.protocols.simple_moves.ExplicitWaterMover, val: float) → None¶: C++: protocols::simple_moves::ExplicitWaterMover::set_clust_radius(double) –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_dwell_cutoff(self: pyrosetta.rosetta.protocols.simple_moves.ExplicitWaterMover, val: float) → None¶: C++: protocols::simple_moves::ExplicitWaterMover::set_dwell_cutoff(double) –> void

set_gen_fixed(*args, **kwargs)¶

Overloaded function.

set_gen_fixed(self: pyrosetta.rosetta.protocols.simple_moves.ExplicitWaterMover, val: bool) -> None

C++: protocols::simple_moves::ExplicitWaterMover::set_gen_fixed(bool) –> void

set_gen_fixed(self: pyrosetta.rosetta.protocols.simple_moves.ExplicitWaterMover, val: pyrosetta.rosetta.utility.vector1_bool) -> None

C++: protocols::simple_moves::ExplicitWaterMover::set_gen_fixed(class utility::vector1<bool, class std::allocator<bool> >) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_lkb_clust_rad(self: pyrosetta.rosetta.protocols.simple_moves.ExplicitWaterMover, val: float) → None¶: C++: protocols::simple_moves::ExplicitWaterMover::set_lkb_clust_rad(double) –> void

set_lkb_overlap_dist(self: pyrosetta.rosetta.protocols.simple_moves.ExplicitWaterMover, val: float) → None¶: C++: protocols::simple_moves::ExplicitWaterMover::set_lkb_overlap_dist(double) –> void

set_lkb_rotset_radius(self: pyrosetta.rosetta.protocols.simple_moves.ExplicitWaterMover, val: float) → None¶: C++: protocols::simple_moves::ExplicitWaterMover::set_lkb_rotset_radius(double) –> void

set_mode(self: pyrosetta.rosetta.protocols.simple_moves.ExplicitWaterMover, val: str) → None¶: C++: protocols::simple_moves::ExplicitWaterMover::set_mode(std::string) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_taskop(self: pyrosetta.rosetta.protocols.simple_moves.ExplicitWaterMover, val: pyrosetta.rosetta.core.pack.task.PackerTask) → None¶: C++: protocols::simple_moves::ExplicitWaterMover::set_taskop(class std::shared_ptr<const class core::pack::task::PackerTask>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

set_watlim_scale(self: pyrosetta.rosetta.protocols.simple_moves.ExplicitWaterMover, val: float) → None¶: C++: protocols::simple_moves::ExplicitWaterMover::set_watlim_scale(double) –> void

setup_pack(self: pyrosetta.rosetta.protocols.simple_moves.ExplicitWaterMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setup the initial packing step

C++: protocols::simple_moves::ExplicitWaterMover::setup_pack(class core::pose::Pose &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

update_packer_task(self: pyrosetta.rosetta.protocols.simple_moves.ExplicitWaterMover, pose: pyrosetta.rosetta.core.pose.Pose, packer_task: pyrosetta.rosetta.core.pack.task.PackerTask) → pyrosetta.rosetta.core.pack.task.PackerTask¶: C++: protocols::simple_moves::ExplicitWaterMover::update_packer_task(const class core::pose::Pose &, class std::shared_ptr<const class core::pack::task::PackerTask> &) –> class std::shared_ptr<class core::pack::task::PackerTask>

class pyrosetta.rosetta.protocols.simple_moves.ExplicitWaterMoverCreator¶

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.simple_moves.ExplicitWaterMoverCreator, : pyrosetta.rosetta.protocols.simple_moves.ExplicitWaterMoverCreator) → pyrosetta.rosetta.protocols.simple_moves.ExplicitWaterMoverCreator¶: C++: protocols::simple_moves::ExplicitWaterMoverCreator::operator=(const class protocols::simple_moves::ExplicitWaterMoverCreator &) –> class protocols::simple_moves::ExplicitWaterMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.simple_moves.ExplicitWaterMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::ExplicitWaterMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.simple_moves.ExplicitWaterMoverCreator) → str¶: C++: protocols::simple_moves::ExplicitWaterMoverCreator::keyname() const –> std::string

static mover_name() → str¶: C++: protocols::simple_moves::ExplicitWaterMoverCreator::mover_name() –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.simple_moves.ExplicitWaterMoverCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::ExplicitWaterMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.simple_moves.FavorSequenceProfile¶

Bases: Mover

apply(self: pyrosetta.rosetta.protocols.simple_moves.FavorSequenceProfile, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::simple_moves::FavorSequenceProfile::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.FavorSequenceProfile, : pyrosetta.rosetta.protocols.simple_moves.FavorSequenceProfile) → pyrosetta.rosetta.protocols.simple_moves.FavorSequenceProfile¶: C++: protocols::simple_moves::FavorSequenceProfile::operator=(const class protocols::simple_moves::FavorSequenceProfile &) –> class protocols::simple_moves::FavorSequenceProfile &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.simple_moves.FavorSequenceProfile) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::FavorSequenceProfile::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.simple_moves.FavorSequenceProfile) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::FavorSequenceProfile::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.simple_moves.FavorSequenceProfile) → str¶: C++: protocols::simple_moves::FavorSequenceProfile::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static mover_name() → str¶: C++: protocols::simple_moves::FavorSequenceProfile::mover_name() –> std::string

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.simple_moves.FavorSequenceProfile, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::simple_moves::FavorSequenceProfile::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::FavorSequenceProfile::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_profile(self: pyrosetta.rosetta.protocols.simple_moves.FavorSequenceProfile, profile: pyrosetta.rosetta.core.sequence.SequenceProfile) → None¶

Set the profile object to use.: Remember to set set_scaling() appropriately for the profile matrix you pass in.

C++: protocols::simple_moves::FavorSequenceProfile::set_profile(class core::sequence::SequenceProfile &) –> void

set_scaling(self: pyrosetta.rosetta.protocols.simple_moves.FavorSequenceProfile, scaling: str) → None¶

What type of manipulation to apply to the profile prior to using it for constraints.

C++: protocols::simple_moves::FavorSequenceProfile::set_scaling(const std::string &) –> void

set_sequence(self: pyrosetta.rosetta.protocols.simple_moves.FavorSequenceProfile, seq: pyrosetta.rosetta.core.sequence.Sequence, matrix: str) → None¶: C++: protocols::simple_moves::FavorSequenceProfile::set_sequence(class core::sequence::Sequence &, std::string) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

set_weight(self: pyrosetta.rosetta.protocols.simple_moves.FavorSequenceProfile, weight: float) → None¶

What multiplication factor to apply to the profile prior to using it for constraints.

C++: protocols::simple_moves::FavorSequenceProfile::set_weight(double) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.simple_moves.FavorSequenceProfileCreator¶

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.simple_moves.FavorSequenceProfileCreator, : pyrosetta.rosetta.protocols.simple_moves.FavorSequenceProfileCreator) → pyrosetta.rosetta.protocols.simple_moves.FavorSequenceProfileCreator¶: C++: protocols::simple_moves::FavorSequenceProfileCreator::operator=(const class protocols::simple_moves::FavorSequenceProfileCreator &) –> class protocols::simple_moves::FavorSequenceProfileCreator &

create_mover(self: pyrosetta.rosetta.protocols.simple_moves.FavorSequenceProfileCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::FavorSequenceProfileCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.simple_moves.FavorSequenceProfileCreator) → str¶: C++: protocols::simple_moves::FavorSequenceProfileCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.simple_moves.FavorSequenceProfileCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::FavorSequenceProfileCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.simple_moves.FavorSymmetricSequence¶

Bases: Mover

apply(self: pyrosetta.rosetta.protocols.simple_moves.FavorSymmetricSequence, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::simple_moves::FavorSymmetricSequence::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.FavorSymmetricSequence, : pyrosetta.rosetta.protocols.simple_moves.FavorSymmetricSequence) → pyrosetta.rosetta.protocols.simple_moves.FavorSymmetricSequence¶: C++: protocols::simple_moves::FavorSymmetricSequence::operator=(const class protocols::simple_moves::FavorSymmetricSequence &) –> class protocols::simple_moves::FavorSymmetricSequence &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.simple_moves.FavorSymmetricSequence) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::FavorSymmetricSequence::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶

Generates a new Mover object freshly created with the default ctor.

C++: protocols::moves::Mover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.simple_moves.FavorSymmetricSequence) → str¶: C++: protocols::simple_moves::FavorSymmetricSequence::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static mover_name() → str¶: C++: protocols::simple_moves::FavorSymmetricSequence::mover_name() –> std::string

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.simple_moves.FavorSymmetricSequence, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::simple_moves::FavorSymmetricSequence::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::FavorSymmetricSequence::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.simple_moves.FavorSymmetricSequenceCreator¶

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.simple_moves.FavorSymmetricSequenceCreator, : pyrosetta.rosetta.protocols.simple_moves.FavorSymmetricSequenceCreator) → pyrosetta.rosetta.protocols.simple_moves.FavorSymmetricSequenceCreator¶: C++: protocols::simple_moves::FavorSymmetricSequenceCreator::operator=(const class protocols::simple_moves::FavorSymmetricSequenceCreator &) –> class protocols::simple_moves::FavorSymmetricSequenceCreator &

create_mover(self: pyrosetta.rosetta.protocols.simple_moves.FavorSymmetricSequenceCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::FavorSymmetricSequenceCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.simple_moves.FavorSymmetricSequenceCreator) → str¶: C++: protocols::simple_moves::FavorSymmetricSequenceCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.simple_moves.FavorSymmetricSequenceCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::FavorSymmetricSequenceCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.simple_moves.FoldTreeFromMotif¶

Bases: Mover

apply(self: pyrosetta.rosetta.protocols.simple_moves.FoldTreeFromMotif, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::simple_moves::FoldTreeFromMotif::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.FoldTreeFromMotif, : pyrosetta.rosetta.protocols.simple_moves.FoldTreeFromMotif) → pyrosetta.rosetta.protocols.simple_moves.FoldTreeFromMotif¶: C++: protocols::simple_moves::FoldTreeFromMotif::operator=(const class protocols::simple_moves::FoldTreeFromMotif &) –> class protocols::simple_moves::FoldTreeFromMotif &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.simple_moves.FoldTreeFromMotif) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::FoldTreeFromMotif::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.simple_moves.FoldTreeFromMotif) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::FoldTreeFromMotif::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.simple_moves.FoldTreeFromMotif) → str¶: C++: protocols::simple_moves::FoldTreeFromMotif::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static mover_name() → str¶: C++: protocols::simple_moves::FoldTreeFromMotif::mover_name() –> std::string

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.simple_moves.FoldTreeFromMotif, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::simple_moves::FoldTreeFromMotif::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::FoldTreeFromMotif::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

residue_selector(self: pyrosetta.rosetta.protocols.simple_moves.FoldTreeFromMotif, selector_in: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) → None¶: C++: protocols::simple_moves::FoldTreeFromMotif::residue_selector(const class std::shared_ptr<const class core::select::residue_selector::ResidueSelector> &) –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.simple_moves.FoldTreeFromMotifCreator¶

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.simple_moves.FoldTreeFromMotifCreator, : pyrosetta.rosetta.protocols.simple_moves.FoldTreeFromMotifCreator) → pyrosetta.rosetta.protocols.simple_moves.FoldTreeFromMotifCreator¶: C++: protocols::simple_moves::FoldTreeFromMotifCreator::operator=(const class protocols::simple_moves::FoldTreeFromMotifCreator &) –> class protocols::simple_moves::FoldTreeFromMotifCreator &

create_mover(self: pyrosetta.rosetta.protocols.simple_moves.FoldTreeFromMotifCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::FoldTreeFromMotifCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.simple_moves.FoldTreeFromMotifCreator) → str¶: C++: protocols::simple_moves::FoldTreeFromMotifCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.simple_moves.FoldTreeFromMotifCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::FoldTreeFromMotifCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.simple_moves.FragmentCost¶

Bases: pybind11_object

assign(self: pyrosetta.rosetta.protocols.simple_moves.FragmentCost, : pyrosetta.rosetta.protocols.simple_moves.FragmentCost) → pyrosetta.rosetta.protocols.simple_moves.FragmentCost¶: C++: protocols::simple_moves::FragmentCost::operator=(const class protocols::simple_moves::FragmentCost &) –> class protocols::simple_moves::FragmentCost &

cutoff(self: pyrosetta.rosetta.protocols.simple_moves.FragmentCost) → float¶: C++: protocols::simple_moves::FragmentCost::cutoff() const –> double

score(self: pyrosetta.rosetta.protocols.simple_moves.FragmentCost, : pyrosetta.rosetta.core.fragment.Frame, pose: pyrosetta.rosetta.core.pose.Pose, scores: pyrosetta.rosetta.utility.vector1_double) → None¶: C++: protocols::simple_moves::FragmentCost::score(const class core::fragment::Frame &, const class core::pose::Pose &, class utility::vector1<double, class std::allocator<double> > &) –> void

type(self: pyrosetta.rosetta.protocols.simple_moves.FragmentCost) → str¶: C++: protocols::simple_moves::FragmentCost::type() –> const std::string &

class pyrosetta.rosetta.protocols.simple_moves.FragmentMover¶

Bases: MoveMapMover

abstract base class for FragmentMovers

apply(*args, **kwargs)¶

Overloaded function.

apply(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover, : pyrosetta.rosetta.core.pose.Pose) -> None
apply(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover, : pyrosetta.rosetta.core.pose.Pose, pos: int) -> bool

apply a fragment at pos to movemable dofs

C++: protocols::simple_moves::FragmentMover::apply(class core::pose::Pose &, unsigned long) const –> bool

apply_at_all_positions(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover, : pyrosetta.rosetta.core.pose.Pose) → int¶

apply at all movemable positions — honors movemap

C++: protocols::simple_moves::FragmentMover::apply_at_all_positions(class core::pose::Pose &) const –> unsigned long

assign(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover, : pyrosetta.rosetta.protocols.simple_moves.FragmentMover) → pyrosetta.rosetta.protocols.simple_moves.FragmentMover¶: C++: protocols::simple_moves::FragmentMover::operator=(const class protocols::simple_moves::FragmentMover &) –> class protocols::simple_moves::FragmentMover &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶

Return a clone of the Mover object.

C++: protocols::moves::Mover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fragments(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover) → pyrosetta.rosetta.core.fragment.FragSet¶

accessor to the fragment set

C++: protocols::simple_moves::FragmentMover::fragments() const –> class std::shared_ptr<const class core::fragment::FragSet>

fresh_instance(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶

Generates a new Mover object freshly created with the default ctor.

C++: protocols::moves::Mover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover) → str¶: C++: protocols::simple_moves::FragmentMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

initialize(self: pyrosetta.rosetta.protocols.moves.MoveMapMover, : pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::moves::MoveMapMover::initialize(class core::pose::Pose &) –> void

insert_map(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover) → pyrosetta.rosetta.utility.vector1_unsigned_long¶: C++: protocols::simple_moves::FragmentMover::insert_map() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

insert_size(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover) → pyrosetta.rosetta.utility.vector1_unsigned_long¶: C++: protocols::simple_moves::FragmentMover::insert_size() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

movemap(*args, **kwargs)¶

Overloaded function.

movemap(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover, : pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.core.kinematics.MoveMap

C++: protocols::simple_moves::FragmentMover::movemap(const class core::pose::Pose &) const –> class std::shared_ptr<const class core::kinematics::MoveMap>

movemap(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover) -> pyrosetta.rosetta.core.kinematics.MoveMap

C++: protocols::simple_moves::FragmentMover::movemap() const –> class std::shared_ptr<const class core::kinematics::MoveMap>

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.

C++: protocols::moves::Mover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_fragments(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover, new_frags_: pyrosetta.rosetta.core.fragment.FragSet) → None¶

setter for the fragment set

C++: protocols::simple_moves::FragmentMover::set_fragments(class std::shared_ptr<const class core::fragment::FragSet>) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_movemap(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover, movemap: pyrosetta.rosetta.core.kinematics.MoveMap) → None¶

setter for the movemap

C++: protocols::simple_moves::FragmentMover::set_movemap(class std::shared_ptr<const class core::kinematics::MoveMap>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.simple_moves.GunnCost¶

Bases: FragmentCost

assign(self: pyrosetta.rosetta.protocols.simple_moves.GunnCost, : pyrosetta.rosetta.protocols.simple_moves.GunnCost) → pyrosetta.rosetta.protocols.simple_moves.GunnCost¶: C++: protocols::simple_moves::GunnCost::operator=(const class protocols::simple_moves::GunnCost &) –> class protocols::simple_moves::GunnCost &

compute_gunn(*args, **kwargs)¶

Overloaded function.

compute_gunn(self: pyrosetta.rosetta.protocols.simple_moves.GunnCost, frame: pyrosetta.rosetta.core.fragment.Frame, frag_num: int, data: pyrosetta.rosetta.protocols.simple_moves.GunnTuple) -> None

C++: protocols::simple_moves::GunnCost::compute_gunn(const class core::fragment::Frame &, unsigned long, struct protocols::simple_moves::GunnTuple &) –> void

compute_gunn(self: pyrosetta.rosetta.protocols.simple_moves.GunnCost, pose: pyrosetta.rosetta.core.pose.Pose, begin: int, end: int, data: pyrosetta.rosetta.protocols.simple_moves.GunnTuple) -> None

C++: protocols::simple_moves::GunnCost::compute_gunn(const class core::pose::Pose &, unsigned long, unsigned long, struct protocols::simple_moves::GunnTuple &) –> void

cutoff(self: pyrosetta.rosetta.protocols.simple_moves.FragmentCost) → float¶: C++: protocols::simple_moves::FragmentCost::cutoff() const –> double

property frag_cache_¶

score(self: pyrosetta.rosetta.protocols.simple_moves.GunnCost, : pyrosetta.rosetta.core.fragment.Frame, pose: pyrosetta.rosetta.core.pose.Pose, scores: pyrosetta.rosetta.utility.vector1_double) → None¶: C++: protocols::simple_moves::GunnCost::score(const class core::fragment::Frame &, const class core::pose::Pose &, class utility::vector1<double, class std::allocator<double> > &) –> void

score_tuple(self: pyrosetta.rosetta.protocols.simple_moves.GunnCost, g1: pyrosetta.rosetta.protocols.simple_moves.GunnTuple, g2: pyrosetta.rosetta.protocols.simple_moves.GunnTuple) → float¶: C++: protocols::simple_moves::GunnCost::score_tuple(const struct protocols::simple_moves::GunnTuple &, const struct protocols::simple_moves::GunnTuple &) –> double

type(self: pyrosetta.rosetta.protocols.simple_moves.FragmentCost) → str¶: C++: protocols::simple_moves::FragmentCost::type() –> const std::string &

class pyrosetta.rosetta.protocols.simple_moves.GunnTuple¶

Bases: pybind11_object

assign(self: pyrosetta.rosetta.protocols.simple_moves.GunnTuple, : pyrosetta.rosetta.protocols.simple_moves.GunnTuple) → pyrosetta.rosetta.protocols.simple_moves.GunnTuple¶: C++: protocols::simple_moves::GunnTuple::operator=(const struct protocols::simple_moves::GunnTuple &) –> struct protocols::simple_moves::GunnTuple &

property q1¶

property q2¶

property q3¶

property q4¶

property q5¶

property q6¶

class pyrosetta.rosetta.protocols.simple_moves.IonizableResidue¶

Bases: pybind11_object

acid_base_coefficient(self: pyrosetta.rosetta.protocols.simple_moves.IonizableResidue) → float¶: C++: protocols::simple_moves::IonizableResidue::acid_base_coefficient() –> double

add_ionized_restype(self: pyrosetta.rosetta.protocols.simple_moves.IonizableResidue, restype: str) → None¶: C++: protocols::simple_moves::IonizableResidue::add_ionized_restype(std::string) –> void

add_neutral_restype(self: pyrosetta.rosetta.protocols.simple_moves.IonizableResidue, restype: str) → None¶: C++: protocols::simple_moves::IonizableResidue::add_neutral_restype(std::string) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.IonizableResidue, : pyrosetta.rosetta.protocols.simple_moves.IonizableResidue) → pyrosetta.rosetta.protocols.simple_moves.IonizableResidue¶: C++: protocols::simple_moves::IonizableResidue::operator=(const class protocols::simple_moves::IonizableResidue &) –> class protocols::simple_moves::IonizableResidue &

ionized_restypes(self: pyrosetta.rosetta.protocols.simple_moves.IonizableResidue) → pyrosetta.rosetta.utility.vector1_std_string¶: C++: protocols::simple_moves::IonizableResidue::ionized_restypes() –> class utility::vector1<std::string, class std::allocator<std::string > > &

name3(self: pyrosetta.rosetta.protocols.simple_moves.IonizableResidue) → str¶: C++: protocols::simple_moves::IonizableResidue::name3() –> std::string

neutral_restypes(self: pyrosetta.rosetta.protocols.simple_moves.IonizableResidue) → pyrosetta.rosetta.utility.vector1_std_string¶: C++: protocols::simple_moves::IonizableResidue::neutral_restypes() –> class utility::vector1<std::string, class std::allocator<std::string > > &

ref_pKa(self: pyrosetta.rosetta.protocols.simple_moves.IonizableResidue) → float¶: C++: protocols::simple_moves::IonizableResidue::ref_pKa() –> double

class pyrosetta.rosetta.protocols.simple_moves.LoadPDBMover¶

Bases: Mover

append(*args, **kwargs)¶

Overloaded function.

append(self: pyrosetta.rosetta.protocols.simple_moves.LoadPDBMover) -> bool

C++: protocols::simple_moves::LoadPDBMover::append() const –> bool

append(self: pyrosetta.rosetta.protocols.simple_moves.LoadPDBMover, setting: bool) -> None

C++: protocols::simple_moves::LoadPDBMover::append(bool) –> void

apply(self: pyrosetta.rosetta.protocols.simple_moves.LoadPDBMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::simple_moves::LoadPDBMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.LoadPDBMover, : pyrosetta.rosetta.protocols.simple_moves.LoadPDBMover) → pyrosetta.rosetta.protocols.simple_moves.LoadPDBMover¶: C++: protocols::simple_moves::LoadPDBMover::operator=(const class protocols::simple_moves::LoadPDBMover &) –> class protocols::simple_moves::LoadPDBMover &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.simple_moves.LoadPDBMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::LoadPDBMover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

filename(*args, **kwargs)¶

Overloaded function.

filename(self: pyrosetta.rosetta.protocols.simple_moves.LoadPDBMover) -> str

C++: protocols::simple_moves::LoadPDBMover::filename() const –> std::string

filename(self: pyrosetta.rosetta.protocols.simple_moves.LoadPDBMover, f: str) -> None

C++: protocols::simple_moves::LoadPDBMover::filename(const std::string &) –> void

fresh_instance(self: pyrosetta.rosetta.protocols.simple_moves.LoadPDBMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::LoadPDBMover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.simple_moves.LoadPDBMover) → str¶: C++: protocols::simple_moves::LoadPDBMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static mover_name() → str¶: C++: protocols::simple_moves::LoadPDBMover::mover_name() –> std::string

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.simple_moves.LoadPDBMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::simple_moves::LoadPDBMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::LoadPDBMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.simple_moves.LoadPDBMoverCreator¶

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.simple_moves.LoadPDBMoverCreator, : pyrosetta.rosetta.protocols.simple_moves.LoadPDBMoverCreator) → pyrosetta.rosetta.protocols.simple_moves.LoadPDBMoverCreator¶: C++: protocols::simple_moves::LoadPDBMoverCreator::operator=(const class protocols::simple_moves::LoadPDBMoverCreator &) –> class protocols::simple_moves::LoadPDBMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.simple_moves.LoadPDBMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::LoadPDBMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.simple_moves.LoadPDBMoverCreator) → str¶: C++: protocols::simple_moves::LoadPDBMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.simple_moves.LoadPDBMoverCreator, xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::LoadPDBMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover¶

Bases: Mover

This BS class exists to route around a hard-coded pseudo-Mover in the APPLY_TO_POSE section of the Parser. At XRW2 we needed to move junk out of Parser to use the protocols::moves::MoverFactory instead.

apply(self: pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::simple_moves::LoadUnboundRotMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover, : pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover) → pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover¶: C++: protocols::simple_moves::LoadUnboundRotMover::operator=(const class protocols::simple_moves::LoadUnboundRotMover &) –> class protocols::simple_moves::LoadUnboundRotMover &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::LoadUnboundRotMover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::LoadUnboundRotMover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover) → str¶: C++: protocols::simple_moves::LoadUnboundRotMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static mover_name() → str¶: C++: protocols::simple_moves::LoadUnboundRotMover::mover_name() –> std::string

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶

parse XML (specifically in the context of the parser/scripting scheme)

C++: protocols::simple_moves::LoadUnboundRotMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::LoadUnboundRotMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMoverCreator¶

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMoverCreator, : pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMoverCreator) → pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMoverCreator¶: C++: protocols::simple_moves::LoadUnboundRotMoverCreator::operator=(const class protocols::simple_moves::LoadUnboundRotMoverCreator &) –> class protocols::simple_moves::LoadUnboundRotMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::LoadUnboundRotMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMoverCreator) → str¶: C++: protocols::simple_moves::LoadUnboundRotMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMoverCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::LoadUnboundRotMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.simple_moves.LoggedFragmentMover¶

Bases: ClassicFragmentMover

class Item¶

Bases: pybind11_object

property frag_num¶

property frame_pos¶

apply(*args, **kwargs)¶

Overloaded function.

apply(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, : pyrosetta.rosetta.core.pose.Pose, pos: int) -> bool
apply(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, : pyrosetta.rosetta.core.pose.Pose) -> None

Applies classic fragment insertion based on a FragSet

example:
mover_3mer.apply(pose)

See also:
ClassicFragmentMover Pose ConstantLengthFragSet

C++: protocols::simple_moves::ClassicFragmentMover::apply(class core::pose::Pose &) –> void

apply_at_all_positions(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover, : pyrosetta.rosetta.core.pose.Pose) → int¶

apply at all movemable positions — honors movemap

C++: protocols::simple_moves::FragmentMover::apply_at_all_positions(class core::pose::Pose &) const –> unsigned long

apply_fragment(self: pyrosetta.rosetta.protocols.simple_moves.LoggedFragmentMover, frame: pyrosetta.rosetta.core.fragment.Frame, frag_num: int, movemap: pyrosetta.rosetta.core.kinematics.MoveMap, pose: pyrosetta.rosetta.core.pose.Pose) → bool¶: C++: protocols::simple_moves::LoggedFragmentMover::apply_fragment(const class core::fragment::Frame &, unsigned long, const class core::kinematics::MoveMap &, class core::pose::Pose &) const –> bool

assign(self: pyrosetta.rosetta.protocols.simple_moves.LoggedFragmentMover, : pyrosetta.rosetta.protocols.simple_moves.LoggedFragmentMover) → pyrosetta.rosetta.protocols.simple_moves.LoggedFragmentMover¶: C++: protocols::simple_moves::LoggedFragmentMover::operator=(const class protocols::simple_moves::LoggedFragmentMover &) –> class protocols::simple_moves::LoggedFragmentMover &

check_ss(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover) → bool¶

accessor

C++: protocols::simple_moves::ClassicFragmentMover::check_ss() const –> bool

choose_fragment(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, : pyrosetta.rosetta.core.fragment.FrameList, : pyrosetta.rosetta.core.pose.Pose, frame_num: int, frag_num: int) → bool¶

given FrameList and pose, this method yields a fragment ( frame_num/ frag_num);: return false if nothing suitable is found

C++: protocols::simple_moves::ClassicFragmentMover::choose_fragment(const class core::fragment::FrameList &, const class core::pose::Pose &, unsigned long &, unsigned long &) const –> bool

choose_window_length(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, : pyrosetta.rosetta.core.pose.Pose, window_length: int) → bool¶

yields a length (window_length) of the fragment window to sample from: ( return false, if no suitable length is found )

C++: protocols::simple_moves::ClassicFragmentMover::choose_window_length(const class core::pose::Pose &, unsigned long &) const –> bool

choose_window_start(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, : pyrosetta.rosetta.core.pose.Pose, window_length: int, window_start: int) → bool¶

yields a start position (window_start) for fragment window to sample from: ( return false, if nothing suitable is found )

C++: protocols::simple_moves::ClassicFragmentMover::choose_window_start(const class core::pose::Pose &, unsigned long, unsigned long &) const –> bool

clear(self: pyrosetta.rosetta.protocols.simple_moves.LoggedFragmentMover) → None¶: C++: protocols::simple_moves::LoggedFragmentMover::clear() –> void

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::ClassicFragmentMover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

define_start_window(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, window_start: int) → None¶

apply fragment at predefined position

C++: protocols::simple_moves::ClassicFragmentMover::define_start_window(unsigned long) –> void

enable_end_bias_check(*args, **kwargs)¶

Overloaded function.

enable_end_bias_check(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover) -> None
enable_end_bias_check(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, setting: bool) -> None

C++: protocols::simple_moves::ClassicFragmentMover::enable_end_bias_check(bool) –> void

end_bias(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover) → float¶: C++: protocols::simple_moves::ClassicFragmentMover::end_bias() const –> double

end_bias_check(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, : pyrosetta.rosetta.core.pose.Pose, window_start: int) → bool¶: C++: protocols::simple_moves::ClassicFragmentMover::end_bias_check(const class core::pose::Pose &, unsigned long) const –> bool

end_bias_check_enabled(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover) → bool¶: C++: protocols::simple_moves::ClassicFragmentMover::end_bias_check_enabled() const –> bool

fragments(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover) → pyrosetta.rosetta.core.fragment.FragSet¶

accessor to the fragment set

C++: protocols::simple_moves::FragmentMover::fragments() const –> class std::shared_ptr<const class core::fragment::FragSet>

fresh_instance(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::ClassicFragmentMover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.simple_moves.LoggedFragmentMover) → str¶: C++: protocols::simple_moves::LoggedFragmentMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

initialize(self: pyrosetta.rosetta.protocols.moves.MoveMapMover, : pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::moves::MoveMapMover::initialize(class core::pose::Pose &) –> void

insert_map(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover) → pyrosetta.rosetta.utility.vector1_unsigned_long¶: C++: protocols::simple_moves::FragmentMover::insert_map() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

insert_size(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover) → pyrosetta.rosetta.utility.vector1_unsigned_long¶: C++: protocols::simple_moves::FragmentMover::insert_size() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

movemap(*args, **kwargs)¶

Overloaded function.

movemap(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover, : pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.core.kinematics.MoveMap

C++: protocols::simple_moves::FragmentMover::movemap(const class core::pose::Pose &) const –> class std::shared_ptr<const class core::kinematics::MoveMap>

movemap(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover) -> pyrosetta.rosetta.core.kinematics.MoveMap

C++: protocols::simple_moves::FragmentMover::movemap() const –> class std::shared_ptr<const class core::kinematics::MoveMap>

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

on_new_fragments(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover) → None¶

is called from set_fragments()

C++: protocols::simple_moves::ClassicFragmentMover::on_new_fragments() –> void

parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.

C++: protocols::moves::Mover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_check_ss(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, setting: bool) → None¶

check_ss controls whether fragment insertions are rejected that create short helices (<3) or strands (<2)

C++: protocols::simple_moves::ClassicFragmentMover::set_check_ss(bool) –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_end_bias(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, setting: float) → None¶: C++: protocols::simple_moves::ClassicFragmentMover::set_end_bias(double) –> void

set_fragments(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover, new_frags_: pyrosetta.rosetta.core.fragment.FragSet) → None¶

setter for the fragment set

C++: protocols::simple_moves::FragmentMover::set_fragments(class std::shared_ptr<const class core::fragment::FragSet>) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_min_frag_length(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, setting: int) → None¶

min_frag_length controls the behaviour fragset->region()

C++: protocols::simple_moves::ClassicFragmentMover::set_min_frag_length(unsigned long) –> void

set_min_overlap(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, setting: int) → None¶

min_overlap controls the behaviour fragset->region()

C++: protocols::simple_moves::ClassicFragmentMover::set_min_overlap(unsigned long) –> void

set_movemap(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover, movemap: pyrosetta.rosetta.core.kinematics.MoveMap) → None¶

setter for the movemap

C++: protocols::simple_moves::FragmentMover::set_movemap(class std::shared_ptr<const class core::kinematics::MoveMap>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(self: pyrosetta.rosetta.protocols.simple_moves.LoggedFragmentMover, : pyrosetta.rosetta.std.ostream) → None¶: C++: protocols::simple_moves::LoggedFragmentMover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

valid_ss(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, new_ss: str) → bool¶

returns true if the ss string is acceptable

C++: protocols::simple_moves::ClassicFragmentMover::valid_ss(const std::string &) const –> bool

class pyrosetta.rosetta.protocols.simple_moves.MembraneTopology¶

Bases: Mover

A mover to change one torsion angle

apply(self: pyrosetta.rosetta.protocols.simple_moves.MembraneTopology, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::simple_moves::MembraneTopology::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.MembraneTopology, : pyrosetta.rosetta.protocols.simple_moves.MembraneTopology) → pyrosetta.rosetta.protocols.simple_moves.MembraneTopology¶: C++: protocols::simple_moves::MembraneTopology::operator=(const class protocols::simple_moves::MembraneTopology &) –> class protocols::simple_moves::MembraneTopology &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.simple_moves.MembraneTopology) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::MembraneTopology::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.simple_moves.MembraneTopology) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::MembraneTopology::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.simple_moves.MembraneTopology) → str¶: C++: protocols::simple_moves::MembraneTopology::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static mover_name() → str¶: C++: protocols::simple_moves::MembraneTopology::mover_name() –> std::string

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.simple_moves.MembraneTopology, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::simple_moves::MembraneTopology::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::MembraneTopology::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

span_file(*args, **kwargs)¶

Overloaded function.

span_file(self: pyrosetta.rosetta.protocols.simple_moves.MembraneTopology) -> str

C++: protocols::simple_moves::MembraneTopology::span_file() const –> std::string

span_file(self: pyrosetta.rosetta.protocols.simple_moves.MembraneTopology, s: str) -> None

C++: protocols::simple_moves::MembraneTopology::span_file(const std::string &) –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.simple_moves.MembraneTopologyCreator¶

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.simple_moves.MembraneTopologyCreator, : pyrosetta.rosetta.protocols.simple_moves.MembraneTopologyCreator) → pyrosetta.rosetta.protocols.simple_moves.MembraneTopologyCreator¶: C++: protocols::simple_moves::MembraneTopologyCreator::operator=(const class protocols::simple_moves::MembraneTopologyCreator &) –> class protocols::simple_moves::MembraneTopologyCreator &

create_mover(self: pyrosetta.rosetta.protocols.simple_moves.MembraneTopologyCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::MembraneTopologyCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.simple_moves.MembraneTopologyCreator) → str¶: C++: protocols::simple_moves::MembraneTopologyCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.simple_moves.MembraneTopologyCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::MembraneTopologyCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.simple_moves.MissingDensityToJumpMover¶

Bases: Mover

apply(self: pyrosetta.rosetta.protocols.simple_moves.MissingDensityToJumpMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::simple_moves::MissingDensityToJumpMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.MissingDensityToJumpMover, : pyrosetta.rosetta.protocols.simple_moves.MissingDensityToJumpMover) → pyrosetta.rosetta.protocols.simple_moves.MissingDensityToJumpMover¶: C++: protocols::simple_moves::MissingDensityToJumpMover::operator=(const class protocols::simple_moves::MissingDensityToJumpMover &) –> class protocols::simple_moves::MissingDensityToJumpMover &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.simple_moves.MissingDensityToJumpMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::MissingDensityToJumpMover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.simple_moves.MissingDensityToJumpMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::MissingDensityToJumpMover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.simple_moves.MissingDensityToJumpMover) → str¶: C++: protocols::simple_moves::MissingDensityToJumpMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.

C++: protocols::moves::Mover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover¶

Bases: Mover

Adds variant types to selected residues

apply(self: pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::simple_moves::ModifyVariantTypeMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover, : pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover) → pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover¶: C++: protocols::simple_moves::ModifyVariantTypeMover::operator=(const class protocols::simple_moves::ModifyVariantTypeMover &) –> class protocols::simple_moves::ModifyVariantTypeMover &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::ModifyVariantTypeMover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::ModifyVariantTypeMover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover) → str¶: C++: protocols::simple_moves::ModifyVariantTypeMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static mover_name() → str¶: C++: protocols::simple_moves::ModifyVariantTypeMover::mover_name() –> std::string

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::simple_moves::ModifyVariantTypeMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::ModifyVariantTypeMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

residue_selector(self: pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶

Get the ResidueSelector used by this mover.

C++: protocols::simple_moves::ModifyVariantTypeMover::residue_selector() const –> class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>

set_add_target_types(self: pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover, types_in: pyrosetta.rosetta.utility.vector1_std_string) → None¶

Set the types to add.

Vikram K. Mulligan (vmullig.edu).

C++: protocols::simple_moves::ModifyVariantTypeMover::set_add_target_types(const class utility::vector1<std::string, class std::allocator<std::string > > &) –> void

set_additional_type_to_add(self: pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover, type_in: str) → None¶

Append a single type to the list to add.

Vikram K. Mulligan (vmullig.edu).

C++: protocols::simple_moves::ModifyVariantTypeMover::set_additional_type_to_add(const std::string &) –> void

set_additional_type_to_remove(self: pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover, type_in: str) → None¶

Append a single type to the list to remove.

Vikram K. Mulligan (vmullig.edu).

C++: protocols::simple_moves::ModifyVariantTypeMover::set_additional_type_to_remove(const std::string &) –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_remove_target_types(self: pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover, types_in: pyrosetta.rosetta.utility.vector1_std_string) → None¶

Set the types to remove.

Vikram K. Mulligan (vmullig.edu).

C++: protocols::simple_moves::ModifyVariantTypeMover::set_remove_target_types(const class utility::vector1<std::string, class std::allocator<std::string > > &) –> void

set_residue_selector(self: pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover, selector_in: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) → None¶

Set the ResidueSelector used by this mover.

C++: protocols::simple_moves::ModifyVariantTypeMover::set_residue_selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

set_update_polymer_bond_dependent_atoms(self: pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover, setting: bool) → None¶

Set whether polymer bond-dependent atoms should be updated after updating variant types.

Defaults to true. Set this to false to preserve polymer bond-dependent atom positions.

Vikram K. Mulligan (vmullig.edu).

C++: protocols::simple_moves::ModifyVariantTypeMover::set_update_polymer_bond_dependent_atoms(const bool) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

update_polymer_bond_dependent_atoms(self: pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover) → bool¶

Get whether polymer bond-dependent atoms should be updated after updating variant types.

Vikram K. Mulligan (vmullig.edu).

C++: protocols::simple_moves::ModifyVariantTypeMover::update_polymer_bond_dependent_atoms() const –> bool

class pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMoverCreator¶

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMoverCreator, : pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMoverCreator) → pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMoverCreator¶: C++: protocols::simple_moves::ModifyVariantTypeMoverCreator::operator=(const class protocols::simple_moves::ModifyVariantTypeMoverCreator &) –> class protocols::simple_moves::ModifyVariantTypeMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::ModifyVariantTypeMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMoverCreator) → str¶: C++: protocols::simple_moves::ModifyVariantTypeMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMoverCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::ModifyVariantTypeMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.simple_moves.MutateResidue¶

Bases: Mover

A mover to mutate a single residue

apply(self: pyrosetta.rosetta.protocols.simple_moves.MutateResidue, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::simple_moves::MutateResidue::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.MutateResidue, : pyrosetta.rosetta.protocols.simple_moves.MutateResidue) → pyrosetta.rosetta.protocols.simple_moves.MutateResidue¶: C++: protocols::simple_moves::MutateResidue::operator=(const class protocols::simple_moves::MutateResidue &) –> class protocols::simple_moves::MutateResidue &

break_disulfide_bonds(self: pyrosetta.rosetta.protocols.simple_moves.MutateResidue) → bool¶

Get whether disulfide bonds are properly broken when

mutating from a disulfide-bonded cysteine to anything else.

True by default. If false, the other cysteine will still think that it is disulfide-bonded to something, and scoring will fail.

Vikram K. Mulligan (vmulligan.org).

C++: protocols::simple_moves::MutateResidue::break_disulfide_bonds() const –> bool

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.simple_moves.MutateResidue) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::MutateResidue::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.simple_moves.MutateResidue) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::MutateResidue::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.simple_moves.MutateResidue) → str¶: C++: protocols::simple_moves::MutateResidue::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static mover_name() → str¶: C++: protocols::simple_moves::MutateResidue::mover_name() –> std::string

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.simple_moves.MutateResidue, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::simple_moves::MutateResidue::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

preserve_atom_coords(self: pyrosetta.rosetta.protocols.simple_moves.MutateResidue) → bool¶

Get whether the mover should try to preserve atoms’ xyz coordinates or not.

Vikram K. Mulligan (vmullig.edu)

C++: protocols::simple_moves::MutateResidue::preserve_atom_coords() –> bool

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::MutateResidue::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

res_name(self: pyrosetta.rosetta.protocols.simple_moves.MutateResidue) → str¶

Get the residue to mutate to.

This is the full name, not the three-letter code.

Vikram K. Mulligan (vmullig.edu)

C++: protocols::simple_moves::MutateResidue::res_name() –> std::string

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_break_disulfide_bonds(self: pyrosetta.rosetta.protocols.simple_moves.MutateResidue, setting: bool) → None¶

Set whether disulfide bonds are properly broken when

mutating from a disulfide-bonded cysteine to anything else.

True by default. If false, the other cysteine will still think that it is disulfide-bonded to something, and scoring will fail.

Vikram K. Mulligan (vmulligan.org).

C++: protocols::simple_moves::MutateResidue::set_break_disulfide_bonds(const bool) –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_preserve_atom_coords(self: pyrosetta.rosetta.protocols.simple_moves.MutateResidue, val: bool) → None¶

Set whether the mover should try to preserve atoms’ xyz coordinates or not.

Vikram K. Mulligan (vmullig.edu)

C++: protocols::simple_moves::MutateResidue::set_preserve_atom_coords(const bool) –> void

set_res_name(*args, **kwargs)¶

Overloaded function.

set_res_name(self: pyrosetta.rosetta.protocols.simple_moves.MutateResidue, name_in: str) -> None

Set the residue to mutate to.

This is the full name, not the three-letter code.

Vikram K. Mulligan (vmullig.edu)

C++: protocols::simple_moves::MutateResidue::set_res_name(const std::string &) –> void

set_res_name(self: pyrosetta.rosetta.protocols.simple_moves.MutateResidue, aa: pyrosetta.rosetta.core.chemical.AA) -> None

C++: protocols::simple_moves::MutateResidue::set_res_name(const enum core::chemical::AA &) –> void

set_selector(self: pyrosetta.rosetta.protocols.simple_moves.MutateResidue, selector_in: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) → None¶

Set a selector if specified by the user

C++: protocols::simple_moves::MutateResidue::set_selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

set_target(*args, **kwargs)¶

Overloaded function.

set_target(self: pyrosetta.rosetta.protocols.simple_moves.MutateResidue, target_in: str) -> None

Set this mover’s target residue index.

Vikram K. Mulligan (vmullig.edu)

C++: protocols::simple_moves::MutateResidue::set_target(const std::string &) –> void

set_target(self: pyrosetta.rosetta.protocols.simple_moves.MutateResidue, target_in: int) -> None

Set this mover’s target residue index, based on the Rosetta indexing.

C++: protocols::simple_moves::MutateResidue::set_target(const unsigned long) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

set_update_polymer_dependent(self: pyrosetta.rosetta.protocols.simple_moves.MutateResidue, setting: bool) → None¶

Set whether this mover updates polymer-dependent atoms in the residue that it mutates.

Vikram K. Mulligan (vmullig.edu)

C++: protocols::simple_moves::MutateResidue::set_update_polymer_dependent(const bool) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

target(self: pyrosetta.rosetta.protocols.simple_moves.MutateResidue) → str¶

Get this mover’s target residue index.

Vikram K. Mulligan (vmullig.edu)

C++: protocols::simple_moves::MutateResidue::target() const –> std::string

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

update_polymer_dependent(self: pyrosetta.rosetta.protocols.simple_moves.MutateResidue) → bool¶

Set whether this mover updates polymer-dependent atoms in the residue that it mutates.

Vikram K. Mulligan (vmullig.edu)

C++: protocols::simple_moves::MutateResidue::update_polymer_dependent() const –> bool

class pyrosetta.rosetta.protocols.simple_moves.MutateResidueCreator¶

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.simple_moves.MutateResidueCreator, : pyrosetta.rosetta.protocols.simple_moves.MutateResidueCreator) → pyrosetta.rosetta.protocols.simple_moves.MutateResidueCreator¶: C++: protocols::simple_moves::MutateResidueCreator::operator=(const class protocols::simple_moves::MutateResidueCreator &) –> class protocols::simple_moves::MutateResidueCreator &

create_mover(self: pyrosetta.rosetta.protocols.simple_moves.MutateResidueCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::MutateResidueCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.simple_moves.MutateResidueCreator) → str¶: C++: protocols::simple_moves::MutateResidueCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.simple_moves.MutateResidueCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::MutateResidueCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.simple_moves.PDBReloadMover¶

Bases: Mover

apply(self: pyrosetta.rosetta.protocols.simple_moves.PDBReloadMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::simple_moves::PDBReloadMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.PDBReloadMover, : pyrosetta.rosetta.protocols.simple_moves.PDBReloadMover) → pyrosetta.rosetta.protocols.simple_moves.PDBReloadMover¶: C++: protocols::simple_moves::PDBReloadMover::operator=(const class protocols::simple_moves::PDBReloadMover &) –> class protocols::simple_moves::PDBReloadMover &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.simple_moves.PDBReloadMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::PDBReloadMover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.simple_moves.PDBReloadMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::PDBReloadMover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.simple_moves.PDBReloadMover) → str¶: C++: protocols::simple_moves::PDBReloadMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static mover_name() → str¶: C++: protocols::simple_moves::PDBReloadMover::mover_name() –> std::string

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.simple_moves.PDBReloadMover, tag: pyrosetta.rosetta.utility.tag.Tag, data_map: pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::simple_moves::PDBReloadMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::PDBReloadMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.simple_moves.PDBReloadMoverCreator¶

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.simple_moves.PDBReloadMoverCreator, : pyrosetta.rosetta.protocols.simple_moves.PDBReloadMoverCreator) → pyrosetta.rosetta.protocols.simple_moves.PDBReloadMoverCreator¶: C++: protocols::simple_moves::PDBReloadMoverCreator::operator=(const class protocols::simple_moves::PDBReloadMoverCreator &) –> class protocols::simple_moves::PDBReloadMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.simple_moves.PDBReloadMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::PDBReloadMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.simple_moves.PDBReloadMoverCreator) → str¶: C++: protocols::simple_moves::PDBReloadMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.simple_moves.PDBReloadMoverCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::PDBReloadMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.simple_moves.PSSM2BfactorMover¶

Bases: Mover

apply(self: pyrosetta.rosetta.protocols.simple_moves.PSSM2BfactorMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::simple_moves::PSSM2BfactorMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.PSSM2BfactorMover, : pyrosetta.rosetta.protocols.simple_moves.PSSM2BfactorMover) → pyrosetta.rosetta.protocols.simple_moves.PSSM2BfactorMover¶: C++: protocols::simple_moves::PSSM2BfactorMover::operator=(const class protocols::simple_moves::PSSM2BfactorMover &) –> class protocols::simple_moves::PSSM2BfactorMover &

chain_num(*args, **kwargs)¶

Overloaded function.

chain_num(self: pyrosetta.rosetta.protocols.simple_moves.PSSM2BfactorMover) -> float

C++: protocols::simple_moves::PSSM2BfactorMover::chain_num() const –> double

chain_num(self: pyrosetta.rosetta.protocols.simple_moves.PSSM2BfactorMover, s: int) -> None

C++: protocols::simple_moves::PSSM2BfactorMover::chain_num(const unsigned long) –> void

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.simple_moves.PSSM2BfactorMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::PSSM2BfactorMover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.simple_moves.PSSM2BfactorMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::PSSM2BfactorMover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.simple_moves.PSSM2BfactorMover) → str¶: C++: protocols::simple_moves::PSSM2BfactorMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

max_value(*args, **kwargs)¶

Overloaded function.

max_value(self: pyrosetta.rosetta.protocols.simple_moves.PSSM2BfactorMover) -> float

C++: protocols::simple_moves::PSSM2BfactorMover::max_value() const –> double

max_value(self: pyrosetta.rosetta.protocols.simple_moves.PSSM2BfactorMover, s: float) -> None

C++: protocols::simple_moves::PSSM2BfactorMover::max_value(const double) –> void

min_value(*args, **kwargs)¶

Overloaded function.

min_value(self: pyrosetta.rosetta.protocols.simple_moves.PSSM2BfactorMover) -> float

C++: protocols::simple_moves::PSSM2BfactorMover::min_value() const –> double

min_value(self: pyrosetta.rosetta.protocols.simple_moves.PSSM2BfactorMover, s: float) -> None

C++: protocols::simple_moves::PSSM2BfactorMover::min_value(const double) –> void

static mover_name() → str¶: C++: protocols::simple_moves::PSSM2BfactorMover::mover_name() –> std::string

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.simple_moves.PSSM2BfactorMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::simple_moves::PSSM2BfactorMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::PSSM2BfactorMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.simple_moves.PSSM2BfactorMoverCreator¶

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.simple_moves.PSSM2BfactorMoverCreator, : pyrosetta.rosetta.protocols.simple_moves.PSSM2BfactorMoverCreator) → pyrosetta.rosetta.protocols.simple_moves.PSSM2BfactorMoverCreator¶: C++: protocols::simple_moves::PSSM2BfactorMoverCreator::operator=(const class protocols::simple_moves::PSSM2BfactorMoverCreator &) –> class protocols::simple_moves::PSSM2BfactorMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.simple_moves.PSSM2BfactorMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::PSSM2BfactorMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.simple_moves.PSSM2BfactorMoverCreator) → str¶: C++: protocols::simple_moves::PSSM2BfactorMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.simple_moves.PSSM2BfactorMoverCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::PSSM2BfactorMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.simple_moves.PeptideStapleMover¶

Bases: Mover

apply(self: pyrosetta.rosetta.protocols.simple_moves.PeptideStapleMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::simple_moves::PeptideStapleMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.PeptideStapleMover, : pyrosetta.rosetta.protocols.simple_moves.PeptideStapleMover) → pyrosetta.rosetta.protocols.simple_moves.PeptideStapleMover¶: C++: protocols::simple_moves::PeptideStapleMover::operator=(const class protocols::simple_moves::PeptideStapleMover &) –> class protocols::simple_moves::PeptideStapleMover &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.simple_moves.PeptideStapleMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::PeptideStapleMover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶

Generates a new Mover object freshly created with the default ctor.

C++: protocols::moves::Mover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.simple_moves.PeptideStapleMover) → str¶: C++: protocols::simple_moves::PeptideStapleMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.

C++: protocols::moves::Mover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.simple_moves.PeriodicBoxMover¶

Bases: Mover

apply(self: pyrosetta.rosetta.protocols.simple_moves.PeriodicBoxMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::simple_moves::PeriodicBoxMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.PeriodicBoxMover, : pyrosetta.rosetta.protocols.simple_moves.PeriodicBoxMover) → pyrosetta.rosetta.protocols.simple_moves.PeriodicBoxMover¶: C++: protocols::simple_moves::PeriodicBoxMover::operator=(const class protocols::simple_moves::PeriodicBoxMover &) –> class protocols::simple_moves::PeriodicBoxMover &

change_volume_move(self: pyrosetta.rosetta.protocols.simple_moves.PeriodicBoxMover, pose: pyrosetta.rosetta.core.pose.Pose, : int, : bool) → None¶: C++: protocols::simple_moves::PeriodicBoxMover::change_volume_move(class core::pose::Pose &, unsigned long, bool &) –> void

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.simple_moves.PeriodicBoxMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::PeriodicBoxMover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.simple_moves.PeriodicBoxMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::PeriodicBoxMover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.simple_moves.PeriodicBoxMover) → str¶: C++: protocols::simple_moves::PeriodicBoxMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static mover_name() → str¶: C++: protocols::simple_moves::PeriodicBoxMover::mover_name() –> std::string

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.simple_moves.PeriodicBoxMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::simple_moves::PeriodicBoxMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

perturb_molecule_move(self: pyrosetta.rosetta.protocols.simple_moves.PeriodicBoxMover, pose: pyrosetta.rosetta.core.pose.Pose, : int, : bool) → None¶: C++: protocols::simple_moves::PeriodicBoxMover::perturb_molecule_move(class core::pose::Pose &, unsigned long, bool &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::PeriodicBoxMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

setup_pose(self: pyrosetta.rosetta.protocols.simple_moves.PeriodicBoxMover, pose: pyrosetta.rosetta.core.pose.Pose, : float, : int) → None¶: C++: protocols::simple_moves::PeriodicBoxMover::setup_pose(class core::pose::Pose &, double &, unsigned long &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.simple_moves.PeriodicBoxMoverCreator¶

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.simple_moves.PeriodicBoxMoverCreator, : pyrosetta.rosetta.protocols.simple_moves.PeriodicBoxMoverCreator) → pyrosetta.rosetta.protocols.simple_moves.PeriodicBoxMoverCreator¶: C++: protocols::simple_moves::PeriodicBoxMoverCreator::operator=(const class protocols::simple_moves::PeriodicBoxMoverCreator &) –> class protocols::simple_moves::PeriodicBoxMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.simple_moves.PeriodicBoxMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::PeriodicBoxMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.simple_moves.PeriodicBoxMoverCreator) → str¶: C++: protocols::simple_moves::PeriodicBoxMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.simple_moves.PeriodicBoxMoverCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::PeriodicBoxMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.simple_moves.PoseFromPoseResourceMover¶

Bases: Mover

Mover that shuttles a Pose from a PoseResource into the DataMap when its parse_my_tag method is invoked

apply(self: pyrosetta.rosetta.protocols.simple_moves.PoseFromPoseResourceMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

No op – this “mover” does all it’s going to ever do during its parse_my_tag method.

C++: protocols::simple_moves::PoseFromPoseResourceMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.PoseFromPoseResourceMover, : pyrosetta.rosetta.protocols.simple_moves.PoseFromPoseResourceMover) → pyrosetta.rosetta.protocols.simple_moves.PoseFromPoseResourceMover¶: C++: protocols::simple_moves::PoseFromPoseResourceMover::operator=(const class protocols::simple_moves::PoseFromPoseResourceMover &) –> class protocols::simple_moves::PoseFromPoseResourceMover &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.simple_moves.PoseFromPoseResourceMover) → pyrosetta.rosetta.protocols.moves.Mover¶

required in the context of the parser/scripting scheme

C++: protocols::simple_moves::PoseFromPoseResourceMover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.simple_moves.PoseFromPoseResourceMover) → pyrosetta.rosetta.protocols.moves.Mover¶

required in the context of the parser/scripting scheme

C++: protocols::simple_moves::PoseFromPoseResourceMover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.simple_moves.PoseFromPoseResourceMover) → str¶: C++: protocols::simple_moves::PoseFromPoseResourceMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static mover_name() → str¶: C++: protocols::simple_moves::PoseFromPoseResourceMover::mover_name() –> std::string

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.simple_moves.PoseFromPoseResourceMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

parse XML tag (to use this Mover in Rosetta Scripts)

C++: protocols::simple_moves::PoseFromPoseResourceMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::PoseFromPoseResourceMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.simple_moves.PoseFromPoseResourceMover) -> None
show(self: pyrosetta.rosetta.protocols.simple_moves.PoseFromPoseResourceMover, output: pyrosetta.rosetta.std.ostream) -> None

C++: protocols::simple_moves::PoseFromPoseResourceMover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.simple_moves.PoseFromPoseResourceMoverCreator¶

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.simple_moves.PoseFromPoseResourceMoverCreator, : pyrosetta.rosetta.protocols.simple_moves.PoseFromPoseResourceMoverCreator) → pyrosetta.rosetta.protocols.simple_moves.PoseFromPoseResourceMoverCreator¶: C++: protocols::simple_moves::PoseFromPoseResourceMoverCreator::operator=(const class protocols::simple_moves::PoseFromPoseResourceMoverCreator &) –> class protocols::simple_moves::PoseFromPoseResourceMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.simple_moves.PoseFromPoseResourceMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::PoseFromPoseResourceMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.simple_moves.PoseFromPoseResourceMoverCreator) → str¶: C++: protocols::simple_moves::PoseFromPoseResourceMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.simple_moves.PoseFromPoseResourceMoverCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::PoseFromPoseResourceMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.simple_moves.ProlineFixMover¶

Bases: Mover

apply(self: pyrosetta.rosetta.protocols.simple_moves.ProlineFixMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::simple_moves::ProlineFixMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.ProlineFixMover, : pyrosetta.rosetta.protocols.simple_moves.ProlineFixMover) → pyrosetta.rosetta.protocols.simple_moves.ProlineFixMover¶: C++: protocols::simple_moves::ProlineFixMover::operator=(const class protocols::simple_moves::ProlineFixMover &) –> class protocols::simple_moves::ProlineFixMover &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶

Return a clone of the Mover object.

C++: protocols::moves::Mover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶

Generates a new Mover object freshly created with the default ctor.

C++: protocols::moves::Mover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.simple_moves.ProlineFixMover) → str¶: C++: protocols::simple_moves::ProlineFixMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.

C++: protocols::moves::Mover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover¶

Bases: Mover

Simple class that flips a random omega selected from a movemap 180 degrees

apply(self: pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::simple_moves::RandomOmegaFlipMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover, : pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover) → pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover¶: C++: protocols::simple_moves::RandomOmegaFlipMover::operator=(const class protocols::simple_moves::RandomOmegaFlipMover &) –> class protocols::simple_moves::RandomOmegaFlipMover &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::RandomOmegaFlipMover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::RandomOmegaFlipMover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover) → str¶: C++: protocols::simple_moves::RandomOmegaFlipMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

movemap_factory(self: pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover, new_movemap_factory: pyrosetta.rosetta.core.select.movemap.MoveMapFactory) → None¶: C++: protocols::simple_moves::RandomOmegaFlipMover::movemap_factory(class std::shared_ptr<const class core::select::movemap::MoveMapFactory>) –> void

static mover_name() → str¶: C++: protocols::simple_moves::RandomOmegaFlipMover::mover_name() –> std::string

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::simple_moves::RandomOmegaFlipMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::RandomOmegaFlipMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMoverCreator¶

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMoverCreator, : pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMoverCreator) → pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMoverCreator¶: C++: protocols::simple_moves::RandomOmegaFlipMoverCreator::operator=(const class protocols::simple_moves::RandomOmegaFlipMoverCreator &) –> class protocols::simple_moves::RandomOmegaFlipMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::RandomOmegaFlipMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMoverCreator) → str¶: C++: protocols::simple_moves::RandomOmegaFlipMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMoverCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::RandomOmegaFlipMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover¶

Bases: Mover

Simple class that randomly purturbs a random torsion selected from a movemap

apply(self: pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::simple_moves::RandomTorsionMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover, : pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover) → pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover¶: C++: protocols::simple_moves::RandomTorsionMover::operator=(const class protocols::simple_moves::RandomTorsionMover &) –> class protocols::simple_moves::RandomTorsionMover &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::RandomTorsionMover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::RandomTorsionMover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover) → str¶: C++: protocols::simple_moves::RandomTorsionMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

movemap_factory(self: pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover, new_movemap_factory: pyrosetta.rosetta.core.select.movemap.MoveMapFactory) → None¶: C++: protocols::simple_moves::RandomTorsionMover::movemap_factory(class std::shared_ptr<const class core::select::movemap::MoveMapFactory>) –> void

static mover_name() → str¶: C++: protocols::simple_moves::RandomTorsionMover::mover_name() –> std::string

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::simple_moves::RandomTorsionMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::RandomTorsionMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMoverCreator¶

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMoverCreator, : pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMoverCreator) → pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMoverCreator¶: C++: protocols::simple_moves::RandomTorsionMoverCreator::operator=(const class protocols::simple_moves::RandomTorsionMoverCreator &) –> class protocols::simple_moves::RandomTorsionMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::RandomTorsionMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMoverCreator) → str¶: C++: protocols::simple_moves::RandomTorsionMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMoverCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::RandomTorsionMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.simple_moves.RepeatPropagationMover¶

Bases: Mover

apply(self: pyrosetta.rosetta.protocols.simple_moves.RepeatPropagationMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::simple_moves::RepeatPropagationMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.RepeatPropagationMover, : pyrosetta.rosetta.protocols.simple_moves.RepeatPropagationMover) → pyrosetta.rosetta.protocols.simple_moves.RepeatPropagationMover¶: C++: protocols::simple_moves::RepeatPropagationMover::operator=(const class protocols::simple_moves::RepeatPropagationMover &) –> class protocols::simple_moves::RepeatPropagationMover &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.simple_moves.RepeatPropagationMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::RepeatPropagationMover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶

Generates a new Mover object freshly created with the default ctor.

C++: protocols::moves::Mover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.simple_moves.RepeatPropagationMover) → str¶: C++: protocols::simple_moves::RepeatPropagationMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static mover_name() → str¶: C++: protocols::simple_moves::RepeatPropagationMover::mover_name() –> std::string

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.simple_moves.RepeatPropagationMover, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::simple_moves::RepeatPropagationMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::RepeatPropagationMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.simple_moves.RepeatPropagationMoverCreator¶

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.simple_moves.RepeatPropagationMoverCreator, : pyrosetta.rosetta.protocols.simple_moves.RepeatPropagationMoverCreator) → pyrosetta.rosetta.protocols.simple_moves.RepeatPropagationMoverCreator¶: C++: protocols::simple_moves::RepeatPropagationMoverCreator::operator=(const class protocols::simple_moves::RepeatPropagationMoverCreator &) –> class protocols::simple_moves::RepeatPropagationMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.simple_moves.RepeatPropagationMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::RepeatPropagationMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.simple_moves.RepeatPropagationMoverCreator) → str¶: C++: protocols::simple_moves::RepeatPropagationMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.simple_moves.RepeatPropagationMoverCreator, xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::RepeatPropagationMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA¶

Bases: Mover

scale density map intensities to match a pose’s

apply(self: pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA, : pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::simple_moves::ReportEffectivePKA::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA, : pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA) → pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA¶: C++: protocols::simple_moves::ReportEffectivePKA::operator=(const class protocols::simple_moves::ReportEffectivePKA &) –> class protocols::simple_moves::ReportEffectivePKA &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::ReportEffectivePKA::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::ReportEffectivePKA::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA) → str¶: C++: protocols::simple_moves::ReportEffectivePKA::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

init(self: pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA) → None¶: C++: protocols::simple_moves::ReportEffectivePKA::init() –> void

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static mover_name() → str¶: C++: protocols::simple_moves::ReportEffectivePKA::mover_name() –> std::string

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::simple_moves::ReportEffectivePKA::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::ReportEffectivePKA::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

task_factory(*args, **kwargs)¶

Overloaded function.

task_factory(self: pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA, task_factory: pyrosetta.rosetta.core.pack.task.TaskFactory) -> None

C++: protocols::simple_moves::ReportEffectivePKA::task_factory(class std::shared_ptr<class core::pack::task::TaskFactory>) –> void

task_factory(self: pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA) -> pyrosetta.rosetta.core.pack.task.TaskFactory

C++: protocols::simple_moves::ReportEffectivePKA::task_factory() const –> class std::shared_ptr<class core::pack::task::TaskFactory>

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKACreator¶

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKACreator, : pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKACreator) → pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKACreator¶: C++: protocols::simple_moves::ReportEffectivePKACreator::operator=(const class protocols::simple_moves::ReportEffectivePKACreator &) –> class protocols::simple_moves::ReportEffectivePKACreator &

create_mover(self: pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKACreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::ReportEffectivePKACreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKACreator) → str¶: C++: protocols::simple_moves::ReportEffectivePKACreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKACreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::ReportEffectivePKACreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.simple_moves.ReportXYZ¶

Bases: Mover

apply(self: pyrosetta.rosetta.protocols.simple_moves.ReportXYZ, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::simple_moves::ReportXYZ::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.ReportXYZ, : pyrosetta.rosetta.protocols.simple_moves.ReportXYZ) → pyrosetta.rosetta.protocols.simple_moves.ReportXYZ¶: C++: protocols::simple_moves::ReportXYZ::operator=(const class protocols::simple_moves::ReportXYZ &) –> class protocols::simple_moves::ReportXYZ &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.simple_moves.ReportXYZ) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::ReportXYZ::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.simple_moves.ReportXYZ) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::ReportXYZ::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.simple_moves.ReportXYZ) → str¶: C++: protocols::simple_moves::ReportXYZ::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static mover_name() → str¶: C++: protocols::simple_moves::ReportXYZ::mover_name() –> std::string

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.simple_moves.ReportXYZ, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::simple_moves::ReportXYZ::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::ReportXYZ::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.simple_moves.ReportXYZCreator¶

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.simple_moves.ReportXYZCreator, : pyrosetta.rosetta.protocols.simple_moves.ReportXYZCreator) → pyrosetta.rosetta.protocols.simple_moves.ReportXYZCreator¶: C++: protocols::simple_moves::ReportXYZCreator::operator=(const class protocols::simple_moves::ReportXYZCreator &) –> class protocols::simple_moves::ReportXYZCreator &

create_mover(self: pyrosetta.rosetta.protocols.simple_moves.ReportXYZCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::ReportXYZCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.simple_moves.ReportXYZCreator) → str¶: C++: protocols::simple_moves::ReportXYZCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.simple_moves.ReportXYZCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::ReportXYZCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.simple_moves.RepulsiveOnlyMover¶

Bases: Mover

this mover replace designated residues with glycines, and then assigns a “REPLONLY” residue type to those glycines. Those “REPLONLY” residues will make only repulsive contributions to the overall energy.

apply(self: pyrosetta.rosetta.protocols.simple_moves.RepulsiveOnlyMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::simple_moves::RepulsiveOnlyMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.RepulsiveOnlyMover, : pyrosetta.rosetta.protocols.simple_moves.RepulsiveOnlyMover) → pyrosetta.rosetta.protocols.simple_moves.RepulsiveOnlyMover¶: C++: protocols::simple_moves::RepulsiveOnlyMover::operator=(const class protocols::simple_moves::RepulsiveOnlyMover &) –> class protocols::simple_moves::RepulsiveOnlyMover &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶

Return a clone of the Mover object.

C++: protocols::moves::Mover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶

Generates a new Mover object freshly created with the default ctor.

C++: protocols::moves::Mover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.simple_moves.RepulsiveOnlyMover) → str¶: C++: protocols::simple_moves::RepulsiveOnlyMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.

C++: protocols::moves::Mover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_mutate_to_glycine(self: pyrosetta.rosetta.protocols.simple_moves.RepulsiveOnlyMover, setting: bool) → None¶: C++: protocols::simple_moves::RepulsiveOnlyMover::set_mutate_to_glycine(bool) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.simple_moves.ResTypeFragmentMover¶

Bases: ClassicFragmentMover

apply(*args, **kwargs)¶

Overloaded function.

apply(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, : pyrosetta.rosetta.core.pose.Pose, pos: int) -> bool
apply(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, : pyrosetta.rosetta.core.pose.Pose) -> None

Applies classic fragment insertion based on a FragSet

example:
mover_3mer.apply(pose)

See also:
ClassicFragmentMover Pose ConstantLengthFragSet

C++: protocols::simple_moves::ClassicFragmentMover::apply(class core::pose::Pose &) –> void

apply_at_all_positions(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover, : pyrosetta.rosetta.core.pose.Pose) → int¶

apply at all movemable positions — honors movemap

C++: protocols::simple_moves::FragmentMover::apply_at_all_positions(class core::pose::Pose &) const –> unsigned long

apply_fragment(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, frame: pyrosetta.rosetta.core.fragment.Frame, frag_num: int, movemap: pyrosetta.rosetta.core.kinematics.MoveMap, pose: pyrosetta.rosetta.core.pose.Pose) → bool¶

apply the chosen fragment,

this can be overloaded to change action, e.,g., WobbleMover introduces chain-break before fragment insertion and does ccd-loop closure afterwards

C++: protocols::simple_moves::ClassicFragmentMover::apply_fragment(const class core::fragment::Frame &, unsigned long, const class core::kinematics::MoveMap &, class core::pose::Pose &) const –> bool

assign(self: pyrosetta.rosetta.protocols.simple_moves.ResTypeFragmentMover, : pyrosetta.rosetta.protocols.simple_moves.ResTypeFragmentMover) → pyrosetta.rosetta.protocols.simple_moves.ResTypeFragmentMover¶: C++: protocols::simple_moves::ResTypeFragmentMover::operator=(const class protocols::simple_moves::ResTypeFragmentMover &) –> class protocols::simple_moves::ResTypeFragmentMover &

check_ss(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover) → bool¶

accessor

C++: protocols::simple_moves::ClassicFragmentMover::check_ss() const –> bool

choose_fragment(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, : pyrosetta.rosetta.core.fragment.FrameList, : pyrosetta.rosetta.core.pose.Pose, frame_num: int, frag_num: int) → bool¶

given FrameList and pose, this method yields a fragment ( frame_num/ frag_num);: return false if nothing suitable is found

C++: protocols::simple_moves::ClassicFragmentMover::choose_fragment(const class core::fragment::FrameList &, const class core::pose::Pose &, unsigned long &, unsigned long &) const –> bool

choose_window_length(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, : pyrosetta.rosetta.core.pose.Pose, window_length: int) → bool¶

yields a length (window_length) of the fragment window to sample from: ( return false, if no suitable length is found )

C++: protocols::simple_moves::ClassicFragmentMover::choose_window_length(const class core::pose::Pose &, unsigned long &) const –> bool

choose_window_start(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, : pyrosetta.rosetta.core.pose.Pose, window_length: int, window_start: int) → bool¶

yields a start position (window_start) for fragment window to sample from: ( return false, if nothing suitable is found )

C++: protocols::simple_moves::ClassicFragmentMover::choose_window_start(const class core::pose::Pose &, unsigned long, unsigned long &) const –> bool

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::ClassicFragmentMover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

define_start_window(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, window_start: int) → None¶

apply fragment at predefined position

C++: protocols::simple_moves::ClassicFragmentMover::define_start_window(unsigned long) –> void

enable_end_bias_check(*args, **kwargs)¶

Overloaded function.

enable_end_bias_check(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover) -> None
enable_end_bias_check(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, setting: bool) -> None

C++: protocols::simple_moves::ClassicFragmentMover::enable_end_bias_check(bool) –> void

end_bias(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover) → float¶: C++: protocols::simple_moves::ClassicFragmentMover::end_bias() const –> double

end_bias_check(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, : pyrosetta.rosetta.core.pose.Pose, window_start: int) → bool¶: C++: protocols::simple_moves::ClassicFragmentMover::end_bias_check(const class core::pose::Pose &, unsigned long) const –> bool

end_bias_check_enabled(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover) → bool¶: C++: protocols::simple_moves::ClassicFragmentMover::end_bias_check_enabled() const –> bool

fragments(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover) → pyrosetta.rosetta.core.fragment.FragSet¶

accessor to the fragment set

C++: protocols::simple_moves::FragmentMover::fragments() const –> class std::shared_ptr<const class core::fragment::FragSet>

fresh_instance(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::ClassicFragmentMover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover) → str¶: C++: protocols::simple_moves::ClassicFragmentMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

initialize(self: pyrosetta.rosetta.protocols.moves.MoveMapMover, : pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::moves::MoveMapMover::initialize(class core::pose::Pose &) –> void

insert_map(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover) → pyrosetta.rosetta.utility.vector1_unsigned_long¶: C++: protocols::simple_moves::FragmentMover::insert_map() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

insert_size(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover) → pyrosetta.rosetta.utility.vector1_unsigned_long¶: C++: protocols::simple_moves::FragmentMover::insert_size() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

movemap(*args, **kwargs)¶

Overloaded function.

movemap(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover, : pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.core.kinematics.MoveMap

C++: protocols::simple_moves::FragmentMover::movemap(const class core::pose::Pose &) const –> class std::shared_ptr<const class core::kinematics::MoveMap>

movemap(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover) -> pyrosetta.rosetta.core.kinematics.MoveMap

C++: protocols::simple_moves::FragmentMover::movemap() const –> class std::shared_ptr<const class core::kinematics::MoveMap>

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

on_new_fragments(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover) → None¶

is called from set_fragments()

C++: protocols::simple_moves::ClassicFragmentMover::on_new_fragments() –> void

parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.

C++: protocols::moves::Mover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_check_ss(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, setting: bool) → None¶

check_ss controls whether fragment insertions are rejected that create short helices (<3) or strands (<2)

C++: protocols::simple_moves::ClassicFragmentMover::set_check_ss(bool) –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_end_bias(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, setting: float) → None¶: C++: protocols::simple_moves::ClassicFragmentMover::set_end_bias(double) –> void

set_fragments(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover, new_frags_: pyrosetta.rosetta.core.fragment.FragSet) → None¶

setter for the fragment set

C++: protocols::simple_moves::FragmentMover::set_fragments(class std::shared_ptr<const class core::fragment::FragSet>) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_min_frag_length(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, setting: int) → None¶

min_frag_length controls the behaviour fragset->region()

C++: protocols::simple_moves::ClassicFragmentMover::set_min_frag_length(unsigned long) –> void

set_min_overlap(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, setting: int) → None¶

min_overlap controls the behaviour fragset->region()

C++: protocols::simple_moves::ClassicFragmentMover::set_min_overlap(unsigned long) –> void

set_movemap(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover, movemap: pyrosetta.rosetta.core.kinematics.MoveMap) → None¶

setter for the movemap

C++: protocols::simple_moves::FragmentMover::set_movemap(class std::shared_ptr<const class core::kinematics::MoveMap>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

shared_from_this(self: pyrosetta.rosetta.protocols.simple_moves.ResTypeFragmentMover) → pyrosetta.rosetta.protocols.simple_moves.ResTypeFragmentMover¶: C++: protocols::simple_moves::ResTypeFragmentMover::shared_from_this() –> class std::shared_ptr<class protocols::simple_moves::ResTypeFragmentMover>

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover) -> None
show(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, output: pyrosetta.rosetta.std.ostream) -> None

C++: protocols::simple_moves::ClassicFragmentMover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

valid_ss(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, new_ss: str) → bool¶

returns true if the ss string is acceptable

C++: protocols::simple_moves::ClassicFragmentMover::valid_ss(const std::string &) const –> bool

class pyrosetta.rosetta.protocols.simple_moves.ResetFoldTree¶

Bases: Mover

apply(self: pyrosetta.rosetta.protocols.simple_moves.ResetFoldTree, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::simple_moves::ResetFoldTree::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.ResetFoldTree, : pyrosetta.rosetta.protocols.simple_moves.ResetFoldTree) → pyrosetta.rosetta.protocols.simple_moves.ResetFoldTree¶: C++: protocols::simple_moves::ResetFoldTree::operator=(const class protocols::simple_moves::ResetFoldTree &) –> class protocols::simple_moves::ResetFoldTree &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.simple_moves.ResetFoldTree) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::ResetFoldTree::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.simple_moves.ResetFoldTree) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::ResetFoldTree::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.simple_moves.ResetFoldTree) → str¶: C++: protocols::simple_moves::ResetFoldTree::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static mover_name() → str¶: C++: protocols::simple_moves::ResetFoldTree::mover_name() –> std::string

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.simple_moves.ResetFoldTree, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::simple_moves::ResetFoldTree::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::ResetFoldTree::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.simple_moves.ResetFoldTreeCreator¶

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.simple_moves.ResetFoldTreeCreator, : pyrosetta.rosetta.protocols.simple_moves.ResetFoldTreeCreator) → pyrosetta.rosetta.protocols.simple_moves.ResetFoldTreeCreator¶: C++: protocols::simple_moves::ResetFoldTreeCreator::operator=(const class protocols::simple_moves::ResetFoldTreeCreator &) –> class protocols::simple_moves::ResetFoldTreeCreator &

create_mover(self: pyrosetta.rosetta.protocols.simple_moves.ResetFoldTreeCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::ResetFoldTreeCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.simple_moves.ResetFoldTreeCreator) → str¶: C++: protocols::simple_moves::ResetFoldTreeCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.simple_moves.ResetFoldTreeCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::ResetFoldTreeCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.simple_moves.ResetFullModelInfoMover¶

Bases: Mover

Ensure synchronized full model info

apply(self: pyrosetta.rosetta.protocols.simple_moves.ResetFullModelInfoMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Apply the mover

C++: protocols::simple_moves::ResetFullModelInfoMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.ResetFullModelInfoMover, : pyrosetta.rosetta.protocols.simple_moves.ResetFullModelInfoMover) → pyrosetta.rosetta.protocols.simple_moves.ResetFullModelInfoMover¶: C++: protocols::simple_moves::ResetFullModelInfoMover::operator=(const class protocols::simple_moves::ResetFullModelInfoMover &) –> class protocols::simple_moves::ResetFullModelInfoMover &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.simple_moves.ResetFullModelInfoMover) → pyrosetta.rosetta.protocols.moves.Mover¶

required in the context of the parser/scripting scheme

C++: protocols::simple_moves::ResetFullModelInfoMover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.simple_moves.ResetFullModelInfoMover) → pyrosetta.rosetta.protocols.moves.Mover¶

required in the context of the parser/scripting scheme

C++: protocols::simple_moves::ResetFullModelInfoMover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.simple_moves.ResetFullModelInfoMover) → str¶: C++: protocols::simple_moves::ResetFullModelInfoMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static mover_name() → str¶: C++: protocols::simple_moves::ResetFullModelInfoMover::mover_name() –> std::string

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.simple_moves.ResetFullModelInfoMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

parse XML tag (to use this Mover in Rosetta Scripts)

C++: protocols::simple_moves::ResetFullModelInfoMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::ResetFullModelInfoMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.simple_moves.ResetFullModelInfoMover) -> None
show(self: pyrosetta.rosetta.protocols.simple_moves.ResetFullModelInfoMover, output: pyrosetta.rosetta.std.ostream) -> None

C++: protocols::simple_moves::ResetFullModelInfoMover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.simple_moves.ResetFullModelInfoMoverCreator¶

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.simple_moves.ResetFullModelInfoMoverCreator, : pyrosetta.rosetta.protocols.simple_moves.ResetFullModelInfoMoverCreator) → pyrosetta.rosetta.protocols.simple_moves.ResetFullModelInfoMoverCreator¶: C++: protocols::simple_moves::ResetFullModelInfoMoverCreator::operator=(const class protocols::simple_moves::ResetFullModelInfoMoverCreator &) –> class protocols::simple_moves::ResetFullModelInfoMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.simple_moves.ResetFullModelInfoMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::ResetFullModelInfoMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.simple_moves.ResetFullModelInfoMoverCreator) → str¶: C++: protocols::simple_moves::ResetFullModelInfoMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.simple_moves.ResetFullModelInfoMoverCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::ResetFullModelInfoMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover¶

Bases: Mover

This class takes two poses, one at instantiation and one at apply. It copies the residue type set and chi information from its kept pose to the apply pose. The intended purpose is for “returning” known sidechains to a pose that was temporarily in centroid mode, although it may work with other residue type sets.

property allow_chi_copy_¶

apply(self: pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::simple_moves::ReturnSidechainMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::operator=(const class protocols::moves::Mover &) –> class protocols::moves::Mover &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::ReturnSidechainMover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

property copy_all_chi_¶

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::ReturnSidechainMover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_end_res(self: pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover) → int¶: C++: protocols::simple_moves::ReturnSidechainMover::get_end_res() const –> unsigned long

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover) → str¶: C++: protocols::simple_moves::ReturnSidechainMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_start_res(self: pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover) → int¶: C++: protocols::simple_moves::ReturnSidechainMover::get_start_res() const –> unsigned long

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.

C++: protocols::moves::Mover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover) -> None
show(self: pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover, output: pyrosetta.rosetta.std.ostream) -> None

C++: protocols::simple_moves::ReturnSidechainMover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.simple_moves.RingConformationMover¶

Bases: Mover

Based on a given MoveMap, this mover selects movable cyclic residues and flips their rings to an idealized ring conformer.

apply(self: pyrosetta.rosetta.protocols.simple_moves.RingConformationMover, input_pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Apply the corresponding move to <input_pose>.

C++: protocols::simple_moves::RingConformationMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.RingConformationMover, object_to_copy: pyrosetta.rosetta.protocols.simple_moves.RingConformationMover) → pyrosetta.rosetta.protocols.simple_moves.RingConformationMover¶: C++: protocols::simple_moves::RingConformationMover::operator=(const class protocols::simple_moves::RingConformationMover &) –> class protocols::simple_moves::RingConformationMover &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.simple_moves.RingConformationMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::RingConformationMover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.simple_moves.RingConformationMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::RingConformationMover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.simple_moves.RingConformationMover) → str¶

Return the name of the Mover.

C++: protocols::simple_moves::RingConformationMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

movemap(*args, **kwargs)¶

Overloaded function.

movemap(self: pyrosetta.rosetta.protocols.simple_moves.RingConformationMover, pose: pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.core.kinematics.MoveMap

Get the current MoveMap, creating it if needed.

C++: protocols::simple_moves::RingConformationMover::movemap(const class core::pose::Pose &) –> class std::shared_ptr<const class core::kinematics::MoveMap>

movemap(self: pyrosetta.rosetta.protocols.simple_moves.RingConformationMover, new_movemap: pyrosetta.rosetta.core.kinematics.MoveMap) -> None

Set the MoveMap.

C++: protocols::simple_moves::RingConformationMover::movemap(class std::shared_ptr<class core::kinematics::MoveMap>) –> void

movemap_factory(self: pyrosetta.rosetta.protocols.simple_moves.RingConformationMover, new_movemap_factory: pyrosetta.rosetta.core.select.movemap.MoveMapFactory) → None¶

Set the MoveMapFactory.

C++: protocols::simple_moves::RingConformationMover::movemap_factory(class std::shared_ptr<const class core::select::movemap::MoveMapFactory>) –> void

static mover_name() → str¶: C++: protocols::simple_moves::RingConformationMover::mover_name() –> std::string

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.simple_moves.RingConformationMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::simple_moves::RingConformationMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.simple_moves.RingConformationMover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide the citation.

C++: protocols::simple_moves::RingConformationMover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::RingConformationMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None¶

Register options with the option system.

C++: protocols::simple_moves::RingConformationMover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

sample_all_conformers(*args, **kwargs)¶

Overloaded function.

sample_all_conformers(self: pyrosetta.rosetta.protocols.simple_moves.RingConformationMover) -> bool

Get whether or not this Mover will sample all ring conformers, regardless of energy.

C++: protocols::simple_moves::RingConformationMover::sample_all_conformers() const –> bool

sample_all_conformers(self: pyrosetta.rosetta.protocols.simple_moves.RingConformationMover, setting: bool) -> None

Set whether or not this Mover will sample all ring conformers, regardless of energy.

C++: protocols::simple_moves::RingConformationMover::sample_all_conformers(bool) –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.simple_moves.RingConformationMover) -> None
show(self: pyrosetta.rosetta.protocols.simple_moves.RingConformationMover, output: pyrosetta.rosetta.std.ostream) -> None

Generate string representation of RingConformationMover for debugging purposes.

C++: protocols::simple_moves::RingConformationMover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.simple_moves.RingConformationMoverCreator¶

Bases: MoverCreator

MoverCreator allowing the MoverFactory to create a RingConformationMover

assign(self: pyrosetta.rosetta.protocols.simple_moves.RingConformationMoverCreator, : pyrosetta.rosetta.protocols.simple_moves.RingConformationMoverCreator) → pyrosetta.rosetta.protocols.simple_moves.RingConformationMoverCreator¶: C++: protocols::simple_moves::RingConformationMoverCreator::operator=(const class protocols::simple_moves::RingConformationMoverCreator &) –> class protocols::simple_moves::RingConformationMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.simple_moves.RingConformationMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover¶

Return an up-casted owning pointer (MoverOP) to the mover.

C++: protocols::simple_moves::RingConformationMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.simple_moves.RingConformationMoverCreator) → str¶

Return the key name for the associated Mover (RingConformationMover).

C++: protocols::simple_moves::RingConformationMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.simple_moves.RingConformationMoverCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::RingConformationMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.simple_moves.SampleSequenceFromProbabilities¶

Bases: Mover

A class to sample sequences from a PerResidueProbabilitiesMetric and thread them onto the pose.

apply(self: pyrosetta.rosetta.protocols.simple_moves.SampleSequenceFromProbabilities, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Apply the mover

C++: protocols::simple_moves::SampleSequenceFromProbabilities::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.SampleSequenceFromProbabilities, : pyrosetta.rosetta.protocols.simple_moves.SampleSequenceFromProbabilities) → pyrosetta.rosetta.protocols.simple_moves.SampleSequenceFromProbabilities¶: C++: protocols::simple_moves::SampleSequenceFromProbabilities::operator=(const class protocols::simple_moves::SampleSequenceFromProbabilities &) –> class protocols::simple_moves::SampleSequenceFromProbabilities &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.simple_moves.SampleSequenceFromProbabilities) → pyrosetta.rosetta.protocols.moves.Mover¶

required in the context of the parser/scripting scheme

C++: protocols::simple_moves::SampleSequenceFromProbabilities::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.simple_moves.SampleSequenceFromProbabilities) → pyrosetta.rosetta.protocols.moves.Mover¶

required in the context of the parser/scripting scheme

C++: protocols::simple_moves::SampleSequenceFromProbabilities::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.simple_moves.SampleSequenceFromProbabilities) → str¶: C++: protocols::simple_moves::SampleSequenceFromProbabilities::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static mover_name() → str¶: C++: protocols::simple_moves::SampleSequenceFromProbabilities::mover_name() –> std::string

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.simple_moves.SampleSequenceFromProbabilities, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

parse XML tag (to use this Mover in Rosetta Scripts)

C++: protocols::simple_moves::SampleSequenceFromProbabilities::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.simple_moves.SampleSequenceFromProbabilities, citations: pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

This mover is unpublished. It returns Moritz Ertelt as its author.

C++: protocols::simple_moves::SampleSequenceFromProbabilities::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::SampleSequenceFromProbabilities::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_aa_temp(self: pyrosetta.rosetta.protocols.simple_moves.SampleSequenceFromProbabilities, aa_temp: float) → None¶

Set the amino acid temperature option

C++: protocols::simple_moves::SampleSequenceFromProbabilities::set_aa_temp(double) –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_delta_prob_cutoff(self: pyrosetta.rosetta.protocols.simple_moves.SampleSequenceFromProbabilities, delta_prob_cutoff: float) → None¶

Set the delta probability cutoff option

C++: protocols::simple_moves::SampleSequenceFromProbabilities::set_delta_prob_cutoff(double) –> void

set_fail_on_missing_cache(self: pyrosetta.rosetta.protocols.simple_moves.SampleSequenceFromProbabilities, fail: bool) → None¶

If use_cache is set to false, do we fail if no data is found in the pose?: Default True

C++: protocols::simple_moves::SampleSequenceFromProbabilities::set_fail_on_missing_cache(bool) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_max_mutations(self: pyrosetta.rosetta.protocols.simple_moves.SampleSequenceFromProbabilities, max_mutations: int) → None¶

Set the maximum number of mutations allowed option

C++: protocols::simple_moves::SampleSequenceFromProbabilities::set_max_mutations(unsigned long) –> void

set_metric(self: pyrosetta.rosetta.protocols.simple_moves.SampleSequenceFromProbabilities, metric: pyrosetta.rosetta.core.simple_metrics.PerResidueProbabilitiesMetric) → None¶

Set the PerResidueProbabilitiesMetric that will be used to calculate the pseudo-perplexity.

C++: protocols::simple_moves::SampleSequenceFromProbabilities::set_metric(class std::shared_ptr<const class core::simple_metrics::PerResidueProbabilitiesMetric>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_packing(self: pyrosetta.rosetta.protocols.simple_moves.SampleSequenceFromProbabilities, packing: bool) → None¶

Set a bool to define whether we repack

C++: protocols::simple_moves::SampleSequenceFromProbabilities::set_packing(bool) –> void

set_pos_temp(self: pyrosetta.rosetta.protocols.simple_moves.SampleSequenceFromProbabilities, pos_temp: float) → None¶

Set the positional temperature option

C++: protocols::simple_moves::SampleSequenceFromProbabilities::set_pos_temp(double) –> void

set_prob_cutoff(self: pyrosetta.rosetta.protocols.simple_moves.SampleSequenceFromProbabilities, prob_cutoff: float) → None¶

Set the probability cutoff option

C++: protocols::simple_moves::SampleSequenceFromProbabilities::set_prob_cutoff(double) –> void

set_task_factory(self: pyrosetta.rosetta.protocols.simple_moves.SampleSequenceFromProbabilities, task_factory: pyrosetta.rosetta.core.pack.task.TaskFactory) → None¶

Set the taskfactory option

C++: protocols::simple_moves::SampleSequenceFromProbabilities::set_task_factory(class std::shared_ptr<class core::pack::task::TaskFactory> &) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

set_use_cached_data(*args, **kwargs)¶

Overloaded function.

set_use_cached_data(self: pyrosetta.rosetta.protocols.simple_moves.SampleSequenceFromProbabilities, use_cache: bool) -> None
set_use_cached_data(self: pyrosetta.rosetta.protocols.simple_moves.SampleSequenceFromProbabilities, use_cache: bool, prefix: str) -> None
set_use_cached_data(self: pyrosetta.rosetta.protocols.simple_moves.SampleSequenceFromProbabilities, use_cache: bool, prefix: str, suffix: str) -> None

Set a boolean to attempt to find cached data matching the name/custom_type of the passed in simple_metric.

Optionally pass any set prefix/suffix.

This will allow the filter to re-use previously calculated data.

C++: protocols::simple_moves::SampleSequenceFromProbabilities::set_use_cached_data(bool, const std::string &, const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.simple_moves.SampleSequenceFromProbabilities) -> None
show(self: pyrosetta.rosetta.protocols.simple_moves.SampleSequenceFromProbabilities, output: pyrosetta.rosetta.std.ostream) -> None

C++: protocols::simple_moves::SampleSequenceFromProbabilities::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.simple_moves.SampleSequenceFromProbabilitiesCreator¶

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.simple_moves.SampleSequenceFromProbabilitiesCreator, : pyrosetta.rosetta.protocols.simple_moves.SampleSequenceFromProbabilitiesCreator) → pyrosetta.rosetta.protocols.simple_moves.SampleSequenceFromProbabilitiesCreator¶: C++: protocols::simple_moves::SampleSequenceFromProbabilitiesCreator::operator=(const class protocols::simple_moves::SampleSequenceFromProbabilitiesCreator &) –> class protocols::simple_moves::SampleSequenceFromProbabilitiesCreator &

create_mover(self: pyrosetta.rosetta.protocols.simple_moves.SampleSequenceFromProbabilitiesCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::SampleSequenceFromProbabilitiesCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.simple_moves.SampleSequenceFromProbabilitiesCreator) → str¶: C++: protocols::simple_moves::SampleSequenceFromProbabilitiesCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.simple_moves.SampleSequenceFromProbabilitiesCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::SampleSequenceFromProbabilitiesCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.simple_moves.SaveProbabilitiesMetricMover¶

Bases: Mover

A class to save a PerResidueProbabilitiesMetric to a weight file.

apply(self: pyrosetta.rosetta.protocols.simple_moves.SaveProbabilitiesMetricMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Apply the mover

C++: protocols::simple_moves::SaveProbabilitiesMetricMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.SaveProbabilitiesMetricMover, : pyrosetta.rosetta.protocols.simple_moves.SaveProbabilitiesMetricMover) → pyrosetta.rosetta.protocols.simple_moves.SaveProbabilitiesMetricMover¶: C++: protocols::simple_moves::SaveProbabilitiesMetricMover::operator=(const class protocols::simple_moves::SaveProbabilitiesMetricMover &) –> class protocols::simple_moves::SaveProbabilitiesMetricMover &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.simple_moves.SaveProbabilitiesMetricMover) → pyrosetta.rosetta.protocols.moves.Mover¶

required in the context of the parser/scripting scheme

C++: protocols::simple_moves::SaveProbabilitiesMetricMover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

convert the map of probabilities to one of logits for writing out to a PSSM

C++: protocols::simple_moves::SaveProbabilitiesMetricMover::convert_probabilities_to_logits(const class std::map<unsigned long, class std::map<enum core::chemical::AA, double, struct std::less<enum core::chemical::AA>, class std::allocator<struct std::pair<const enum core::chemical::AA, double> > >, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, class std::map<enum core::chemical::AA, double, struct std::less<enum core::chemical::AA>, class std::allocator<struct std::pair<const enum core::chemical::AA, double> > > > > > &) –> class std::map<unsigned long, class std::map<enum core::chemical::AA, double, struct std::less<enum core::chemical::AA>, class std::allocator<struct std::pair<const enum core::chemical::AA, double> > >, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, class std::map<enum core::chemical::AA, double, struct std::less<enum core::chemical::AA>, class std::allocator<struct std::pair<const enum core::chemical::AA, double> > > > > >

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.simple_moves.SaveProbabilitiesMetricMover) → pyrosetta.rosetta.protocols.moves.Mover¶

required in the context of the parser/scripting scheme

C++: protocols::simple_moves::SaveProbabilitiesMetricMover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.simple_moves.SaveProbabilitiesMetricMover) → str¶: C++: protocols::simple_moves::SaveProbabilitiesMetricMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

static get_selection_sequence(pose_sequence: str, position_map: pyrosetta.rosetta.std.map_unsigned_long_std_map_core_chemical_AA_double_std_less_core_chemical_AA_std_allocator_std_pair_const_core_chemical_AA_double_t_std_allocator_std_pair_const_unsigned_long_std_map_core_chemical_AA_double_std_less_core_chemical_AA_std_allocator_std_pair_const_core_chemical_AA_double_t) → str¶

Get the sequence of the selection present in the probability map

C++: protocols::simple_moves::SaveProbabilitiesMetricMover::get_selection_sequence(const std::string &, const class std::map<unsigned long, class std::map<enum core::chemical::AA, double, struct std::less<enum core::chemical::AA>, class std::allocator<struct std::pair<const enum core::chemical::AA, double> > >, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, class std::map<enum core::chemical::AA, double, struct std::less<enum core::chemical::AA>, class std::allocator<struct std::pair<const enum core::chemical::AA, double> > > > > > &) –> std::string

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static mover_name() → str¶: C++: protocols::simple_moves::SaveProbabilitiesMetricMover::mover_name() –> std::string

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.simple_moves.SaveProbabilitiesMetricMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

parse XML tag (to use this Mover in Rosetta Scripts)

C++: protocols::simple_moves::SaveProbabilitiesMetricMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.simple_moves.SaveProbabilitiesMetricMover, citations: pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

This mover is unpublished. It returns moritzertelt as its author.

C++: protocols::simple_moves::SaveProbabilitiesMetricMover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::SaveProbabilitiesMetricMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

static save_aa_probabilities_to_file(weights_file: str, prob_set: pyrosetta.rosetta.std.map_unsigned_long_std_map_core_chemical_AA_double_std_less_core_chemical_AA_std_allocator_std_pair_const_core_chemical_AA_double_t_std_allocator_std_pair_const_unsigned_long_std_map_core_chemical_AA_double_std_less_core_chemical_AA_std_allocator_std_pair_const_core_chemical_AA_double_t) → None¶

Save a set of amino acid probabilities to a weight file with formatting: PoseNum ResidueType Weight

C++: protocols::simple_moves::SaveProbabilitiesMetricMover::save_aa_probabilities_to_file(const std::string &, const class std::map<unsigned long, class std::map<enum core::chemical::AA, double, struct std::less<enum core::chemical::AA>, class std::allocator<struct std::pair<const enum core::chemical::AA, double> > >, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, class std::map<enum core::chemical::AA, double, struct std::less<enum core::chemical::AA>, class std::allocator<struct std::pair<const enum core::chemical::AA, double> > > > > > &) –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_fail_on_missing_cache(self: pyrosetta.rosetta.protocols.simple_moves.SaveProbabilitiesMetricMover, fail: bool) → None¶

If use_cache is set to false, do we fail if no data is found in the pose?: Default True

C++: protocols::simple_moves::SaveProbabilitiesMetricMover::set_fail_on_missing_cache(bool) –> void

set_filename(self: pyrosetta.rosetta.protocols.simple_moves.SaveProbabilitiesMetricMover, filename: str) → None¶

Set the name of the output file.

C++: protocols::simple_moves::SaveProbabilitiesMetricMover::set_filename(const std::string &) –> void

set_filetype(self: pyrosetta.rosetta.protocols.simple_moves.SaveProbabilitiesMetricMover, filetype: str) → None¶

Set the type of the output file.

C++: protocols::simple_moves::SaveProbabilitiesMetricMover::set_filetype(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_metric(self: pyrosetta.rosetta.protocols.simple_moves.SaveProbabilitiesMetricMover, metric: pyrosetta.rosetta.core.simple_metrics.PerResidueProbabilitiesMetric) → None¶

Set the PerResidueProbabilitiesMetric that will be used to calculate the pseudo-perplexity.

C++: protocols::simple_moves::SaveProbabilitiesMetricMover::set_metric(class std::shared_ptr<const class core::simple_metrics::PerResidueProbabilitiesMetric>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

set_use_cached_data(*args, **kwargs)¶

Overloaded function.

set_use_cached_data(self: pyrosetta.rosetta.protocols.simple_moves.SaveProbabilitiesMetricMover, use_cache: bool) -> None
set_use_cached_data(self: pyrosetta.rosetta.protocols.simple_moves.SaveProbabilitiesMetricMover, use_cache: bool, prefix: str) -> None
set_use_cached_data(self: pyrosetta.rosetta.protocols.simple_moves.SaveProbabilitiesMetricMover, use_cache: bool, prefix: str, suffix: str) -> None

Set a boolean to attempt to find cached data matching the name/custom_type of the passed in simple_metric.

Optionally pass any set prefix/suffix.

This will allow the filter to re-use previously calculated data.

C++: protocols::simple_moves::SaveProbabilitiesMetricMover::set_use_cached_data(bool, const std::string &, const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.simple_moves.SaveProbabilitiesMetricMoverCreator¶

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.simple_moves.SaveProbabilitiesMetricMoverCreator, : pyrosetta.rosetta.protocols.simple_moves.SaveProbabilitiesMetricMoverCreator) → pyrosetta.rosetta.protocols.simple_moves.SaveProbabilitiesMetricMoverCreator¶: C++: protocols::simple_moves::SaveProbabilitiesMetricMoverCreator::operator=(const class protocols::simple_moves::SaveProbabilitiesMetricMoverCreator &) –> class protocols::simple_moves::SaveProbabilitiesMetricMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.simple_moves.SaveProbabilitiesMetricMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::SaveProbabilitiesMetricMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.simple_moves.SaveProbabilitiesMetricMoverCreator) → str¶: C++: protocols::simple_moves::SaveProbabilitiesMetricMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.simple_moves.SaveProbabilitiesMetricMoverCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::SaveProbabilitiesMetricMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.simple_moves.SaveSequenceToCommentsMover¶

Bases: Mover

apply(self: pyrosetta.rosetta.protocols.simple_moves.SaveSequenceToCommentsMover, : pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::simple_moves::SaveSequenceToCommentsMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.SaveSequenceToCommentsMover, : pyrosetta.rosetta.protocols.simple_moves.SaveSequenceToCommentsMover) → pyrosetta.rosetta.protocols.simple_moves.SaveSequenceToCommentsMover¶: C++: protocols::simple_moves::SaveSequenceToCommentsMover::operator=(const class protocols::simple_moves::SaveSequenceToCommentsMover &) –> class protocols::simple_moves::SaveSequenceToCommentsMover &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.simple_moves.SaveSequenceToCommentsMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::SaveSequenceToCommentsMover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.simple_moves.SaveSequenceToCommentsMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::SaveSequenceToCommentsMover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.simple_moves.SaveSequenceToCommentsMover) → str¶: C++: protocols::simple_moves::SaveSequenceToCommentsMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static mover_name() → str¶: C++: protocols::simple_moves::SaveSequenceToCommentsMover::mover_name() –> std::string

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.simple_moves.SaveSequenceToCommentsMover, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::simple_moves::SaveSequenceToCommentsMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::SaveSequenceToCommentsMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

save_seq_name(*args, **kwargs)¶

Overloaded function.

save_seq_name(self: pyrosetta.rosetta.protocols.simple_moves.SaveSequenceToCommentsMover) -> str

C++: protocols::simple_moves::SaveSequenceToCommentsMover::save_seq_name() const –> std::string

save_seq_name(self: pyrosetta.rosetta.protocols.simple_moves.SaveSequenceToCommentsMover, s: str) -> None

C++: protocols::simple_moves::SaveSequenceToCommentsMover::save_seq_name(const std::string &) –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.simple_moves.SaveSequenceToCommentsMoverCreator¶

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.simple_moves.SaveSequenceToCommentsMoverCreator, : pyrosetta.rosetta.protocols.simple_moves.SaveSequenceToCommentsMoverCreator) → pyrosetta.rosetta.protocols.simple_moves.SaveSequenceToCommentsMoverCreator¶: C++: protocols::simple_moves::SaveSequenceToCommentsMoverCreator::operator=(const class protocols::simple_moves::SaveSequenceToCommentsMoverCreator &) –> class protocols::simple_moves::SaveSequenceToCommentsMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.simple_moves.SaveSequenceToCommentsMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::SaveSequenceToCommentsMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.simple_moves.SaveSequenceToCommentsMoverCreator) → str¶: C++: protocols::simple_moves::SaveSequenceToCommentsMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.simple_moves.SaveSequenceToCommentsMoverCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::SaveSequenceToCommentsMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.simple_moves.ScoreMover¶

Bases: Mover

apply(self: pyrosetta.rosetta.protocols.simple_moves.ScoreMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::simple_moves::ScoreMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.ScoreMover, : pyrosetta.rosetta.protocols.simple_moves.ScoreMover) → pyrosetta.rosetta.protocols.simple_moves.ScoreMover¶: C++: protocols::simple_moves::ScoreMover::operator=(const class protocols::simple_moves::ScoreMover &) –> class protocols::simple_moves::ScoreMover &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.simple_moves.ScoreMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::ScoreMover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.simple_moves.ScoreMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::ScoreMover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.simple_moves.ScoreMover) → str¶: C++: protocols::simple_moves::ScoreMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

insert_rms(self: pyrosetta.rosetta.protocols.simple_moves.ScoreMover, rms: float) → None¶

add an rms to the score_map: TODO possibly find a better way to do this? for now, there are too many different rmsd calculation functions to be able to do the actual calculation in the protocols::moves::Mover

C++: protocols::simple_moves::ScoreMover::insert_rms(double) –> void

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static mover_name() → str¶: C++: protocols::simple_moves::ScoreMover::mover_name() –> std::string

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.simple_moves.ScoreMover, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::simple_moves::ScoreMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::ScoreMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None¶: C++: protocols::simple_moves::ScoreMover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

score_function(self: pyrosetta.rosetta.protocols.simple_moves.ScoreMover) → pyrosetta.rosetta.core.scoring.ScoreFunction¶: C++: protocols::simple_moves::ScoreMover::score_function() const –> class std::shared_ptr<class core::scoring::ScoreFunction>

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_score_file(self: pyrosetta.rosetta.protocols.simple_moves.ScoreMover, scorefile: str) → None¶: C++: protocols::simple_moves::ScoreMover::set_score_file(std::string) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

set_verbose(self: pyrosetta.rosetta.protocols.simple_moves.ScoreMover, value: bool) → None¶: C++: protocols::simple_moves::ScoreMover::set_verbose(bool) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.simple_moves.ScoreMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::simple_moves::ScoreMover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.simple_moves.ScoreMoverCreator¶

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.simple_moves.ScoreMoverCreator, : pyrosetta.rosetta.protocols.simple_moves.ScoreMoverCreator) → pyrosetta.rosetta.protocols.simple_moves.ScoreMoverCreator¶: C++: protocols::simple_moves::ScoreMoverCreator::operator=(const class protocols::simple_moves::ScoreMoverCreator &) –> class protocols::simple_moves::ScoreMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.simple_moves.ScoreMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::ScoreMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.simple_moves.ScoreMoverCreator) → str¶: C++: protocols::simple_moves::ScoreMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.simple_moves.ScoreMoverCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::ScoreMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.simple_moves.SequenceProfileMover¶

Bases: Mover

apply(self: pyrosetta.rosetta.protocols.simple_moves.SequenceProfileMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::simple_moves::SequenceProfileMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.SequenceProfileMover, : pyrosetta.rosetta.protocols.simple_moves.SequenceProfileMover) → pyrosetta.rosetta.protocols.simple_moves.SequenceProfileMover¶: C++: protocols::simple_moves::SequenceProfileMover::operator=(const class protocols::simple_moves::SequenceProfileMover &) –> class protocols::simple_moves::SequenceProfileMover &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.simple_moves.SequenceProfileMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::SequenceProfileMover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.simple_moves.SequenceProfileMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::SequenceProfileMover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_cst_file_name(self: pyrosetta.rosetta.protocols.simple_moves.SequenceProfileMover) → str¶: C++: protocols::simple_moves::SequenceProfileMover::get_cst_file_name() const –> const std::string &

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.simple_moves.SequenceProfileMover) → str¶: C++: protocols::simple_moves::SequenceProfileMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_profile_wgt(self: pyrosetta.rosetta.protocols.simple_moves.SequenceProfileMover) → float¶: C++: protocols::simple_moves::SequenceProfileMover::get_profile_wgt() const –> double

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static mover_name() → str¶: C++: protocols::simple_moves::SequenceProfileMover::mover_name() –> std::string

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.simple_moves.SequenceProfileMover, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::simple_moves::SequenceProfileMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::SequenceProfileMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_cst_file_name(self: pyrosetta.rosetta.protocols.simple_moves.SequenceProfileMover, cst_file_name: str) → None¶: C++: protocols::simple_moves::SequenceProfileMover::set_cst_file_name(const std::string &) –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_profile_wgt(self: pyrosetta.rosetta.protocols.simple_moves.SequenceProfileMover, profile_wgt: float) → None¶: C++: protocols::simple_moves::SequenceProfileMover::set_profile_wgt(const double) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.simple_moves.SequenceProfileMoverCreator¶

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.simple_moves.SequenceProfileMoverCreator, : pyrosetta.rosetta.protocols.simple_moves.SequenceProfileMoverCreator) → pyrosetta.rosetta.protocols.simple_moves.SequenceProfileMoverCreator¶: C++: protocols::simple_moves::SequenceProfileMoverCreator::operator=(const class protocols::simple_moves::SequenceProfileMoverCreator &) –> class protocols::simple_moves::SequenceProfileMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.simple_moves.SequenceProfileMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::SequenceProfileMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.simple_moves.SequenceProfileMoverCreator) → str¶: C++: protocols::simple_moves::SequenceProfileMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.simple_moves.SequenceProfileMoverCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::SequenceProfileMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.simple_moves.SetTorsion¶

Bases: Mover

A mover to change one torsion angle

add_perturbation_magnitude(self: pyrosetta.rosetta.protocols.simple_moves.SetTorsion, mag_in: float) → None¶

Add a perturbation magnitude to the list of perturbation magnitudes.

Checks for non-negative magnitude. After this operation, the perturbation_magnitude_ vector is one entry longer.

C++: protocols::simple_moves::SetTorsion::add_perturbation_magnitude(const double &) –> void

add_perturbation_type(self: pyrosetta.rosetta.protocols.simple_moves.SetTorsion, type_in: str) → None¶

Add a perturbation type to the list of perturbation types.

Currently only allows “uniform” or “gaussian”. Checks for proper input. After this operation, the perturbation_type_ vector is one entry longer.

C++: protocols::simple_moves::SetTorsion::add_perturbation_type(const std::string &) –> void

angle(self: pyrosetta.rosetta.protocols.simple_moves.SetTorsion, iset: int, old_angle: float) → float¶

Actually get the value that the torsion will be set to.

Depending on settings, this will look up a value, generate a random value, or perturb an input value.

C++: protocols::simple_moves::SetTorsion::angle(const unsigned long, const double &) const –> double

apply(self: pyrosetta.rosetta.protocols.simple_moves.SetTorsion, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::simple_moves::SetTorsion::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.SetTorsion, : pyrosetta.rosetta.protocols.simple_moves.SetTorsion) → pyrosetta.rosetta.protocols.simple_moves.SetTorsion¶: C++: protocols::simple_moves::SetTorsion::operator=(const class protocols::simple_moves::SetTorsion &) –> class protocols::simple_moves::SetTorsion &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.simple_moves.SetTorsion) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::SetTorsion::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.simple_moves.SetTorsion) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::SetTorsion::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_fold_tree_root(self: pyrosetta.rosetta.protocols.simple_moves.SetTorsion) → int¶

Returns the residue index that will serve as the root of the FoldTree for the SetTorsion operation.

C++: protocols::simple_moves::SetTorsion::get_fold_tree_root() const –> unsigned long

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.simple_moves.SetTorsion) → str¶: C++: protocols::simple_moves::SetTorsion::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static mover_name() → str¶: C++: protocols::simple_moves::SetTorsion::mover_name() –> std::string

n_torsion_sets(self: pyrosetta.rosetta.protocols.simple_moves.SetTorsion) → int¶: C++: protocols::simple_moves::SetTorsion::n_torsion_sets() const –> unsigned long

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.simple_moves.SetTorsion, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::simple_moves::SetTorsion::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

perturbation_magnitude(self: pyrosetta.rosetta.protocols.simple_moves.SetTorsion, index: int) → float¶

Get a perturbation magnitude.

C++: protocols::simple_moves::SetTorsion::perturbation_magnitude(const unsigned long) const –> double

perturbation_type(self: pyrosetta.rosetta.protocols.simple_moves.SetTorsion, index: int) → pyrosetta.rosetta.protocols.simple_moves.TorsionPerturbType¶

Get a perturbation type.

C++: protocols::simple_moves::SetTorsion::perturbation_type(const unsigned long) const –> enum protocols::simple_moves::TorsionPerturbType

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::SetTorsion::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

residue_list(self: pyrosetta.rosetta.protocols.simple_moves.SetTorsion, iset: int, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_unsigned_long¶: C++: protocols::simple_moves::SetTorsion::residue_list(unsigned long, const class core::pose::Pose &) –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_fold_tree_root(self: pyrosetta.rosetta.protocols.simple_moves.SetTorsion, root: int) → None¶

Sets a residue index that will serve as the root of the FoldTree for the SetTorsion operation.

The FoldTree is reset afterwards (i.e. the mover does not permanently change the FoldTree).

C++: protocols::simple_moves::SetTorsion::set_fold_tree_root(const unsigned long) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

static torsion_ct_name(: str) → str¶: C++: protocols::simple_moves::SetTorsion::torsion_ct_name(std::string) –> std::string

torsion_name(self: pyrosetta.rosetta.protocols.simple_moves.SetTorsion, iset: int) → str¶: C++: protocols::simple_moves::SetTorsion::torsion_name(const unsigned long) –> std::string

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.simple_moves.SetTorsionCreator¶

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.simple_moves.SetTorsionCreator, : pyrosetta.rosetta.protocols.simple_moves.SetTorsionCreator) → pyrosetta.rosetta.protocols.simple_moves.SetTorsionCreator¶: C++: protocols::simple_moves::SetTorsionCreator::operator=(const class protocols::simple_moves::SetTorsionCreator &) –> class protocols::simple_moves::SetTorsionCreator &

create_mover(self: pyrosetta.rosetta.protocols.simple_moves.SetTorsionCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::SetTorsionCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.simple_moves.SetTorsionCreator) → str¶: C++: protocols::simple_moves::SetTorsionCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.simple_moves.SetTorsionCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::SetTorsionCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover¶

Bases: Mover

A protocols::moves::Mover that

apply(self: pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::simple_moves::SetupMetalsMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover, : pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover) → pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover¶: C++: protocols::simple_moves::SetupMetalsMover::operator=(const class protocols::simple_moves::SetupMetalsMover &) –> class protocols::simple_moves::SetupMetalsMover &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::SetupMetalsMover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::SetupMetalsMover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_add_constraints(self: pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover) → bool¶: C++: protocols::simple_moves::SetupMetalsMover::get_add_constraints() const –> bool

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_constraints_only(self: pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover) → bool¶: C++: protocols::simple_moves::SetupMetalsMover::get_constraints_only() const –> bool

get_contact_resnums_string(self: pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover) → str¶: C++: protocols::simple_moves::SetupMetalsMover::get_contact_resnums_string() const –> std::string

get_contact_selector(self: pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶: C++: protocols::simple_moves::SetupMetalsMover::get_contact_selector() const –> class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_metal_resnums_string(self: pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover) → str¶: C++: protocols::simple_moves::SetupMetalsMover::get_metal_resnums_string() const –> std::string

get_metal_selector(self: pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶: C++: protocols::simple_moves::SetupMetalsMover::get_metal_selector() const –> class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>

get_metals_angle_constraint_multiplier(self: pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover) → float¶: C++: protocols::simple_moves::SetupMetalsMover::get_metals_angle_constraint_multiplier() const –> double

get_metals_detection_LJ_multiplier(self: pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover) → float¶: C++: protocols::simple_moves::SetupMetalsMover::get_metals_detection_LJ_multiplier() const –> double

get_metals_distance_constraint_multiplier(self: pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover) → float¶: C++: protocols::simple_moves::SetupMetalsMover::get_metals_distance_constraint_multiplier() const –> double

get_name(self: pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover) → str¶: C++: protocols::simple_moves::SetupMetalsMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_remove_hydrogens(self: pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover) → bool¶: C++: protocols::simple_moves::SetupMetalsMover::get_remove_hydrogens() const –> bool

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static mover_name() → str¶: C++: protocols::simple_moves::SetupMetalsMover::mover_name() –> std::string

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶

Called by protocols::moves::MoverFactory when constructing new protocols::moves::Movers. Takes care of the specific mover’s parsing.

C++: protocols::simple_moves::SetupMetalsMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide the citation.

C++: protocols::simple_moves::SetupMetalsMover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::SetupMetalsMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_add_constraints(self: pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover, : bool) → None¶: C++: protocols::simple_moves::SetupMetalsMover::set_add_constraints(bool) –> void

set_constraints_only(self: pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover, : bool) → None¶: C++: protocols::simple_moves::SetupMetalsMover::set_constraints_only(bool) –> void

set_contact_resnums_string(self: pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover, : str) → None¶: C++: protocols::simple_moves::SetupMetalsMover::set_contact_resnums_string(std::string) –> void

set_contact_selector(self: pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover, : pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) → None¶: C++: protocols::simple_moves::SetupMetalsMover::set_contact_selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_metal_resnums_string(self: pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover, : str) → None¶: C++: protocols::simple_moves::SetupMetalsMover::set_metal_resnums_string(std::string) –> void

set_metal_selector(self: pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover, : pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) → None¶: C++: protocols::simple_moves::SetupMetalsMover::set_metal_selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

set_metals_angle_constraint_multiplier(self: pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover, : float) → None¶: C++: protocols::simple_moves::SetupMetalsMover::set_metals_angle_constraint_multiplier(double) –> void

set_metals_detection_LJ_multiplier(self: pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover, : float) → None¶: C++: protocols::simple_moves::SetupMetalsMover::set_metals_detection_LJ_multiplier(double) –> void

set_metals_distance_constraint_multiplier(self: pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover, : float) → None¶: C++: protocols::simple_moves::SetupMetalsMover::set_metals_distance_constraint_multiplier(double) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_remove_hydrogens(self: pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover, : bool) → None¶: C++: protocols::simple_moves::SetupMetalsMover::set_remove_hydrogens(bool) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover) -> None
show(self: pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover, output: pyrosetta.rosetta.std.ostream) -> None

C++: protocols::simple_moves::SetupMetalsMover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMoverCreator¶

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMoverCreator, : pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMoverCreator) → pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMoverCreator¶: C++: protocols::simple_moves::SetupMetalsMoverCreator::operator=(const class protocols::simple_moves::SetupMetalsMoverCreator &) –> class protocols::simple_moves::SetupMetalsMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::SetupMetalsMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMoverCreator) → str¶: C++: protocols::simple_moves::SetupMetalsMoverCreator::keyname() const –> std::string

static mover_name() → str¶: C++: protocols::simple_moves::SetupMetalsMoverCreator::mover_name() –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMoverCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::SetupMetalsMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.simple_moves.ShakeStructureMover¶

Bases: Mover

apply(self: pyrosetta.rosetta.protocols.simple_moves.ShakeStructureMover, p: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::simple_moves::ShakeStructureMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.ShakeStructureMover, : pyrosetta.rosetta.protocols.simple_moves.ShakeStructureMover) → pyrosetta.rosetta.protocols.simple_moves.ShakeStructureMover¶: C++: protocols::simple_moves::ShakeStructureMover::operator=(const class protocols::simple_moves::ShakeStructureMover &) –> class protocols::simple_moves::ShakeStructureMover &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶

Return a clone of the Mover object.

C++: protocols::moves::Mover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶

Generates a new Mover object freshly created with the default ctor.

C++: protocols::moves::Mover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_ensemble_ca_rmsd(self: pyrosetta.rosetta.protocols.simple_moves.ShakeStructureMover) → float¶: C++: protocols::simple_moves::ShakeStructureMover::get_ensemble_ca_rmsd() –> double

get_ensemble_diversity(self: pyrosetta.rosetta.protocols.simple_moves.ShakeStructureMover) → float¶: C++: protocols::simple_moves::ShakeStructureMover::get_ensemble_diversity() –> double

get_harmonic_ca_cst_std_dev(self: pyrosetta.rosetta.protocols.simple_moves.ShakeStructureMover) → float¶: C++: protocols::simple_moves::ShakeStructureMover::get_harmonic_ca_cst_std_dev() –> double

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_mc_temperature(self: pyrosetta.rosetta.protocols.simple_moves.ShakeStructureMover) → float¶: C++: protocols::simple_moves::ShakeStructureMover::get_mc_temperature() –> double

get_min_cst(self: pyrosetta.rosetta.protocols.simple_moves.ShakeStructureMover) → bool¶: C++: protocols::simple_moves::ShakeStructureMover::get_min_cst() –> bool

get_min_scorefunction(self: pyrosetta.rosetta.protocols.simple_moves.ShakeStructureMover) → pyrosetta.rosetta.core.scoring.ScoreFunction¶: C++: protocols::simple_moves::ShakeStructureMover::get_min_scorefunction() –> class std::shared_ptr<class core::scoring::ScoreFunction>

get_minimize_with_cst(self: pyrosetta.rosetta.protocols.simple_moves.ShakeStructureMover) → bool¶: C++: protocols::simple_moves::ShakeStructureMover::get_minimize_with_cst() –> bool

get_name(self: pyrosetta.rosetta.protocols.simple_moves.ShakeStructureMover) → str¶: C++: protocols::simple_moves::ShakeStructureMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_nrounds(self: pyrosetta.rosetta.protocols.simple_moves.ShakeStructureMover) → int¶: C++: protocols::simple_moves::ShakeStructureMover::get_nrounds() –> unsigned long

get_ramp_fa_rep(self: pyrosetta.rosetta.protocols.simple_moves.ShakeStructureMover) → bool¶: C++: protocols::simple_moves::ShakeStructureMover::get_ramp_fa_rep() –> bool

get_rmsd_target_tolerance(self: pyrosetta.rosetta.protocols.simple_moves.ShakeStructureMover) → float¶: C++: protocols::simple_moves::ShakeStructureMover::get_rmsd_target_tolerance() –> double

get_sc_min(self: pyrosetta.rosetta.protocols.simple_moves.ShakeStructureMover) → bool¶: C++: protocols::simple_moves::ShakeStructureMover::get_sc_min() –> bool

get_scorefunction(self: pyrosetta.rosetta.protocols.simple_moves.ShakeStructureMover) → pyrosetta.rosetta.core.scoring.ScoreFunction¶: C++: protocols::simple_moves::ShakeStructureMover::get_scorefunction() –> class std::shared_ptr<class core::scoring::ScoreFunction>

get_scorefunction_initialized(self: pyrosetta.rosetta.protocols.simple_moves.ShakeStructureMover) → bool¶: C++: protocols::simple_moves::ShakeStructureMover::get_scorefunction_initialized() –> bool

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_skip_low_temp_phase(self: pyrosetta.rosetta.protocols.simple_moves.ShakeStructureMover) → bool¶: C++: protocols::simple_moves::ShakeStructureMover::get_skip_low_temp_phase() –> bool

get_testing_phase(self: pyrosetta.rosetta.protocols.simple_moves.ShakeStructureMover) → bool¶: C++: protocols::simple_moves::ShakeStructureMover::get_testing_phase() –> bool

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.

C++: protocols::moves::Mover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_ensemble_diversity(self: pyrosetta.rosetta.protocols.simple_moves.ShakeStructureMover, ca_rmsd: float) → None¶: C++: protocols::simple_moves::ShakeStructureMover::set_ensemble_diversity(double) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_mc_temperature(self: pyrosetta.rosetta.protocols.simple_moves.ShakeStructureMover, temp: float) → None¶: C++: protocols::simple_moves::ShakeStructureMover::set_mc_temperature(double) –> void

set_minimize_with_cst(self: pyrosetta.rosetta.protocols.simple_moves.ShakeStructureMover, truefalse: bool) → None¶: C++: protocols::simple_moves::ShakeStructureMover::set_minimize_with_cst(bool) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_nrounds(self: pyrosetta.rosetta.protocols.simple_moves.ShakeStructureMover, new_nrounds: int) → None¶: C++: protocols::simple_moves::ShakeStructureMover::set_nrounds(int) –> void

set_ramp_fa_rep(self: pyrosetta.rosetta.protocols.simple_moves.ShakeStructureMover, truefalse: bool) → None¶: C++: protocols::simple_moves::ShakeStructureMover::set_ramp_fa_rep(bool) –> void

set_rmsd_target_tolerance(self: pyrosetta.rosetta.protocols.simple_moves.ShakeStructureMover, tol: float) → None¶: C++: protocols::simple_moves::ShakeStructureMover::set_rmsd_target_tolerance(double) –> void

set_sc_min(self: pyrosetta.rosetta.protocols.simple_moves.ShakeStructureMover, truefalse: bool) → None¶: C++: protocols::simple_moves::ShakeStructureMover::set_sc_min(bool) –> void

set_scorefunction(self: pyrosetta.rosetta.protocols.simple_moves.ShakeStructureMover, s: pyrosetta.rosetta.core.scoring.ScoreFunction) → None¶: C++: protocols::simple_moves::ShakeStructureMover::set_scorefunction(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void

set_skip_low_temp_phase(self: pyrosetta.rosetta.protocols.simple_moves.ShakeStructureMover, truefalse: bool) → None¶: C++: protocols::simple_moves::ShakeStructureMover::set_skip_low_temp_phase(bool) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.simple_moves.ShearMover¶

Bases: BackboneMover

A mover that perturbs the phi of residue i and the psi of residue i-1 such that they create a ‘shearing’ effect, minimizing the downstream consequences of this torsional perturbation. The final torsion angle is subject to a metropolis criterion using the rama score to ensure that only favorable backbone torsion angles are being selected. The number of perturbations, and the magnitude of perturbations, and the temperature in the rama check, can all be modified.

Common Methods:: ShearMover.apply

angle_max(*args, **kwargs)¶

Overloaded function.

angle_max(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, angle: float) -> None

Set the maximum angle of perturbation, independent of

secondary structure. new_angle = old_angle +/- ( angle_max/2 )

Example:: bbmover.angle_max(25)
See also:: ShearMover SmallMover

C++: protocols::simple_moves::BackboneMover::angle_max(const double) –> void

angle_max(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, type: str, angle: float) -> None

Sets the max angle of perturbation for residues with <type>

secondary structure. (<type> must be ‘H’, ‘E’, or ‘L’.) new_angle = old_angle +/- ( angle_max/2 )

Example:: bbmover.angle_max(‘H’, 25)
See also:: ShearMover SmallMover

C++: protocols::simple_moves::BackboneMover::angle_max(const char, const double) –> void

angle_max(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, angle_max_in: pyrosetta.rosetta.std.map_char_double) -> None

Sets the max angle of perturbation, for secondary structures: ‘H’, ‘E’, and ‘L’. new_angle = old_angle +/- ( angle_max/2 )

C++: protocols::simple_moves::BackboneMover::angle_max(class std::map<char, double, struct std::less<char>, class std::allocator<struct std::pair<const char, double> > >) –> void

apply(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, : pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::simple_moves::BackboneMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.ShearMover, : pyrosetta.rosetta.protocols.simple_moves.ShearMover) → pyrosetta.rosetta.protocols.simple_moves.ShearMover¶: C++: protocols::simple_moves::ShearMover::operator=(const class protocols::simple_moves::ShearMover &) –> class protocols::simple_moves::ShearMover &

static backbone_mover_complex_type_namer(tag_name: str) → str¶: C++: protocols::simple_moves::BackboneMover::backbone_mover_complex_type_namer(std::string) –> std::string

check_rama(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover) → bool¶: C++: protocols::simple_moves::BackboneMover::check_rama() –> bool

clear(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover) → None¶: C++: protocols::simple_moves::BackboneMover::clear() –> void

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.simple_moves.ShearMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::ShearMover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

static complex_type_generator_for_backbone_mover(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → pyrosetta.rosetta.utility.tag.XMLSchemaComplexTypeGenerator¶: C++: protocols::simple_moves::BackboneMover::complex_type_generator_for_backbone_mover(class utility::tag::XMLSchemaDefinition &) –> class std::shared_ptr<class utility::tag::XMLSchemaComplexTypeGenerator>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

finalize_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, pose: pyrosetta.rosetta.core.pose.Pose, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover) → None¶

Callback executed after all Monte Carlo trials are completed.

C++: protocols::canonical_sampling::ThermodynamicMover::finalize_simulation(class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover &) –> void

fresh_instance(self: pyrosetta.rosetta.protocols.simple_moves.ShearMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::ShearMover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_angle_max(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, type: str) → float¶

Gets the max angle of perturbation for residues with <type>

secondary structure. (<type> must be ‘H’, ‘E’, or ‘L’.)

Example:: bbmover.angle_max(‘H’)
See also:: ShearMover SmallMover

C++: protocols::simple_moves::BackboneMover::get_angle_max(const char) const –> double

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.simple_moves.ShearMover) → str¶: C++: protocols::simple_moves::ShearMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

initialize_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, pose: pyrosetta.rosetta.core.pose.Pose, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover, cycle: int) → None¶

Callback executed before any Monte Carlo trials are attempted.

C++: protocols::canonical_sampling::ThermodynamicMover::initialize_simulation(class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover &, unsigned long) –> void

is_multi_trial(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → bool¶

Return true if the move performs multiple trials on each apply.

last_inner_score_delta_over_temperature()

metropolis_hastings_mover()

set_metropolis_hastings_mover()

C++: protocols::canonical_sampling::ThermodynamicMover::is_multi_trial() –> bool

last_inner_score_delta_over_temperature(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → float¶

If this is a multi-trial move, return the change in internal

score/temperature caused by the last call to apply().

is_multi_trial()

C++: protocols::canonical_sampling::ThermodynamicMover::last_inner_score_delta_over_temperature() –> double

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → float¶

Return the proposal density ratio for last apply method.

C++: protocols::canonical_sampling::ThermodynamicMover::last_proposal_density_ratio() –> double

make_move(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, : pyrosetta.rosetta.core.pose.Pose) → bool¶: C++: protocols::simple_moves::BackboneMover::make_move(class core::pose::Pose &) –> bool

metropolis_hastings_mover(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → pyrosetta.rosetta.std.weak_ptr_protocols_canonical_sampling_MetropolisHastingsMover_t¶

If this is a multi-trial move, return the MetropolisHastingsMover

being used internally.

is_multi_trial()

C++: protocols::canonical_sampling::ThermodynamicMover::metropolis_hastings_mover() –> class std::weak_ptr<class protocols::canonical_sampling::MetropolisHastingsMover>

move_with_rama(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, pose: pyrosetta.rosetta.core.pose.Pose) → bool¶: C++: protocols::simple_moves::BackboneMover::move_with_rama(class core::pose::Pose &) –> bool

move_with_scorefxn(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, pose: pyrosetta.rosetta.core.pose.Pose) → bool¶: C++: protocols::simple_moves::BackboneMover::move_with_scorefxn(class core::pose::Pose &) –> bool

movemap(*args, **kwargs)¶

Overloaded function.

movemap(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, new_movemap: pyrosetta.rosetta.core.kinematics.MoveMap) -> None

C++: protocols::simple_moves::BackboneMover::movemap(class std::shared_ptr<class core::kinematics::MoveMap>) –> void

movemap(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, pose: pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.core.kinematics.MoveMap

Get the movemap for this pose.

C++: protocols::simple_moves::BackboneMover::movemap(const class core::pose::Pose &) –> class std::shared_ptr<const class core::kinematics::MoveMap>

movemap_factory(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, new_movemap_factory: pyrosetta.rosetta.core.select.movemap.MoveMapFactory) → None¶: C++: protocols::simple_moves::BackboneMover::movemap_factory(class std::shared_ptr<const class core::select::movemap::MoveMapFactory>) –> void

static mover_name() → str¶: C++: protocols::simple_moves::ShearMover::mover_name() –> std::string

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

nmoves(*args, **kwargs)¶

Overloaded function.

nmoves(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, nmoves_in: int) -> None

C++: protocols::simple_moves::BackboneMover::nmoves(const unsigned long) –> void

nmoves(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover) -> int

C++: protocols::simple_moves::BackboneMover::nmoves() const –> unsigned long

observe_after_metropolis(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover) → None¶

Callback executed after the Metropolis criterion is evaluated.

C++: protocols::canonical_sampling::ThermodynamicMover::observe_after_metropolis(const class protocols::canonical_sampling::MetropolisHastingsMover &) –> void

parse_my_tag(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::simple_moves::BackboneMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

preserve_detailed_balance(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover) → bool¶

get whether detailed balance is preserved (i.e. no Ramachandran biasing)

C++: protocols::simple_moves::BackboneMover::preserve_detailed_balance() const –> bool

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::ShearMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

scorefxn(*args, **kwargs)¶

Overloaded function.

scorefxn(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover) -> pyrosetta.rosetta.core.scoring.ScoreFunction

If set, this scorefunction will be used instead of the original rama method (default = not set).

C++: protocols::simple_moves::BackboneMover::scorefxn() const –> class std::shared_ptr<class core::scoring::ScoreFunction>

scorefxn(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None

C++: protocols::simple_moves::BackboneMover::scorefxn(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void

selector(*args, **kwargs)¶

Overloaded function.

selector(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover) -> pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

Return the residue selector that can be used to dynamically select residues to perturb: at runtime.

C++: protocols::simple_moves::BackboneMover::selector() const –> class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>

selector(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) -> None

C++: protocols::simple_moves::BackboneMover::selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

set_angles(self: pyrosetta.rosetta.protocols.simple_moves.ShearMover, angle_in: float) → None¶: C++: protocols::simple_moves::ShearMover::set_angles(double) –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_metropolis_hastings_mover(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, metropolis_hastings_mover: pyrosetta.rosetta.std.weak_ptr_protocols_canonical_sampling_MetropolisHastingsMover_t) → None¶

If this is a multi-trial move, set the MetropolisHastingsMover to

be used internally.

is_multi_trial()

C++: protocols::canonical_sampling::ThermodynamicMover::set_metropolis_hastings_mover(class std::weak_ptr<class protocols::canonical_sampling::MetropolisHastingsMover>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_preserve_detailed_balance(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, preserve_detailed_balance: bool) → None¶

set whether detailed balance is preserved (i.e. no Ramachandran biasing)

C++: protocols::simple_moves::BackboneMover::set_preserve_detailed_balance(bool) –> void

set_residue_selector(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) → None¶

Set the ResidueSelector that this mover will use.

Clones the input.

C++: protocols::simple_moves::BackboneMover::set_residue_selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

set_warn_empty_list(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, warn_empty: bool) → None¶

Set to warn of an empty setup list. Default true.

C++: protocols::simple_moves::BackboneMover::set_warn_empty_list(bool) –> void

setup_list(self: pyrosetta.rosetta.protocols.simple_moves.ShearMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::simple_moves::ShearMover::setup_list(class core::pose::Pose &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover) -> None
show(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, output: pyrosetta.rosetta.std.ostream) -> None

C++: protocols::simple_moves::BackboneMover::show(std::ostream &) const –> void

temperature(*args, **kwargs)¶

Overloaded function.

temperature(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, temperature_in: float) -> None

C++: protocols::simple_moves::BackboneMover::temperature(const double) –> void

temperature(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover) -> float

C++: protocols::simple_moves::BackboneMover::temperature() const –> double

test_move(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, : pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::simple_moves::BackboneMover::test_move(class core::pose::Pose &) –> void

torsion_id_ranges(self: pyrosetta.rosetta.protocols.simple_moves.ShearMover, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_core_id_TorsionID_Range¶

get the TorsionIDs perturbed by the mover during moves, along with their ranges

C++: protocols::simple_moves::ShearMover::torsion_id_ranges(class core::pose::Pose &) –> class utility::vector1<class core::id::TorsionID_Range, class std::allocator<class core::id::TorsionID_Range> >

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.simple_moves.ShearMoverCreator¶

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.simple_moves.ShearMoverCreator, : pyrosetta.rosetta.protocols.simple_moves.ShearMoverCreator) → pyrosetta.rosetta.protocols.simple_moves.ShearMoverCreator¶: C++: protocols::simple_moves::ShearMoverCreator::operator=(const class protocols::simple_moves::ShearMoverCreator &) –> class protocols::simple_moves::ShearMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.simple_moves.ShearMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::ShearMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.simple_moves.ShearMoverCreator) → str¶: C++: protocols::simple_moves::ShearMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.simple_moves.ShearMoverCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::ShearMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.simple_moves.ShortBackrubMover¶

Bases: Mover

apply(self: pyrosetta.rosetta.protocols.simple_moves.ShortBackrubMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::simple_moves::ShortBackrubMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.ShortBackrubMover, : pyrosetta.rosetta.protocols.simple_moves.ShortBackrubMover) → pyrosetta.rosetta.protocols.simple_moves.ShortBackrubMover¶: C++: protocols::simple_moves::ShortBackrubMover::operator=(const class protocols::simple_moves::ShortBackrubMover &) –> class protocols::simple_moves::ShortBackrubMover &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.simple_moves.ShortBackrubMover) → pyrosetta.rosetta.protocols.moves.Mover¶

clone this object

C++: protocols::simple_moves::ShortBackrubMover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.simple_moves.ShortBackrubMover) → pyrosetta.rosetta.protocols.moves.Mover¶

create this type of object

C++: protocols::simple_moves::ShortBackrubMover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_backrubmover(self: pyrosetta.rosetta.protocols.simple_moves.ShortBackrubMover) → pyrosetta.rosetta.protocols.backrub.BackrubMover¶: C++: protocols::simple_moves::ShortBackrubMover::get_backrubmover() const –> class std::shared_ptr<class protocols::backrub::BackrubMover>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.simple_moves.ShortBackrubMover) → str¶: C++: protocols::simple_moves::ShortBackrubMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_randomize_resnum(self: pyrosetta.rosetta.protocols.simple_moves.ShortBackrubMover) → bool¶: C++: protocols::simple_moves::ShortBackrubMover::get_randomize_resnum() const –> bool

get_resnum(self: pyrosetta.rosetta.protocols.simple_moves.ShortBackrubMover) → int¶: C++: protocols::simple_moves::ShortBackrubMover::get_resnum() const –> unsigned long

get_rotation_std_dev(self: pyrosetta.rosetta.protocols.simple_moves.ShortBackrubMover) → float¶: C++: protocols::simple_moves::ShortBackrubMover::get_rotation_std_dev() const –> double

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

get_uniform_backrub(self: pyrosetta.rosetta.protocols.simple_moves.ShortBackrubMover) → bool¶: C++: protocols::simple_moves::ShortBackrubMover::get_uniform_backrub() const –> bool

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static mover_name() → str¶: C++: protocols::simple_moves::ShortBackrubMover::mover_name() –> std::string

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.simple_moves.ShortBackrubMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::simple_moves::ShortBackrubMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::ShortBackrubMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.simple_moves.ShortBackrubMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::simple_moves::ShortBackrubMover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_randomize_resnum(self: pyrosetta.rosetta.protocols.simple_moves.ShortBackrubMover, randomize_resnum: bool) → None¶: C++: protocols::simple_moves::ShortBackrubMover::set_randomize_resnum(bool) –> void

set_resnum(self: pyrosetta.rosetta.protocols.simple_moves.ShortBackrubMover, resnum: int) → None¶: C++: protocols::simple_moves::ShortBackrubMover::set_resnum(unsigned long) –> void

set_rotation_std_dev(self: pyrosetta.rosetta.protocols.simple_moves.ShortBackrubMover, rotation_std_dev: float) → None¶: C++: protocols::simple_moves::ShortBackrubMover::set_rotation_std_dev(double) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

set_uniform_backrub(self: pyrosetta.rosetta.protocols.simple_moves.ShortBackrubMover, uniform_backrub: bool) → None¶: C++: protocols::simple_moves::ShortBackrubMover::set_uniform_backrub(bool) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.simple_moves.ShortBackrubMoverCreator¶

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.simple_moves.ShortBackrubMoverCreator, : pyrosetta.rosetta.protocols.simple_moves.ShortBackrubMoverCreator) → pyrosetta.rosetta.protocols.simple_moves.ShortBackrubMoverCreator¶: C++: protocols::simple_moves::ShortBackrubMoverCreator::operator=(const class protocols::simple_moves::ShortBackrubMoverCreator &) –> class protocols::simple_moves::ShortBackrubMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.simple_moves.ShortBackrubMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::ShortBackrubMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.simple_moves.ShortBackrubMoverCreator) → str¶: C++: protocols::simple_moves::ShortBackrubMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.simple_moves.ShortBackrubMoverCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::ShortBackrubMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover¶

Bases: Mover

This mover functions to thread the sequence of a region onto the given pose. Nothing fancy here. For more fancy things see protocols/comparative_modeling.

It does the threading by allowing the task to only enable these residues and then does a repacking. Optionally repack neighbors so we save one more step. A sequence is just a string, additional ‘-’ charactors denote to skip this position in the thread. Default is 5 rounds of packing.

apply(self: pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::simple_moves::SimpleThreadingMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover, : pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover) → pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover¶: C++: protocols::simple_moves::SimpleThreadingMover::operator=(const class protocols::simple_moves::SimpleThreadingMover &) –> class protocols::simple_moves::SimpleThreadingMover &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::SimpleThreadingMover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::SimpleThreadingMover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover) → str¶: C++: protocols::simple_moves::SimpleThreadingMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_neighbor_distance(self: pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover) → float¶: C++: protocols::simple_moves::SimpleThreadingMover::get_neighbor_distance() const –> double

get_pack_neighbors(self: pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover) → bool¶: C++: protocols::simple_moves::SimpleThreadingMover::get_pack_neighbors() const –> bool

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static mover_name() → str¶: C++: protocols::simple_moves::SimpleThreadingMover::mover_name() –> std::string

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::simple_moves::SimpleThreadingMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide the citation.

C++: protocols::simple_moves::SimpleThreadingMover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::SimpleThreadingMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

sequence_mode(self: pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover) → pyrosetta.rosetta.core.simple_metrics.metrics.SequenceMetricMode¶

Get the sequence mode.

Vikram K. Mulligan (vmulligan.org).

C++: protocols::simple_moves::SimpleThreadingMover::sequence_mode() const –> enum core::simple_metrics::metrics::SequenceMetricMode

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_neighbor_distance(self: pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover, neighbor_dis: float) → None¶

Set the packing distance for neighbor pack.

C++: protocols::simple_moves::SimpleThreadingMover::set_neighbor_distance(double) –> void

set_pack_neighbors(self: pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover, pack_neighbors: bool) → None¶

Pack the neighbor residues?

C++: protocols::simple_moves::SimpleThreadingMover::set_pack_neighbors(bool) –> void

set_pack_rounds(self: pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover, pack_rounds: int) → None¶

Set the number of pack rounds.

C++: protocols::simple_moves::SimpleThreadingMover::set_pack_rounds(unsigned long) –> void

set_scorefxn(self: pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) → None¶

Set the scorefunction used for packing.

C++: protocols::simple_moves::SimpleThreadingMover::set_scorefxn(class std::shared_ptr<const class core::scoring::ScoreFunction>) –> void

set_sequence(self: pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover, thread_sequence: str, start_position: int) → None¶

Set the sequence to thread onto the structure used in apply and where to start.

Can have ‘-’ charactors in sequence to denote a gap in the threaded sequence.

C++: protocols::simple_moves::SimpleThreadingMover::set_sequence(std::string, unsigned long) –> void

set_sequence_mode(*args, **kwargs)¶

Overloaded function.

set_sequence_mode(self: pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover, mode_string_in: str) -> None

Set the sequence mode, by string.

This determines how the sequence is interpreted (one-letter codes, three-letter codes, etc.).

Vikram K. Mulligan (vmulligan.org).

C++: protocols::simple_moves::SimpleThreadingMover::set_sequence_mode(const std::string &) –> void

set_sequence_mode(self: pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover, mode_in: pyrosetta.rosetta.core.simple_metrics.metrics.SequenceMetricMode) -> None

Set the sequence mode, by enum.

This determines how the sequence is interpreted (one-letter codes, three-letter codes, etc.).

Vikram K. Mulligan (vmulligan.org).

C++: protocols::simple_moves::SimpleThreadingMover::set_sequence_mode(const enum core::simple_metrics::metrics::SequenceMetricMode) –> void

set_skip_unknown_mutant(self: pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover, setting: bool) → None¶

Set whether we skip unknown residue types, or throw errors.

C++: protocols::simple_moves::SimpleThreadingMover::set_skip_unknown_mutant(const bool) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

skip_unknown_mutant(self: pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover) → bool¶

Get whether we skip unknown residue types, or throw errors.

C++: protocols::simple_moves::SimpleThreadingMover::skip_unknown_mutant() const –> bool

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMoverCreator¶

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMoverCreator, : pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMoverCreator) → pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMoverCreator¶: C++: protocols::simple_moves::SimpleThreadingMoverCreator::operator=(const class protocols::simple_moves::SimpleThreadingMoverCreator &) –> class protocols::simple_moves::SimpleThreadingMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::SimpleThreadingMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMoverCreator) → str¶: C++: protocols::simple_moves::SimpleThreadingMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMoverCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::SimpleThreadingMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.simple_moves.SixDoFGridDockMover¶

Bases: Mover

Class for enumerating docked orientations (3 translations and 3 rotations) between two chains

apply(self: pyrosetta.rosetta.protocols.simple_moves.SixDoFGridDockMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Apply the mover

C++: protocols::simple_moves::SixDoFGridDockMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.SixDoFGridDockMover, : pyrosetta.rosetta.protocols.simple_moves.SixDoFGridDockMover) → pyrosetta.rosetta.protocols.simple_moves.SixDoFGridDockMover¶: C++: protocols::simple_moves::SixDoFGridDockMover::operator=(const class protocols::simple_moves::SixDoFGridDockMover &) –> class protocols::simple_moves::SixDoFGridDockMover &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.simple_moves.SixDoFGridDockMover) → pyrosetta.rosetta.protocols.moves.Mover¶

required in the context of the parser/scripting scheme

C++: protocols::simple_moves::SixDoFGridDockMover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

dof_sample_index(*args, **kwargs)¶

Overloaded function.

dof_sample_index(self: pyrosetta.rosetta.protocols.simple_moves.SixDoFGridDockMover) -> int

C++: protocols::simple_moves::SixDoFGridDockMover::dof_sample_index() const –> unsigned long

dof_sample_index(self: pyrosetta.rosetta.protocols.simple_moves.SixDoFGridDockMover, setting: int) -> None

C++: protocols::simple_moves::SixDoFGridDockMover::dof_sample_index(unsigned long) –> void

fresh_instance(self: pyrosetta.rosetta.protocols.simple_moves.SixDoFGridDockMover) → pyrosetta.rosetta.protocols.moves.Mover¶

required in the context of the parser/scripting scheme

C++: protocols::simple_moves::SixDoFGridDockMover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.simple_moves.SixDoFGridDockMover) → str¶: C++: protocols::simple_moves::SixDoFGridDockMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

lex_position(self: pyrosetta.rosetta.protocols.simple_moves.SixDoFGridDockMover, dof_values: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, index: int, dof: int) → float¶: C++: protocols::simple_moves::SixDoFGridDockMover::lex_position(class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > >, unsigned long, unsigned long) –> double

static mover_name() → str¶: C++: protocols::simple_moves::SixDoFGridDockMover::mover_name() –> std::string

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.simple_moves.SixDoFGridDockMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

parse XML tag (to use this Mover in Rosetta Scripts)

C++: protocols::simple_moves::SixDoFGridDockMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

parse_range(self: pyrosetta.rosetta.protocols.simple_moves.SixDoFGridDockMover, tag: pyrosetta.rosetta.utility.tag.Tag, range_option_name: str) → pyrosetta.rosetta.utility.vector1_double¶: C++: protocols::simple_moves::SixDoFGridDockMover::parse_range(class std::shared_ptr<const class utility::tag::Tag>, std::string) –> class utility::vector1<double, class std::allocator<double> >

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::SixDoFGridDockMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.simple_moves.SixDoFGridDockMover) -> None
show(self: pyrosetta.rosetta.protocols.simple_moves.SixDoFGridDockMover, output: pyrosetta.rosetta.std.ostream) -> None

C++: protocols::simple_moves::SixDoFGridDockMover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.simple_moves.SixDoFGridDockMoverCreator¶

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.simple_moves.SixDoFGridDockMoverCreator, : pyrosetta.rosetta.protocols.simple_moves.SixDoFGridDockMoverCreator) → pyrosetta.rosetta.protocols.simple_moves.SixDoFGridDockMoverCreator¶: C++: protocols::simple_moves::SixDoFGridDockMoverCreator::operator=(const class protocols::simple_moves::SixDoFGridDockMoverCreator &) –> class protocols::simple_moves::SixDoFGridDockMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.simple_moves.SixDoFGridDockMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::SixDoFGridDockMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.simple_moves.SixDoFGridDockMoverCreator) → str¶: C++: protocols::simple_moves::SixDoFGridDockMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.simple_moves.SixDoFGridDockMoverCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::SixDoFGridDockMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.simple_moves.SmallMover¶

Bases: BackboneMover

A mover that makes independent random perturbations of the phi and psi torsion angles of residue i. It selects residue i at random among movable residues (set by its MoveMap), and the final torsion angle is subject to a metropolis criterion using the rama score to ensure that only favorable backbone torsion angles are being selected. The number of perturbations, and the magnitude of perturbations, and the temperature in the rama check, can all be modified.

Common Methods:: SmallMover.apply SmallMover.angle_max

angle_max(*args, **kwargs)¶

Overloaded function.

angle_max(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, angle: float) -> None

Set the maximum angle of perturbation, independent of

secondary structure. new_angle = old_angle +/- ( angle_max/2 )

Example:: bbmover.angle_max(25)
See also:: ShearMover SmallMover

C++: protocols::simple_moves::BackboneMover::angle_max(const double) –> void

angle_max(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, type: str, angle: float) -> None

Sets the max angle of perturbation for residues with <type>

secondary structure. (<type> must be ‘H’, ‘E’, or ‘L’.) new_angle = old_angle +/- ( angle_max/2 )

Example:: bbmover.angle_max(‘H’, 25)
See also:: ShearMover SmallMover

C++: protocols::simple_moves::BackboneMover::angle_max(const char, const double) –> void

angle_max(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, angle_max_in: pyrosetta.rosetta.std.map_char_double) -> None

Sets the max angle of perturbation, for secondary structures: ‘H’, ‘E’, and ‘L’. new_angle = old_angle +/- ( angle_max/2 )

C++: protocols::simple_moves::BackboneMover::angle_max(class std::map<char, double, struct std::less<char>, class std::allocator<struct std::pair<const char, double> > >) –> void

apply(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, : pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::simple_moves::BackboneMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.SmallMover, : pyrosetta.rosetta.protocols.simple_moves.SmallMover) → pyrosetta.rosetta.protocols.simple_moves.SmallMover¶: C++: protocols::simple_moves::SmallMover::operator=(const class protocols::simple_moves::SmallMover &) –> class protocols::simple_moves::SmallMover &

static backbone_mover_complex_type_namer(tag_name: str) → str¶: C++: protocols::simple_moves::BackboneMover::backbone_mover_complex_type_namer(std::string) –> std::string

check_rama(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover) → bool¶: C++: protocols::simple_moves::BackboneMover::check_rama() –> bool

clear(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover) → None¶: C++: protocols::simple_moves::BackboneMover::clear() –> void

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.simple_moves.SmallMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::SmallMover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

static complex_type_generator_for_backbone_mover(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → pyrosetta.rosetta.utility.tag.XMLSchemaComplexTypeGenerator¶: C++: protocols::simple_moves::BackboneMover::complex_type_generator_for_backbone_mover(class utility::tag::XMLSchemaDefinition &) –> class std::shared_ptr<class utility::tag::XMLSchemaComplexTypeGenerator>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

finalize_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, pose: pyrosetta.rosetta.core.pose.Pose, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover) → None¶

Callback executed after all Monte Carlo trials are completed.

C++: protocols::canonical_sampling::ThermodynamicMover::finalize_simulation(class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover &) –> void

fresh_instance(self: pyrosetta.rosetta.protocols.simple_moves.SmallMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::SmallMover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_angle_max(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, type: str) → float¶

Gets the max angle of perturbation for residues with <type>

secondary structure. (<type> must be ‘H’, ‘E’, or ‘L’.)

Example:: bbmover.angle_max(‘H’)
See also:: ShearMover SmallMover

C++: protocols::simple_moves::BackboneMover::get_angle_max(const char) const –> double

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.simple_moves.SmallMover) → str¶: C++: protocols::simple_moves::SmallMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

initialize_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, pose: pyrosetta.rosetta.core.pose.Pose, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover, cycle: int) → None¶

Callback executed before any Monte Carlo trials are attempted.

C++: protocols::canonical_sampling::ThermodynamicMover::initialize_simulation(class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover &, unsigned long) –> void

is_multi_trial(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → bool¶

Return true if the move performs multiple trials on each apply.

last_inner_score_delta_over_temperature()

metropolis_hastings_mover()

set_metropolis_hastings_mover()

C++: protocols::canonical_sampling::ThermodynamicMover::is_multi_trial() –> bool

last_inner_score_delta_over_temperature(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → float¶

If this is a multi-trial move, return the change in internal

score/temperature caused by the last call to apply().

is_multi_trial()

C++: protocols::canonical_sampling::ThermodynamicMover::last_inner_score_delta_over_temperature() –> double

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → float¶

Return the proposal density ratio for last apply method.

C++: protocols::canonical_sampling::ThermodynamicMover::last_proposal_density_ratio() –> double

make_move(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, : pyrosetta.rosetta.core.pose.Pose) → bool¶: C++: protocols::simple_moves::BackboneMover::make_move(class core::pose::Pose &) –> bool

metropolis_hastings_mover(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → pyrosetta.rosetta.std.weak_ptr_protocols_canonical_sampling_MetropolisHastingsMover_t¶

If this is a multi-trial move, return the MetropolisHastingsMover

being used internally.

is_multi_trial()

C++: protocols::canonical_sampling::ThermodynamicMover::metropolis_hastings_mover() –> class std::weak_ptr<class protocols::canonical_sampling::MetropolisHastingsMover>

move_with_rama(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, pose: pyrosetta.rosetta.core.pose.Pose) → bool¶: C++: protocols::simple_moves::BackboneMover::move_with_rama(class core::pose::Pose &) –> bool

move_with_scorefxn(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, pose: pyrosetta.rosetta.core.pose.Pose) → bool¶: C++: protocols::simple_moves::BackboneMover::move_with_scorefxn(class core::pose::Pose &) –> bool

movemap(*args, **kwargs)¶

Overloaded function.

movemap(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, new_movemap: pyrosetta.rosetta.core.kinematics.MoveMap) -> None

C++: protocols::simple_moves::BackboneMover::movemap(class std::shared_ptr<class core::kinematics::MoveMap>) –> void

movemap(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, pose: pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.core.kinematics.MoveMap

Get the movemap for this pose.

C++: protocols::simple_moves::BackboneMover::movemap(const class core::pose::Pose &) –> class std::shared_ptr<const class core::kinematics::MoveMap>

movemap_factory(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, new_movemap_factory: pyrosetta.rosetta.core.select.movemap.MoveMapFactory) → None¶: C++: protocols::simple_moves::BackboneMover::movemap_factory(class std::shared_ptr<const class core::select::movemap::MoveMapFactory>) –> void

static mover_name() → str¶: C++: protocols::simple_moves::SmallMover::mover_name() –> std::string

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

nmoves(*args, **kwargs)¶

Overloaded function.

nmoves(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, nmoves_in: int) -> None

C++: protocols::simple_moves::BackboneMover::nmoves(const unsigned long) –> void

nmoves(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover) -> int

C++: protocols::simple_moves::BackboneMover::nmoves() const –> unsigned long

observe_after_metropolis(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover) → None¶

Callback executed after the Metropolis criterion is evaluated.

C++: protocols::canonical_sampling::ThermodynamicMover::observe_after_metropolis(const class protocols::canonical_sampling::MetropolisHastingsMover &) –> void

parse_my_tag(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::simple_moves::BackboneMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

preserve_detailed_balance(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover) → bool¶

get whether detailed balance is preserved (i.e. no Ramachandran biasing)

C++: protocols::simple_moves::BackboneMover::preserve_detailed_balance() const –> bool

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::SmallMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

scorefxn(*args, **kwargs)¶

Overloaded function.

scorefxn(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover) -> pyrosetta.rosetta.core.scoring.ScoreFunction

If set, this scorefunction will be used instead of the original rama method (default = not set).

C++: protocols::simple_moves::BackboneMover::scorefxn() const –> class std::shared_ptr<class core::scoring::ScoreFunction>

scorefxn(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None

C++: protocols::simple_moves::BackboneMover::scorefxn(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void

selector(*args, **kwargs)¶

Overloaded function.

selector(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover) -> pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

Return the residue selector that can be used to dynamically select residues to perturb: at runtime.

C++: protocols::simple_moves::BackboneMover::selector() const –> class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>

selector(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) -> None

C++: protocols::simple_moves::BackboneMover::selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

set_angles(self: pyrosetta.rosetta.protocols.simple_moves.SmallMover, angle_in: float) → None¶: C++: protocols::simple_moves::SmallMover::set_angles(double) –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_metropolis_hastings_mover(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, metropolis_hastings_mover: pyrosetta.rosetta.std.weak_ptr_protocols_canonical_sampling_MetropolisHastingsMover_t) → None¶

If this is a multi-trial move, set the MetropolisHastingsMover to

be used internally.

is_multi_trial()

C++: protocols::canonical_sampling::ThermodynamicMover::set_metropolis_hastings_mover(class std::weak_ptr<class protocols::canonical_sampling::MetropolisHastingsMover>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_preserve_detailed_balance(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, preserve_detailed_balance: bool) → None¶

set whether detailed balance is preserved (i.e. no Ramachandran biasing)

C++: protocols::simple_moves::BackboneMover::set_preserve_detailed_balance(bool) –> void

set_residue_selector(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) → None¶

Set the ResidueSelector that this mover will use.

Clones the input.

C++: protocols::simple_moves::BackboneMover::set_residue_selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

set_warn_empty_list(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, warn_empty: bool) → None¶

Set to warn of an empty setup list. Default true.

C++: protocols::simple_moves::BackboneMover::set_warn_empty_list(bool) –> void

setup_list(self: pyrosetta.rosetta.protocols.simple_moves.SmallMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::simple_moves::SmallMover::setup_list(class core::pose::Pose &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover) -> None
show(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, output: pyrosetta.rosetta.std.ostream) -> None

C++: protocols::simple_moves::BackboneMover::show(std::ostream &) const –> void

temperature(*args, **kwargs)¶

Overloaded function.

temperature(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, temperature_in: float) -> None

C++: protocols::simple_moves::BackboneMover::temperature(const double) –> void

temperature(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover) -> float

C++: protocols::simple_moves::BackboneMover::temperature() const –> double

test_move(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, : pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::simple_moves::BackboneMover::test_move(class core::pose::Pose &) –> void

torsion_id_ranges(self: pyrosetta.rosetta.protocols.simple_moves.SmallMover, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_core_id_TorsionID_Range¶

get the TorsionIDs perturbed by the mover during moves, along with their ranges

C++: protocols::simple_moves::SmallMover::torsion_id_ranges(class core::pose::Pose &) –> class utility::vector1<class core::id::TorsionID_Range, class std::allocator<class core::id::TorsionID_Range> >

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.simple_moves.SmallMoverCreator¶

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.simple_moves.SmallMoverCreator, : pyrosetta.rosetta.protocols.simple_moves.SmallMoverCreator) → pyrosetta.rosetta.protocols.simple_moves.SmallMoverCreator¶: C++: protocols::simple_moves::SmallMoverCreator::operator=(const class protocols::simple_moves::SmallMoverCreator &) –> class protocols::simple_moves::SmallMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.simple_moves.SmallMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::SmallMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.simple_moves.SmallMoverCreator) → str¶: C++: protocols::simple_moves::SmallMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.simple_moves.SmallMoverCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::SmallMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.simple_moves.SmoothFragmentMover¶

Bases: ClassicFragmentMover

apply(*args, **kwargs)¶

Overloaded function.

apply(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, : pyrosetta.rosetta.core.pose.Pose, pos: int) -> bool
apply(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, : pyrosetta.rosetta.core.pose.Pose) -> None

Applies classic fragment insertion based on a FragSet

example:
mover_3mer.apply(pose)

See also:
ClassicFragmentMover Pose ConstantLengthFragSet

C++: protocols::simple_moves::ClassicFragmentMover::apply(class core::pose::Pose &) –> void

apply_at_all_positions(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover, : pyrosetta.rosetta.core.pose.Pose) → int¶

apply at all movemable positions — honors movemap

C++: protocols::simple_moves::FragmentMover::apply_at_all_positions(class core::pose::Pose &) const –> unsigned long

apply_fragment(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, frame: pyrosetta.rosetta.core.fragment.Frame, frag_num: int, movemap: pyrosetta.rosetta.core.kinematics.MoveMap, pose: pyrosetta.rosetta.core.pose.Pose) → bool¶

apply the chosen fragment,

this can be overloaded to change action, e.,g., WobbleMover introduces chain-break before fragment insertion and does ccd-loop closure afterwards

C++: protocols::simple_moves::ClassicFragmentMover::apply_fragment(const class core::fragment::Frame &, unsigned long, const class core::kinematics::MoveMap &, class core::pose::Pose &) const –> bool

assign(self: pyrosetta.rosetta.protocols.simple_moves.SmoothFragmentMover, : pyrosetta.rosetta.protocols.simple_moves.SmoothFragmentMover) → pyrosetta.rosetta.protocols.simple_moves.SmoothFragmentMover¶: C++: protocols::simple_moves::SmoothFragmentMover::operator=(const class protocols::simple_moves::SmoothFragmentMover &) –> class protocols::simple_moves::SmoothFragmentMover &

check_ss(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover) → bool¶

accessor

C++: protocols::simple_moves::ClassicFragmentMover::check_ss() const –> bool

choose_fragment(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, : pyrosetta.rosetta.core.fragment.FrameList, : pyrosetta.rosetta.core.pose.Pose, frame_num: int, frag_num: int) → bool¶

given FrameList and pose, this method yields a fragment ( frame_num/ frag_num);: return false if nothing suitable is found

C++: protocols::simple_moves::ClassicFragmentMover::choose_fragment(const class core::fragment::FrameList &, const class core::pose::Pose &, unsigned long &, unsigned long &) const –> bool

choose_window_length(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, : pyrosetta.rosetta.core.pose.Pose, window_length: int) → bool¶

yields a length (window_length) of the fragment window to sample from: ( return false, if no suitable length is found )

C++: protocols::simple_moves::ClassicFragmentMover::choose_window_length(const class core::pose::Pose &, unsigned long &) const –> bool

choose_window_start(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, : pyrosetta.rosetta.core.pose.Pose, window_length: int, window_start: int) → bool¶

yields a start position (window_start) for fragment window to sample from: ( return false, if nothing suitable is found )

C++: protocols::simple_moves::ClassicFragmentMover::choose_window_start(const class core::pose::Pose &, unsigned long, unsigned long &) const –> bool

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::ClassicFragmentMover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

define_start_window(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, window_start: int) → None¶

apply fragment at predefined position

C++: protocols::simple_moves::ClassicFragmentMover::define_start_window(unsigned long) –> void

enable_end_bias_check(*args, **kwargs)¶

Overloaded function.

enable_end_bias_check(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover) -> None
enable_end_bias_check(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, setting: bool) -> None

C++: protocols::simple_moves::ClassicFragmentMover::enable_end_bias_check(bool) –> void

end_bias(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover) → float¶: C++: protocols::simple_moves::ClassicFragmentMover::end_bias() const –> double

end_bias_check(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, : pyrosetta.rosetta.core.pose.Pose, window_start: int) → bool¶: C++: protocols::simple_moves::ClassicFragmentMover::end_bias_check(const class core::pose::Pose &, unsigned long) const –> bool

end_bias_check_enabled(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover) → bool¶: C++: protocols::simple_moves::ClassicFragmentMover::end_bias_check_enabled() const –> bool

fragments(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover) → pyrosetta.rosetta.core.fragment.FragSet¶

accessor to the fragment set

C++: protocols::simple_moves::FragmentMover::fragments() const –> class std::shared_ptr<const class core::fragment::FragSet>

fresh_instance(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::ClassicFragmentMover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.simple_moves.SmoothFragmentMover) → str¶: C++: protocols::simple_moves::SmoothFragmentMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

initialize(self: pyrosetta.rosetta.protocols.moves.MoveMapMover, : pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::moves::MoveMapMover::initialize(class core::pose::Pose &) –> void

insert_map(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover) → pyrosetta.rosetta.utility.vector1_unsigned_long¶: C++: protocols::simple_moves::FragmentMover::insert_map() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

insert_size(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover) → pyrosetta.rosetta.utility.vector1_unsigned_long¶: C++: protocols::simple_moves::FragmentMover::insert_size() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

movemap(*args, **kwargs)¶

Overloaded function.

movemap(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover, : pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.core.kinematics.MoveMap

C++: protocols::simple_moves::FragmentMover::movemap(const class core::pose::Pose &) const –> class std::shared_ptr<const class core::kinematics::MoveMap>

movemap(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover) -> pyrosetta.rosetta.core.kinematics.MoveMap

C++: protocols::simple_moves::FragmentMover::movemap() const –> class std::shared_ptr<const class core::kinematics::MoveMap>

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

on_new_fragments(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover) → None¶

is called from set_fragments()

C++: protocols::simple_moves::ClassicFragmentMover::on_new_fragments() –> void

parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.

C++: protocols::moves::Mover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_check_ss(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, setting: bool) → None¶

check_ss controls whether fragment insertions are rejected that create short helices (<3) or strands (<2)

C++: protocols::simple_moves::ClassicFragmentMover::set_check_ss(bool) –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_end_bias(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, setting: float) → None¶: C++: protocols::simple_moves::ClassicFragmentMover::set_end_bias(double) –> void

set_fragments(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover, new_frags_: pyrosetta.rosetta.core.fragment.FragSet) → None¶

setter for the fragment set

C++: protocols::simple_moves::FragmentMover::set_fragments(class std::shared_ptr<const class core::fragment::FragSet>) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_min_frag_length(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, setting: int) → None¶

min_frag_length controls the behaviour fragset->region()

C++: protocols::simple_moves::ClassicFragmentMover::set_min_frag_length(unsigned long) –> void

set_min_overlap(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, setting: int) → None¶

min_overlap controls the behaviour fragset->region()

C++: protocols::simple_moves::ClassicFragmentMover::set_min_overlap(unsigned long) –> void

set_movemap(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover, movemap: pyrosetta.rosetta.core.kinematics.MoveMap) → None¶

setter for the movemap

C++: protocols::simple_moves::FragmentMover::set_movemap(class std::shared_ptr<const class core::kinematics::MoveMap>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

shared_from_this(self: pyrosetta.rosetta.protocols.simple_moves.SmoothFragmentMover) → pyrosetta.rosetta.protocols.simple_moves.SmoothFragmentMover¶: C++: protocols::simple_moves::SmoothFragmentMover::shared_from_this() –> class std::shared_ptr<class protocols::simple_moves::SmoothFragmentMover>

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover) -> None
show(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, output: pyrosetta.rosetta.std.ostream) -> None

C++: protocols::simple_moves::ClassicFragmentMover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

valid_ss(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, new_ss: str) → bool¶

returns true if the ss string is acceptable

C++: protocols::simple_moves::ClassicFragmentMover::valid_ss(const std::string &) const –> bool

class pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover¶

Bases: SymmetricFragmentMover, SmoothFragmentMover

A SymmetricFragmentMover that applies uniform sampling of fragments

apply(*args, **kwargs)¶

Overloaded function.

apply(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, : pyrosetta.rosetta.core.pose.Pose, pos: int) -> bool
apply(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, : pyrosetta.rosetta.core.pose.Pose) -> None

Applies classic fragment insertion based on a FragSet

example:
mover_3mer.apply(pose)

See also:
ClassicFragmentMover Pose ConstantLengthFragSet

C++: protocols::simple_moves::ClassicFragmentMover::apply(class core::pose::Pose &) –> void

apply_at_all_positions(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover, : pyrosetta.rosetta.core.pose.Pose) → int¶

apply at all movemable positions — honors movemap

C++: protocols::simple_moves::FragmentMover::apply_at_all_positions(class core::pose::Pose &) const –> unsigned long

apply_fragment(self: pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover, frame: pyrosetta.rosetta.core.fragment.Frame, frag_num: int, movemap: pyrosetta.rosetta.core.kinematics.MoveMap, pose: pyrosetta.rosetta.core.pose.Pose) → bool¶: C++: protocols::simple_moves::SymmetricFragmentMover::apply_fragment(const class core::fragment::Frame &, unsigned long, const class core::kinematics::MoveMap &, class core::pose::Pose &) const –> bool

assign(self: pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover, : pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover) → pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover¶: C++: protocols::simple_moves::SmoothSymmetricFragmentMover::operator=(const class protocols::simple_moves::SmoothSymmetricFragmentMover &) –> class protocols::simple_moves::SmoothSymmetricFragmentMover &

check_ss(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover) → bool¶

accessor

C++: protocols::simple_moves::ClassicFragmentMover::check_ss() const –> bool

choose_fragment(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, : pyrosetta.rosetta.core.fragment.FrameList, : pyrosetta.rosetta.core.pose.Pose, frame_num: int, frag_num: int) → bool¶

given FrameList and pose, this method yields a fragment ( frame_num/ frag_num);: return false if nothing suitable is found

C++: protocols::simple_moves::ClassicFragmentMover::choose_fragment(const class core::fragment::FrameList &, const class core::pose::Pose &, unsigned long &, unsigned long &) const –> bool

choose_window_length(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, : pyrosetta.rosetta.core.pose.Pose, window_length: int) → bool¶

yields a length (window_length) of the fragment window to sample from: ( return false, if no suitable length is found )

C++: protocols::simple_moves::ClassicFragmentMover::choose_window_length(const class core::pose::Pose &, unsigned long &) const –> bool

choose_window_start(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, : pyrosetta.rosetta.core.pose.Pose, window_length: int, window_start: int) → bool¶

yields a start position (window_start) for fragment window to sample from: ( return false, if nothing suitable is found )

C++: protocols::simple_moves::ClassicFragmentMover::choose_window_start(const class core::pose::Pose &, unsigned long, unsigned long &) const –> bool

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::ClassicFragmentMover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

define_start_window(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, window_start: int) → None¶

apply fragment at predefined position

C++: protocols::simple_moves::ClassicFragmentMover::define_start_window(unsigned long) –> void

enable_end_bias_check(*args, **kwargs)¶

Overloaded function.

enable_end_bias_check(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover) -> None
enable_end_bias_check(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, setting: bool) -> None

C++: protocols::simple_moves::ClassicFragmentMover::enable_end_bias_check(bool) –> void

end_bias(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover) → float¶: C++: protocols::simple_moves::ClassicFragmentMover::end_bias() const –> double

end_bias_check(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, : pyrosetta.rosetta.core.pose.Pose, window_start: int) → bool¶: C++: protocols::simple_moves::ClassicFragmentMover::end_bias_check(const class core::pose::Pose &, unsigned long) const –> bool

end_bias_check_enabled(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover) → bool¶: C++: protocols::simple_moves::ClassicFragmentMover::end_bias_check_enabled() const –> bool

fragments(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover) → pyrosetta.rosetta.core.fragment.FragSet¶

accessor to the fragment set

C++: protocols::simple_moves::FragmentMover::fragments() const –> class std::shared_ptr<const class core::fragment::FragSet>

fresh_instance(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::ClassicFragmentMover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover) → str¶: C++: protocols::simple_moves::SmoothSymmetricFragmentMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

initialize(self: pyrosetta.rosetta.protocols.moves.MoveMapMover, : pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::moves::MoveMapMover::initialize(class core::pose::Pose &) –> void

insert_map(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover) → pyrosetta.rosetta.utility.vector1_unsigned_long¶: C++: protocols::simple_moves::FragmentMover::insert_map() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

insert_size(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover) → pyrosetta.rosetta.utility.vector1_unsigned_long¶: C++: protocols::simple_moves::FragmentMover::insert_size() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

movemap(*args, **kwargs)¶

Overloaded function.

movemap(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover, : pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.core.kinematics.MoveMap

C++: protocols::simple_moves::FragmentMover::movemap(const class core::pose::Pose &) const –> class std::shared_ptr<const class core::kinematics::MoveMap>

movemap(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover) -> pyrosetta.rosetta.core.kinematics.MoveMap

C++: protocols::simple_moves::FragmentMover::movemap() const –> class std::shared_ptr<const class core::kinematics::MoveMap>

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

on_new_fragments(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover) → None¶

is called from set_fragments()

C++: protocols::simple_moves::ClassicFragmentMover::on_new_fragments() –> void

parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.

C++: protocols::moves::Mover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_check_ss(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, setting: bool) → None¶

check_ss controls whether fragment insertions are rejected that create short helices (<3) or strands (<2)

C++: protocols::simple_moves::ClassicFragmentMover::set_check_ss(bool) –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_end_bias(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, setting: float) → None¶: C++: protocols::simple_moves::ClassicFragmentMover::set_end_bias(double) –> void

set_fragments(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover, new_frags_: pyrosetta.rosetta.core.fragment.FragSet) → None¶

setter for the fragment set

C++: protocols::simple_moves::FragmentMover::set_fragments(class std::shared_ptr<const class core::fragment::FragSet>) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_min_frag_length(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, setting: int) → None¶

min_frag_length controls the behaviour fragset->region()

C++: protocols::simple_moves::ClassicFragmentMover::set_min_frag_length(unsigned long) –> void

set_min_overlap(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, setting: int) → None¶

min_overlap controls the behaviour fragset->region()

C++: protocols::simple_moves::ClassicFragmentMover::set_min_overlap(unsigned long) –> void

set_movemap(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover, movemap: pyrosetta.rosetta.core.kinematics.MoveMap) → None¶

setter for the movemap

C++: protocols::simple_moves::FragmentMover::set_movemap(class std::shared_ptr<const class core::kinematics::MoveMap>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

shared_from_this(self: pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover) → pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover¶: C++: protocols::simple_moves::SmoothSymmetricFragmentMover::shared_from_this() –> class std::shared_ptr<class protocols::simple_moves::SmoothSymmetricFragmentMover>

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover) -> None
show(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, output: pyrosetta.rosetta.std.ostream) -> None

C++: protocols::simple_moves::ClassicFragmentMover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

valid_ss(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, new_ss: str) → bool¶

returns true if the ss string is acceptable

C++: protocols::simple_moves::ClassicFragmentMover::valid_ss(const std::string &) const –> bool

class pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot¶

Bases: Mover

A mover to store current residue indices in a map that will be updated as residues are added or deleted, permitting residue indices from the current state to be used to set up movers applied in the future.

apply(self: pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Apply function – actually apply this mover to the pose, modifying the pose.

C++: protocols::simple_moves::StorePoseSnapshot::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot, : pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot) → pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot¶: C++: protocols::simple_moves::StorePoseSnapshot::operator=(const class protocols::simple_moves::StorePoseSnapshot &) –> class protocols::simple_moves::StorePoseSnapshot &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot) → pyrosetta.rosetta.protocols.moves.Mover¶

Makea copy of this mover, and return an owning pointer to the copy.

C++: protocols::simple_moves::StorePoseSnapshot::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot) → pyrosetta.rosetta.protocols.moves.Mover¶

Create a new instance of this mover, initialized to default settings.

C++: protocols::simple_moves::StorePoseSnapshot::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot) → str¶: C++: protocols::simple_moves::StorePoseSnapshot::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static mover_name() → str¶: C++: protocols::simple_moves::StorePoseSnapshot::mover_name() –> std::string

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶

Parse RosettaScripts XML to set up this mover.

This is called at script initialization, long before the apply() function is called.

C++: protocols::simple_moves::StorePoseSnapshot::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::StorePoseSnapshot::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

reference_pose_name(self: pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot) → str¶

Return the name of the reference pose object that will be created and stored in the pose.

C++: protocols::simple_moves::StorePoseSnapshot::reference_pose_name() const –> std::string

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_reference_pose_name(self: pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot, name_in: str) → None¶

Set the name of the reference pose object that will be created and stored in the pose.

C++: protocols::simple_moves::StorePoseSnapshot::set_reference_pose_name(const std::string &) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshotCreator¶

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshotCreator, : pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshotCreator) → pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshotCreator¶: C++: protocols::simple_moves::StorePoseSnapshotCreator::operator=(const class protocols::simple_moves::StorePoseSnapshotCreator &) –> class protocols::simple_moves::StorePoseSnapshotCreator &

create_mover(self: pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshotCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::StorePoseSnapshotCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshotCreator) → str¶: C++: protocols::simple_moves::StorePoseSnapshotCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshotCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::StorePoseSnapshotCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.simple_moves.StructProfileMover¶

Bases: Mover

add_MSAcst_to_pose(self: pyrosetta.rosetta.protocols.simple_moves.StructProfileMover, profile_score: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::simple_moves::StructProfileMover::add_MSAcst_to_pose(class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > >, class core::pose::Pose &) –> void

apply(self: pyrosetta.rosetta.protocols.simple_moves.StructProfileMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::simple_moves::StructProfileMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.StructProfileMover, : pyrosetta.rosetta.protocols.simple_moves.StructProfileMover) → pyrosetta.rosetta.protocols.simple_moves.StructProfileMover¶: C++: protocols::simple_moves::StructProfileMover::operator=(const class protocols::simple_moves::StructProfileMover &) –> class protocols::simple_moves::StructProfileMover &

calc_cenlist(self: pyrosetta.rosetta.protocols.simple_moves.StructProfileMover, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_double¶: C++: protocols::simple_moves::StructProfileMover::calc_cenlist(const class core::pose::Pose &) –> class utility::vector1<double, class std::allocator<double> >

censorFragByBurial(self: pyrosetta.rosetta.protocols.simple_moves.StructProfileMover, cenListFrag: pyrosetta.rosetta.std.vector_double, cenListModel: pyrosetta.rosetta.utility.vector1_double, cenListFragSeq: str) → str¶: C++: protocols::simple_moves::StructProfileMover::censorFragByBurial(class std::vector<double, class std::allocator<double> >, class utility::vector1<double, class std::allocator<double> >, std::string) –> std::string

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.simple_moves.StructProfileMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::StructProfileMover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶

Generates a new Mover object freshly created with the default ctor.

C++: protocols::moves::Mover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

generate_counts(self: pyrosetta.rosetta.protocols.simple_moves.StructProfileMover, top_frag_sequences: pyrosetta.rosetta.utility.vector1_utility_vector1_std_string_std_allocator_std_string_t, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_utility_vector1_unsigned_long_std_allocator_unsigned_long_t¶: C++: protocols::simple_moves::StructProfileMover::generate_counts(class utility::vector1<class utility::vector1<std::string, class std::allocator<std::string > >, class std::allocator<class utility::vector1<std::string, class std::allocator<std::string > > > >, const class core::pose::Pose &) –> class utility::vector1<class utility::vector1<unsigned long, class std::allocator<unsigned long> >, class std::allocator<class utility::vector1<unsigned long, class std::allocator<unsigned long> > > >

generate_profile_score(self: pyrosetta.rosetta.protocols.simple_moves.StructProfileMover, res_per_pos: pyrosetta.rosetta.utility.vector1_utility_vector1_unsigned_long_std_allocator_unsigned_long_t, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t¶: C++: protocols::simple_moves::StructProfileMover::generate_profile_score(class utility::vector1<class utility::vector1<unsigned long, class std::allocator<unsigned long> >, class std::allocator<class utility::vector1<unsigned long, class std::allocator<unsigned long> > > >, const class core::pose::Pose &) –> class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > >

generate_profile_score_wo_background(self: pyrosetta.rosetta.protocols.simple_moves.StructProfileMover, res_per_pos: pyrosetta.rosetta.utility.vector1_utility_vector1_unsigned_long_std_allocator_unsigned_long_t, cenList: pyrosetta.rosetta.utility.vector1_double, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t¶: C++: protocols::simple_moves::StructProfileMover::generate_profile_score_wo_background(class utility::vector1<class utility::vector1<unsigned long, class std::allocator<unsigned long> >, class std::allocator<class utility::vector1<unsigned long, class std::allocator<unsigned long> > > >, class utility::vector1<double, class std::allocator<double> >, const class core::pose::Pose &) –> class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > >

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_cen_deviation(self: pyrosetta.rosetta.protocols.simple_moves.StructProfileMover, cenListFrag: pyrosetta.rosetta.std.vector_double, cenListModel: pyrosetta.rosetta.utility.vector1_double) → float¶: C++: protocols::simple_moves::StructProfileMover::get_cen_deviation(class std::vector<double, class std::allocator<double> >, class utility::vector1<double, class std::allocator<double> >) –> double

get_closest_sequence_at_res(self: pyrosetta.rosetta.protocols.simple_moves.StructProfileMover, pose: pyrosetta.rosetta.core.pose.Pose, res: int, cenList: pyrosetta.rosetta.utility.vector1_double) → pyrosetta.rosetta.utility.vector1_std_string¶: C++: protocols::simple_moves::StructProfileMover::get_closest_sequence_at_res(const class core::pose::Pose &, unsigned long, class utility::vector1<double, class std::allocator<double> >) –> class utility::vector1<std::string, class std::allocator<std::string > >

get_closest_sequences(self: pyrosetta.rosetta.protocols.simple_moves.StructProfileMover, pose: pyrosetta.rosetta.core.pose.Pose, cenList: pyrosetta.rosetta.utility.vector1_double, subset: pyrosetta.rosetta.utility.vector1_bool) → pyrosetta.rosetta.utility.vector1_utility_vector1_std_string_std_allocator_std_string_t¶: C++: protocols::simple_moves::StructProfileMover::get_closest_sequences(const class core::pose::Pose &, class utility::vector1<double, class std::allocator<double> >, const class utility::vector1<bool, class std::allocator<bool> > &) –> class utility::vector1<class utility::vector1<std::string, class std::allocator<std::string > >, class std::allocator<class utility::vector1<std::string, class std::allocator<std::string > > > >

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.simple_moves.StructProfileMover) → str¶: C++: protocols::simple_moves::StructProfileMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static mover_name() → str¶: C++: protocols::simple_moves::StructProfileMover::mover_name() –> std::string

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.simple_moves.StructProfileMover, tag: pyrosetta.rosetta.utility.tag.Tag, datamap: pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::simple_moves::StructProfileMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::StructProfileMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

read_P_AA_SS_cen6(self: pyrosetta.rosetta.protocols.simple_moves.StructProfileMover) → None¶: C++: protocols::simple_moves::StructProfileMover::read_P_AA_SS_cen6() –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

save_MSAcst_file(self: pyrosetta.rosetta.protocols.simple_moves.StructProfileMover, profile_score: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::simple_moves::StructProfileMover::save_MSAcst_file(class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > >, const class core::pose::Pose &) –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_profile_save_name(self: pyrosetta.rosetta.protocols.simple_moves.StructProfileMover, name: str) → None¶: C++: protocols::simple_moves::StructProfileMover::set_profile_save_name(const std::string &) –> void

set_residue_selector(self: pyrosetta.rosetta.protocols.simple_moves.StructProfileMover, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) → None¶: C++: protocols::simple_moves::StructProfileMover::set_residue_selector(const class core::select::residue_selector::ResidueSelector &) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

ss_type_convert(self: pyrosetta.rosetta.protocols.simple_moves.StructProfileMover, ss_type: str) → int¶: C++: protocols::simple_moves::StructProfileMover::ss_type_convert(char) –> unsigned long

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.simple_moves.StructProfileMoverCreator¶

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.simple_moves.StructProfileMoverCreator, : pyrosetta.rosetta.protocols.simple_moves.StructProfileMoverCreator) → pyrosetta.rosetta.protocols.simple_moves.StructProfileMoverCreator¶: C++: protocols::simple_moves::StructProfileMoverCreator::operator=(const class protocols::simple_moves::StructProfileMoverCreator &) –> class protocols::simple_moves::StructProfileMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.simple_moves.StructProfileMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::StructProfileMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.simple_moves.StructProfileMoverCreator) → str¶: C++: protocols::simple_moves::StructProfileMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.simple_moves.StructProfileMoverCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::StructProfileMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover¶

Bases: Mover

Superimpose pose onto reference pose. Default CA only. All residues. Optionally set to superimpose regions or backbone only (N, C, CA, O)

apply(self: pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::simple_moves::SuperimposeMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover, : pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover) → pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover¶: C++: protocols::simple_moves::SuperimposeMover::operator=(const class protocols::simple_moves::SuperimposeMover &) –> class protocols::simple_moves::SuperimposeMover &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::SuperimposeMover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::SuperimposeMover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover) → str¶: C++: protocols::simple_moves::SuperimposeMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static mover_name() → str¶: C++: protocols::simple_moves::SuperimposeMover::mover_name() –> std::string

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover, tag: pyrosetta.rosetta.utility.tag.Tag, data_map: pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::simple_moves::SuperimposeMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::SuperimposeMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_ca_only(self: pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover, setting: bool) → None¶: C++: protocols::simple_moves::SuperimposeMover::set_ca_only(bool) –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_reference_pose(*args, **kwargs)¶

Overloaded function.

set_reference_pose(self: pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover, pose: pyrosetta.rosetta.core.pose.Pose) -> None
set_reference_pose(self: pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover, pose: pyrosetta.rosetta.core.pose.Pose, start: int) -> None
set_reference_pose(self: pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover, pose: pyrosetta.rosetta.core.pose.Pose, start: int, end: int) -> None

C++: protocols::simple_moves::SuperimposeMover::set_reference_pose(const class core::pose::Pose &, unsigned long, unsigned long) –> void

set_target_range(self: pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover, start: int, end: int) → None¶: C++: protocols::simple_moves::SuperimposeMover::set_target_range(unsigned long, unsigned long) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.simple_moves.SuperimposeMoverCreator¶

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.simple_moves.SuperimposeMoverCreator, : pyrosetta.rosetta.protocols.simple_moves.SuperimposeMoverCreator) → pyrosetta.rosetta.protocols.simple_moves.SuperimposeMoverCreator¶: C++: protocols::simple_moves::SuperimposeMoverCreator::operator=(const class protocols::simple_moves::SuperimposeMoverCreator &) –> class protocols::simple_moves::SuperimposeMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.simple_moves.SuperimposeMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::SuperimposeMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.simple_moves.SuperimposeMoverCreator) → str¶: C++: protocols::simple_moves::SuperimposeMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.simple_moves.SuperimposeMoverCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::SuperimposeMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.simple_moves.SwitchChainOrderMover¶

Bases: Mover

apply(self: pyrosetta.rosetta.protocols.simple_moves.SwitchChainOrderMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::simple_moves::SwitchChainOrderMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.SwitchChainOrderMover, : pyrosetta.rosetta.protocols.simple_moves.SwitchChainOrderMover) → pyrosetta.rosetta.protocols.simple_moves.SwitchChainOrderMover¶: C++: protocols::simple_moves::SwitchChainOrderMover::operator=(const class protocols::simple_moves::SwitchChainOrderMover &) –> class protocols::simple_moves::SwitchChainOrderMover &

chain_order(*args, **kwargs)¶

Overloaded function.

chain_order(self: pyrosetta.rosetta.protocols.simple_moves.SwitchChainOrderMover, co: str) -> None

C++: protocols::simple_moves::SwitchChainOrderMover::chain_order(const std::string &) –> void

chain_order(self: pyrosetta.rosetta.protocols.simple_moves.SwitchChainOrderMover, : pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.utility.vector1_unsigned_long

C++: protocols::simple_moves::SwitchChainOrderMover::chain_order(const class core::pose::Pose &) const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.simple_moves.SwitchChainOrderMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::SwitchChainOrderMover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.simple_moves.SwitchChainOrderMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::SwitchChainOrderMover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.simple_moves.SwitchChainOrderMover) → str¶: C++: protocols::simple_moves::SwitchChainOrderMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static mover_name() → str¶: C++: protocols::simple_moves::SwitchChainOrderMover::mover_name() –> std::string

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.simple_moves.SwitchChainOrderMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::simple_moves::SwitchChainOrderMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::SwitchChainOrderMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

scorefxn(*args, **kwargs)¶

Overloaded function.

scorefxn(self: pyrosetta.rosetta.protocols.simple_moves.SwitchChainOrderMover) -> pyrosetta.rosetta.core.scoring.ScoreFunction

C++: protocols::simple_moves::SwitchChainOrderMover::scorefxn() const –> class std::shared_ptr<class core::scoring::ScoreFunction>

scorefxn(self: pyrosetta.rosetta.protocols.simple_moves.SwitchChainOrderMover, s: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None

C++: protocols::simple_moves::SwitchChainOrderMover::scorefxn(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.simple_moves.SwitchChainOrderMoverCreator¶

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.simple_moves.SwitchChainOrderMoverCreator, : pyrosetta.rosetta.protocols.simple_moves.SwitchChainOrderMoverCreator) → pyrosetta.rosetta.protocols.simple_moves.SwitchChainOrderMoverCreator¶: C++: protocols::simple_moves::SwitchChainOrderMoverCreator::operator=(const class protocols::simple_moves::SwitchChainOrderMoverCreator &) –> class protocols::simple_moves::SwitchChainOrderMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.simple_moves.SwitchChainOrderMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::SwitchChainOrderMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.simple_moves.SwitchChainOrderMoverCreator) → str¶: C++: protocols::simple_moves::SwitchChainOrderMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.simple_moves.SwitchChainOrderMoverCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::SwitchChainOrderMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover¶

Bases: Mover

A mover that switches a pose between residue type sets (e.g. centroid and fullatom)

examples:: switch = protocols::simple_moves::SwitchResidueTypeSetMover(“centroid”)
See also:: Pose Residue ResidueType ResidueTypeSet

apply(self: pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Applies ResidueTypeSet converion on the pose

: a single protocols::moves::Mover only converts in ONE direction e.g. to centroid

C++: protocols::simple_moves::SwitchResidueTypeSetMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover, : pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover) → pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover¶: C++: protocols::simple_moves::SwitchResidueTypeSetMover::operator=(const class protocols::simple_moves::SwitchResidueTypeSetMover &) –> class protocols::simple_moves::SwitchResidueTypeSetMover &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::SwitchResidueTypeSetMover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::SwitchResidueTypeSetMover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover) → str¶: C++: protocols::simple_moves::SwitchResidueTypeSetMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_residue_type_set(self: pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover) → str¶: C++: protocols::simple_moves::SwitchResidueTypeSetMover::get_residue_type_set() const –> std::string

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static mover_name() → str¶: C++: protocols::simple_moves::SwitchResidueTypeSetMover::mover_name() –> std::string

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::simple_moves::SwitchResidueTypeSetMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::SwitchResidueTypeSetMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover) -> None
show(self: pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover, output: pyrosetta.rosetta.std.ostream) -> None

C++: protocols::simple_moves::SwitchResidueTypeSetMover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

type_set_tag(self: pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover, type_set_tag_in: str) → None¶: C++: protocols::simple_moves::SwitchResidueTypeSetMover::type_set_tag(const std::string &) –> void

class pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMoverCreator¶

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMoverCreator, : pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMoverCreator) → pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMoverCreator¶: C++: protocols::simple_moves::SwitchResidueTypeSetMoverCreator::operator=(const class protocols::simple_moves::SwitchResidueTypeSetMoverCreator &) –> class protocols::simple_moves::SwitchResidueTypeSetMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::SwitchResidueTypeSetMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMoverCreator) → str¶: C++: protocols::simple_moves::SwitchResidueTypeSetMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMoverCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::SwitchResidueTypeSetMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover¶

Bases: ClassicFragmentMover

A SymmetricFragmentMover that applies uniform sampling of fragments

apply(*args, **kwargs)¶

Overloaded function.

apply(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, : pyrosetta.rosetta.core.pose.Pose, pos: int) -> bool
apply(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, : pyrosetta.rosetta.core.pose.Pose) -> None

Applies classic fragment insertion based on a FragSet

example:
mover_3mer.apply(pose)

See also:
ClassicFragmentMover Pose ConstantLengthFragSet

C++: protocols::simple_moves::ClassicFragmentMover::apply(class core::pose::Pose &) –> void

apply_at_all_positions(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover, : pyrosetta.rosetta.core.pose.Pose) → int¶

apply at all movemable positions — honors movemap

C++: protocols::simple_moves::FragmentMover::apply_at_all_positions(class core::pose::Pose &) const –> unsigned long

apply_fragment(self: pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover, frame: pyrosetta.rosetta.core.fragment.Frame, frag_num: int, movemap: pyrosetta.rosetta.core.kinematics.MoveMap, pose: pyrosetta.rosetta.core.pose.Pose) → bool¶: C++: protocols::simple_moves::SymmetricFragmentMover::apply_fragment(const class core::fragment::Frame &, unsigned long, const class core::kinematics::MoveMap &, class core::pose::Pose &) const –> bool

assign(self: pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover, : pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover) → pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover¶: C++: protocols::simple_moves::SymmetricFragmentMover::operator=(const class protocols::simple_moves::SymmetricFragmentMover &) –> class protocols::simple_moves::SymmetricFragmentMover &

check_ss(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover) → bool¶

accessor

C++: protocols::simple_moves::ClassicFragmentMover::check_ss() const –> bool

choose_fragment(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, : pyrosetta.rosetta.core.fragment.FrameList, : pyrosetta.rosetta.core.pose.Pose, frame_num: int, frag_num: int) → bool¶

given FrameList and pose, this method yields a fragment ( frame_num/ frag_num);: return false if nothing suitable is found

C++: protocols::simple_moves::ClassicFragmentMover::choose_fragment(const class core::fragment::FrameList &, const class core::pose::Pose &, unsigned long &, unsigned long &) const –> bool

choose_window_length(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, : pyrosetta.rosetta.core.pose.Pose, window_length: int) → bool¶

yields a length (window_length) of the fragment window to sample from: ( return false, if no suitable length is found )

C++: protocols::simple_moves::ClassicFragmentMover::choose_window_length(const class core::pose::Pose &, unsigned long &) const –> bool

choose_window_start(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, : pyrosetta.rosetta.core.pose.Pose, window_length: int, window_start: int) → bool¶

yields a start position (window_start) for fragment window to sample from: ( return false, if nothing suitable is found )

C++: protocols::simple_moves::ClassicFragmentMover::choose_window_start(const class core::pose::Pose &, unsigned long, unsigned long &) const –> bool

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::ClassicFragmentMover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

define_start_window(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, window_start: int) → None¶

apply fragment at predefined position

C++: protocols::simple_moves::ClassicFragmentMover::define_start_window(unsigned long) –> void

enable_end_bias_check(*args, **kwargs)¶

Overloaded function.

enable_end_bias_check(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover) -> None
enable_end_bias_check(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, setting: bool) -> None

C++: protocols::simple_moves::ClassicFragmentMover::enable_end_bias_check(bool) –> void

end_bias(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover) → float¶: C++: protocols::simple_moves::ClassicFragmentMover::end_bias() const –> double

end_bias_check(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, : pyrosetta.rosetta.core.pose.Pose, window_start: int) → bool¶: C++: protocols::simple_moves::ClassicFragmentMover::end_bias_check(const class core::pose::Pose &, unsigned long) const –> bool

end_bias_check_enabled(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover) → bool¶: C++: protocols::simple_moves::ClassicFragmentMover::end_bias_check_enabled() const –> bool

fragments(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover) → pyrosetta.rosetta.core.fragment.FragSet¶

accessor to the fragment set

C++: protocols::simple_moves::FragmentMover::fragments() const –> class std::shared_ptr<const class core::fragment::FragSet>

fresh_instance(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::ClassicFragmentMover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover) → str¶: C++: protocols::simple_moves::SymmetricFragmentMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

initialize(self: pyrosetta.rosetta.protocols.moves.MoveMapMover, : pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::moves::MoveMapMover::initialize(class core::pose::Pose &) –> void

insert_map(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover) → pyrosetta.rosetta.utility.vector1_unsigned_long¶: C++: protocols::simple_moves::FragmentMover::insert_map() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

insert_size(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover) → pyrosetta.rosetta.utility.vector1_unsigned_long¶: C++: protocols::simple_moves::FragmentMover::insert_size() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

movemap(*args, **kwargs)¶

Overloaded function.

movemap(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover, : pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.core.kinematics.MoveMap

C++: protocols::simple_moves::FragmentMover::movemap(const class core::pose::Pose &) const –> class std::shared_ptr<const class core::kinematics::MoveMap>

movemap(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover) -> pyrosetta.rosetta.core.kinematics.MoveMap

C++: protocols::simple_moves::FragmentMover::movemap() const –> class std::shared_ptr<const class core::kinematics::MoveMap>

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

on_new_fragments(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover) → None¶

is called from set_fragments()

C++: protocols::simple_moves::ClassicFragmentMover::on_new_fragments() –> void

parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.

C++: protocols::moves::Mover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_check_ss(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, setting: bool) → None¶

check_ss controls whether fragment insertions are rejected that create short helices (<3) or strands (<2)

C++: protocols::simple_moves::ClassicFragmentMover::set_check_ss(bool) –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_end_bias(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, setting: float) → None¶: C++: protocols::simple_moves::ClassicFragmentMover::set_end_bias(double) –> void

set_fragments(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover, new_frags_: pyrosetta.rosetta.core.fragment.FragSet) → None¶

setter for the fragment set

C++: protocols::simple_moves::FragmentMover::set_fragments(class std::shared_ptr<const class core::fragment::FragSet>) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_min_frag_length(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, setting: int) → None¶

min_frag_length controls the behaviour fragset->region()

C++: protocols::simple_moves::ClassicFragmentMover::set_min_frag_length(unsigned long) –> void

set_min_overlap(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, setting: int) → None¶

min_overlap controls the behaviour fragset->region()

C++: protocols::simple_moves::ClassicFragmentMover::set_min_overlap(unsigned long) –> void

set_movemap(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover, movemap: pyrosetta.rosetta.core.kinematics.MoveMap) → None¶

setter for the movemap

C++: protocols::simple_moves::FragmentMover::set_movemap(class std::shared_ptr<const class core::kinematics::MoveMap>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

shared_from_this(self: pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover) → pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover¶: C++: protocols::simple_moves::SymmetricFragmentMover::shared_from_this() –> class std::shared_ptr<class protocols::simple_moves::SymmetricFragmentMover>

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover) -> None
show(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, output: pyrosetta.rosetta.std.ostream) -> None

C++: protocols::simple_moves::ClassicFragmentMover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

valid_ss(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, new_ss: str) → bool¶

returns true if the ss string is acceptable

C++: protocols::simple_moves::ClassicFragmentMover::valid_ss(const std::string &) const –> bool

class pyrosetta.rosetta.protocols.simple_moves.TailsScoreMover¶

Bases: ScoreMover

apply(self: pyrosetta.rosetta.protocols.simple_moves.TailsScoreMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::simple_moves::TailsScoreMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.TailsScoreMover, : pyrosetta.rosetta.protocols.simple_moves.TailsScoreMover) → pyrosetta.rosetta.protocols.simple_moves.TailsScoreMover¶: C++: protocols::simple_moves::TailsScoreMover::operator=(const class protocols::simple_moves::TailsScoreMover &) –> class protocols::simple_moves::TailsScoreMover &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.simple_moves.ScoreMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::ScoreMover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.simple_moves.ScoreMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::ScoreMover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.simple_moves.TailsScoreMover) → str¶: C++: protocols::simple_moves::TailsScoreMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

insert_rms(self: pyrosetta.rosetta.protocols.simple_moves.ScoreMover, rms: float) → None¶

add an rms to the score_map: TODO possibly find a better way to do this? for now, there are too many different rmsd calculation functions to be able to do the actual calculation in the protocols::moves::Mover

C++: protocols::simple_moves::ScoreMover::insert_rms(double) –> void

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static mover_name() → str¶: C++: protocols::simple_moves::ScoreMover::mover_name() –> std::string

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.simple_moves.ScoreMover, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::simple_moves::ScoreMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::ScoreMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None¶: C++: protocols::simple_moves::ScoreMover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

score_function(self: pyrosetta.rosetta.protocols.simple_moves.ScoreMover) → pyrosetta.rosetta.core.scoring.ScoreFunction¶: C++: protocols::simple_moves::ScoreMover::score_function() const –> class std::shared_ptr<class core::scoring::ScoreFunction>

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_score_file(self: pyrosetta.rosetta.protocols.simple_moves.ScoreMover, scorefile: str) → None¶: C++: protocols::simple_moves::ScoreMover::set_score_file(std::string) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

set_verbose(self: pyrosetta.rosetta.protocols.simple_moves.ScoreMover, value: bool) → None¶: C++: protocols::simple_moves::ScoreMover::set_verbose(bool) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.simple_moves.ScoreMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::simple_moves::ScoreMover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.simple_moves.ThermodynamicData¶

Bases: pybind11_object

structure that stores data during simulation

intraE and interE are incorrect for now;

assign(self: pyrosetta.rosetta.protocols.simple_moves.ThermodynamicData, : pyrosetta.rosetta.protocols.simple_moves.ThermodynamicData) → pyrosetta.rosetta.protocols.simple_moves.ThermodynamicData¶: C++: protocols::simple_moves::ThermodynamicData::operator=(const struct protocols::simple_moves::ThermodynamicData &) –> struct protocols::simple_moves::ThermodynamicData &

property centralE¶

property density¶

property interE¶

property intraE¶

property volume¶

class pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover¶

Bases: Mover

This mover rotates a specific AtomTree Torsion degree of freedom (any valid 4-body torsion). It can rotate by a fixed amount, within a range, or randomly. Optionally, the mover will attempt to internally score the move with MMTorsionEnergy (similar to check_rama in Small/ShearMover). The mover will print a warning message at apply time if the specified DOF is bad. For now this mover only allows one DOF; if you want to have it consider multiple DOF’s that might be a good idea. The DOF is determined by a set of 4 atoms; this allows the mover to check the validity of the DOF. I found it conceptually simpler to think about the 4 atoms involved in the torsion than try to trace DOF_IDs.

apply(self: pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::simple_moves::TorsionDOFMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover, : pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover) → pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover¶: C++: protocols::simple_moves::TorsionDOFMover::operator=(const class protocols::simple_moves::TorsionDOFMover &) –> class protocols::simple_moves::TorsionDOFMover &

check_mmt(*args, **kwargs)¶

Overloaded function.

check_mmt(self: pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover, setting: bool) -> None

(de)activate scoring check

C++: protocols::simple_moves::TorsionDOFMover::check_mmt(const bool) –> void

check_mmt(self: pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover) -> bool

getter for scoring check

C++: protocols::simple_moves::TorsionDOFMover::check_mmt() const –> bool

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶

Return a clone of the Mover object.

C++: protocols::moves::Mover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶

Generates a new Mover object freshly created with the default ctor.

C++: protocols::moves::Mover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_DOF(self: pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover, atom1: pyrosetta.rosetta.core.id.AtomID, atom2: pyrosetta.rosetta.core.id.AtomID, atom3: pyrosetta.rosetta.core.id.AtomID, atom4: pyrosetta.rosetta.core.id.AtomID) → None¶

return DOF

C++: protocols::simple_moves::TorsionDOFMover::get_DOF(class core::id::AtomID &, class core::id::AtomID &, class core::id::AtomID &, class core::id::AtomID &) const –> void

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_angle_range(self: pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover, upper: float, lower: float) → None¶

return range of allowed angles

C++: protocols::simple_moves::TorsionDOFMover::get_angle_range(double &, double &) const –> void

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover) → str¶: C++: protocols::simple_moves::TorsionDOFMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.

C++: protocols::moves::Mover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_DOF(self: pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover, atom1: pyrosetta.rosetta.core.id.AtomID, atom2: pyrosetta.rosetta.core.id.AtomID, atom3: pyrosetta.rosetta.core.id.AtomID, atom4: pyrosetta.rosetta.core.id.AtomID) → None¶

change the torsion DOF under consideration

C++: protocols::simple_moves::TorsionDOFMover::set_DOF(const class core::id::AtomID &, const class core::id::AtomID &, const class core::id::AtomID &, const class core::id::AtomID &) –> void

set_angle_range(self: pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover, upper: float, lower: float) → None¶

///////////////////////////////getters, setters////////////////////////////////////////

set range of desired change - on [180, -180) degrees

C++: protocols::simple_moves::TorsionDOFMover::set_angle_range(const double, const double) –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

temp(*args, **kwargs)¶

Overloaded function.

temp(self: pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover, setting: float) -> None

set temperature for scoring check

C++: protocols::simple_moves::TorsionDOFMover::temp(const double) –> void

temp(self: pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover) -> float

getter for temperature for scoring check

C++: protocols::simple_moves::TorsionDOFMover::temp() const –> double

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

tries(*args, **kwargs)¶

Overloaded function.

tries(self: pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover, setting: int) -> None

set number of tries

C++: protocols::simple_moves::TorsionDOFMover::tries(const unsigned long) –> void

tries(self: pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover) -> int

getter for number of tries

C++: protocols::simple_moves::TorsionDOFMover::tries() const –> unsigned long

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.simple_moves.TorsionPerturbType¶

Bases: pybind11_object

Members:

perturbtorsion_uniform

perturbtorsion_gaussian

perturbtorsion_unknown

property name¶

perturbtorsion_gaussian = <TorsionPerturbType.perturbtorsion_gaussian: 2>¶

perturbtorsion_uniform = <TorsionPerturbType.perturbtorsion_uniform: 1>¶

perturbtorsion_unknown = <TorsionPerturbType.perturbtorsion_unknown: 3>¶

property value¶

class pyrosetta.rosetta.protocols.simple_moves.TorsionSetMover¶

Bases: Mover

apply(self: pyrosetta.rosetta.protocols.simple_moves.TorsionSetMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Apply function: apply this mover to a pose.

C++: protocols::simple_moves::TorsionSetMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.TorsionSetMover, : pyrosetta.rosetta.protocols.simple_moves.TorsionSetMover) → pyrosetta.rosetta.protocols.simple_moves.TorsionSetMover¶: C++: protocols::simple_moves::TorsionSetMover::operator=(const class protocols::simple_moves::TorsionSetMover &) –> class protocols::simple_moves::TorsionSetMover &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.simple_moves.TorsionSetMover) → pyrosetta.rosetta.protocols.moves.Mover¶

Clone function: create a copy of this object and return an owning pointer to the copy.

C++: protocols::simple_moves::TorsionSetMover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶

Generates a new Mover object freshly created with the default ctor.

C++: protocols::moves::Mover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.simple_moves.TorsionSetMover) → str¶: C++: protocols::simple_moves::TorsionSetMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.

C++: protocols::moves::Mover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.simple_moves.Tumble¶

Bases: Mover

apply(self: pyrosetta.rosetta.protocols.simple_moves.Tumble, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::simple_moves::Tumble::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.Tumble, : pyrosetta.rosetta.protocols.simple_moves.Tumble) → pyrosetta.rosetta.protocols.simple_moves.Tumble¶: C++: protocols::simple_moves::Tumble::operator=(const class protocols::simple_moves::Tumble &) –> class protocols::simple_moves::Tumble &

center_of_mass(self: pyrosetta.rosetta.protocols.simple_moves.Tumble, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.numeric.xyzVector_double_t¶: C++: protocols::simple_moves::Tumble::center_of_mass(const class core::pose::Pose &) –> class numeric::xyzVector<double>

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.simple_moves.Tumble) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::Tumble::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.simple_moves.Tumble) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::Tumble::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.simple_moves.Tumble) → str¶: C++: protocols::simple_moves::Tumble::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static mover_name() → str¶: C++: protocols::simple_moves::Tumble::mover_name() –> std::string

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.simple_moves.Tumble, tag: pyrosetta.rosetta.utility.tag.Tag, datamap: pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::simple_moves::Tumble::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::Tumble::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.simple_moves.TumbleCreator¶

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.simple_moves.TumbleCreator, : pyrosetta.rosetta.protocols.simple_moves.TumbleCreator) → pyrosetta.rosetta.protocols.simple_moves.TumbleCreator¶: C++: protocols::simple_moves::TumbleCreator::operator=(const class protocols::simple_moves::TumbleCreator &) –> class protocols::simple_moves::TumbleCreator &

create_mover(self: pyrosetta.rosetta.protocols.simple_moves.TumbleCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::TumbleCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.simple_moves.TumbleCreator) → str¶: C++: protocols::simple_moves::TumbleCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.simple_moves.TumbleCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::TumbleCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.simple_moves.UniformRotationMover¶

Bases: Mover

Uniform Rotation Mover

apply(self: pyrosetta.rosetta.protocols.simple_moves.UniformRotationMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Apply Rotation

Rotate the membrane to the new normal position

C++: protocols::simple_moves::UniformRotationMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.UniformRotationMover, src: pyrosetta.rosetta.protocols.simple_moves.UniformRotationMover) → pyrosetta.rosetta.protocols.simple_moves.UniformRotationMover¶

Assignment Operator

Make a deep copy of this mover object, overriding the assignment operator

C++: protocols::simple_moves::UniformRotationMover::operator=(const class protocols::simple_moves::UniformRotationMover &) –> class protocols::simple_moves::UniformRotationMover &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶

Return a clone of the Mover object.

C++: protocols::moves::Mover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶

Generates a new Mover object freshly created with the default ctor.

C++: protocols::moves::Mover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.simple_moves.UniformRotationMover) → str¶

Get the name of this mover

C++: protocols::simple_moves::UniformRotationMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.

C++: protocols::moves::Mover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.simple_moves.UniformTranslationMover¶

Bases: Mover

Uniform Translation Mover

apply(self: pyrosetta.rosetta.protocols.simple_moves.UniformTranslationMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Apply Translation to membrane position

Translate membrane position to new center

C++: protocols::simple_moves::UniformTranslationMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.UniformTranslationMover, src: pyrosetta.rosetta.protocols.simple_moves.UniformTranslationMover) → pyrosetta.rosetta.protocols.simple_moves.UniformTranslationMover¶

Assignment Operator

Make a deep copy of this mover object, overriding the assignment operator

C++: protocols::simple_moves::UniformTranslationMover::operator=(const class protocols::simple_moves::UniformTranslationMover &) –> class protocols::simple_moves::UniformTranslationMover &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶

Return a clone of the Mover object.

C++: protocols::moves::Mover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶

Generates a new Mover object freshly created with the default ctor.

C++: protocols::moves::Mover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.simple_moves.UniformTranslationMover) → str¶

Get the name of this mover

C++: protocols::simple_moves::UniformTranslationMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.

C++: protocols::moves::Mover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.simple_moves.VirtualRootMover¶

Bases: Mover

apply(self: pyrosetta.rosetta.protocols.simple_moves.VirtualRootMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::simple_moves::VirtualRootMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.VirtualRootMover, : pyrosetta.rosetta.protocols.simple_moves.VirtualRootMover) → pyrosetta.rosetta.protocols.simple_moves.VirtualRootMover¶: C++: protocols::simple_moves::VirtualRootMover::operator=(const class protocols::simple_moves::VirtualRootMover &) –> class protocols::simple_moves::VirtualRootMover &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.simple_moves.VirtualRootMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::VirtualRootMover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.simple_moves.VirtualRootMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::VirtualRootMover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.simple_moves.VirtualRootMover) → str¶: C++: protocols::simple_moves::VirtualRootMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static mover_name() → str¶: C++: protocols::simple_moves::VirtualRootMover::mover_name() –> std::string

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.simple_moves.VirtualRootMover, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::simple_moves::VirtualRootMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::VirtualRootMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_removable(self: pyrosetta.rosetta.protocols.simple_moves.VirtualRootMover, removable: bool) → None¶: C++: protocols::simple_moves::VirtualRootMover::set_removable(const bool) –> void

set_remove(self: pyrosetta.rosetta.protocols.simple_moves.VirtualRootMover, remove: bool) → None¶: C++: protocols::simple_moves::VirtualRootMover::set_remove(const bool) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.simple_moves.VirtualRootMoverCreator¶

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.simple_moves.VirtualRootMoverCreator, : pyrosetta.rosetta.protocols.simple_moves.VirtualRootMoverCreator) → pyrosetta.rosetta.protocols.simple_moves.VirtualRootMoverCreator¶: C++: protocols::simple_moves::VirtualRootMoverCreator::operator=(const class protocols::simple_moves::VirtualRootMoverCreator &) –> class protocols::simple_moves::VirtualRootMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.simple_moves.VirtualRootMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::VirtualRootMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.simple_moves.VirtualRootMoverCreator) → str¶: C++: protocols::simple_moves::VirtualRootMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.simple_moves.VirtualRootMoverCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::VirtualRootMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.simple_moves.WaterRot¶

Bases: pybind11_object

property aa_¶

property aatm_¶

property abase1_¶

property abase2_¶

assign(self: pyrosetta.rosetta.protocols.simple_moves.WaterRot, : pyrosetta.rosetta.protocols.simple_moves.WaterRot) → pyrosetta.rosetta.protocols.simple_moves.WaterRot¶: C++: protocols::simple_moves::WaterRot::operator=(const struct protocols::simple_moves::WaterRot &) –> struct protocols::simple_moves::WaterRot &

property coords_¶

class pyrosetta.rosetta.protocols.simple_moves.WaterRotsDB¶

Bases: pybind11_object

initialize(self: pyrosetta.rosetta.protocols.simple_moves.WaterRotsDB) → None¶: C++: protocols::simple_moves::WaterRotsDB::initialize() –> void

is_initialized(self: pyrosetta.rosetta.protocols.simple_moves.WaterRotsDB) → bool¶: C++: protocols::simple_moves::WaterRotsDB::is_initialized() –> bool

ligand_rot(self: pyrosetta.rosetta.protocols.simple_moves.WaterRotsDB, i: int) → pyrosetta.rosetta.protocols.simple_moves.WaterRot¶: C++: protocols::simple_moves::WaterRotsDB::ligand_rot(unsigned long) –> const struct protocols::simple_moves::WaterRot &

n_ligand_rots(self: pyrosetta.rosetta.protocols.simple_moves.WaterRotsDB) → int¶: C++: protocols::simple_moves::WaterRotsDB::n_ligand_rots() –> unsigned long

n_protein_rots(self: pyrosetta.rosetta.protocols.simple_moves.WaterRotsDB) → int¶: C++: protocols::simple_moves::WaterRotsDB::n_protein_rots() –> unsigned long

protein_rot(self: pyrosetta.rosetta.protocols.simple_moves.WaterRotsDB, i: int) → pyrosetta.rosetta.protocols.simple_moves.WaterRot¶: C++: protocols::simple_moves::WaterRotsDB::protein_rot(unsigned long) –> const struct protocols::simple_moves::WaterRot &

class pyrosetta.rosetta.protocols.simple_moves.WobbleMover¶

Bases: SmoothFragmentMover

A protocols::moves::Mover class for a classic-wobble analog: a smooth move followed by ccd closure

a smooth fragment is chosen according to the FragmentCost Functor;: a cutpoint is inserted just in front of or just after the fragment a loop is defined around the fragment and cutpoint to be closed with ccd: a cut_Cterm insertion: —-lfff bbb—- f: fragment_res b: buffer_res -: immovable residues a !cut_Cterm insertion: —bbb fffl—

the number of b resiudes is controlled by buffer_length_ (default 3); the move is used by apply() (inherited from FragmentMover). the insertion and loop closure is implemented in the virtual method apply_fragment().

apply(*args, **kwargs)¶

Overloaded function.

apply(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, : pyrosetta.rosetta.core.pose.Pose, pos: int) -> bool
apply(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, : pyrosetta.rosetta.core.pose.Pose) -> None

Applies classic fragment insertion based on a FragSet

example:
mover_3mer.apply(pose)

See also:
ClassicFragmentMover Pose ConstantLengthFragSet

C++: protocols::simple_moves::ClassicFragmentMover::apply(class core::pose::Pose &) –> void

apply_at_all_positions(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover, : pyrosetta.rosetta.core.pose.Pose) → int¶

apply at all movemable positions — honors movemap

C++: protocols::simple_moves::FragmentMover::apply_at_all_positions(class core::pose::Pose &) const –> unsigned long

apply_fragment(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, frame: pyrosetta.rosetta.core.fragment.Frame, frag_num: int, movemap: pyrosetta.rosetta.core.kinematics.MoveMap, pose: pyrosetta.rosetta.core.pose.Pose) → bool¶

apply the chosen fragment,

this can be overloaded to change action, e.,g., WobbleMover introduces chain-break before fragment insertion and does ccd-loop closure afterwards

C++: protocols::simple_moves::ClassicFragmentMover::apply_fragment(const class core::fragment::Frame &, unsigned long, const class core::kinematics::MoveMap &, class core::pose::Pose &) const –> bool

assign(self: pyrosetta.rosetta.protocols.simple_moves.WobbleMover, : pyrosetta.rosetta.protocols.simple_moves.WobbleMover) → pyrosetta.rosetta.protocols.simple_moves.WobbleMover¶: C++: protocols::simple_moves::WobbleMover::operator=(const class protocols::simple_moves::WobbleMover &) –> class protocols::simple_moves::WobbleMover &

check_ss(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover) → bool¶

accessor

C++: protocols::simple_moves::ClassicFragmentMover::check_ss() const –> bool

choose_fragment(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, : pyrosetta.rosetta.core.fragment.FrameList, : pyrosetta.rosetta.core.pose.Pose, frame_num: int, frag_num: int) → bool¶

given FrameList and pose, this method yields a fragment ( frame_num/ frag_num);: return false if nothing suitable is found

C++: protocols::simple_moves::ClassicFragmentMover::choose_fragment(const class core::fragment::FrameList &, const class core::pose::Pose &, unsigned long &, unsigned long &) const –> bool

choose_window_length(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, : pyrosetta.rosetta.core.pose.Pose, window_length: int) → bool¶

yields a length (window_length) of the fragment window to sample from: ( return false, if no suitable length is found )

C++: protocols::simple_moves::ClassicFragmentMover::choose_window_length(const class core::pose::Pose &, unsigned long &) const –> bool

choose_window_start(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, : pyrosetta.rosetta.core.pose.Pose, window_length: int, window_start: int) → bool¶

yields a start position (window_start) for fragment window to sample from: ( return false, if nothing suitable is found )

C++: protocols::simple_moves::ClassicFragmentMover::choose_window_start(const class core::pose::Pose &, unsigned long, unsigned long &) const –> bool

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::ClassicFragmentMover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

define_start_window(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, window_start: int) → None¶

apply fragment at predefined position

C++: protocols::simple_moves::ClassicFragmentMover::define_start_window(unsigned long) –> void

enable_end_bias_check(*args, **kwargs)¶

Overloaded function.

enable_end_bias_check(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover) -> None
enable_end_bias_check(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, setting: bool) -> None

C++: protocols::simple_moves::ClassicFragmentMover::enable_end_bias_check(bool) –> void

end_bias(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover) → float¶: C++: protocols::simple_moves::ClassicFragmentMover::end_bias() const –> double

end_bias_check(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, : pyrosetta.rosetta.core.pose.Pose, window_start: int) → bool¶: C++: protocols::simple_moves::ClassicFragmentMover::end_bias_check(const class core::pose::Pose &, unsigned long) const –> bool

end_bias_check_enabled(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover) → bool¶: C++: protocols::simple_moves::ClassicFragmentMover::end_bias_check_enabled() const –> bool

fragments(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover) → pyrosetta.rosetta.core.fragment.FragSet¶

accessor to the fragment set

C++: protocols::simple_moves::FragmentMover::fragments() const –> class std::shared_ptr<const class core::fragment::FragSet>

fresh_instance(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::ClassicFragmentMover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.simple_moves.WobbleMover) → str¶: C++: protocols::simple_moves::WobbleMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

initialize(self: pyrosetta.rosetta.protocols.moves.MoveMapMover, : pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::moves::MoveMapMover::initialize(class core::pose::Pose &) –> void

insert_map(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover) → pyrosetta.rosetta.utility.vector1_unsigned_long¶: C++: protocols::simple_moves::FragmentMover::insert_map() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

insert_size(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover) → pyrosetta.rosetta.utility.vector1_unsigned_long¶: C++: protocols::simple_moves::FragmentMover::insert_size() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

movemap(*args, **kwargs)¶

Overloaded function.

movemap(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover, : pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.core.kinematics.MoveMap

C++: protocols::simple_moves::FragmentMover::movemap(const class core::pose::Pose &) const –> class std::shared_ptr<const class core::kinematics::MoveMap>

movemap(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover) -> pyrosetta.rosetta.core.kinematics.MoveMap

C++: protocols::simple_moves::FragmentMover::movemap() const –> class std::shared_ptr<const class core::kinematics::MoveMap>

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

on_new_fragments(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover) → None¶

is called from set_fragments()

C++: protocols::simple_moves::ClassicFragmentMover::on_new_fragments() –> void

parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.

C++: protocols::moves::Mover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_buffer_length(self: pyrosetta.rosetta.protocols.simple_moves.WobbleMover, setting: int) → None¶: C++: protocols::simple_moves::WobbleMover::set_buffer_length(unsigned long) –> void

set_check_ss(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, setting: bool) → None¶

check_ss controls whether fragment insertions are rejected that create short helices (<3) or strands (<2)

C++: protocols::simple_moves::ClassicFragmentMover::set_check_ss(bool) –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_end_bias(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, setting: float) → None¶: C++: protocols::simple_moves::ClassicFragmentMover::set_end_bias(double) –> void

set_fragments(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover, new_frags_: pyrosetta.rosetta.core.fragment.FragSet) → None¶

setter for the fragment set

C++: protocols::simple_moves::FragmentMover::set_fragments(class std::shared_ptr<const class core::fragment::FragSet>) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_min_frag_length(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, setting: int) → None¶

min_frag_length controls the behaviour fragset->region()

C++: protocols::simple_moves::ClassicFragmentMover::set_min_frag_length(unsigned long) –> void

set_min_overlap(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, setting: int) → None¶

min_overlap controls the behaviour fragset->region()

C++: protocols::simple_moves::ClassicFragmentMover::set_min_overlap(unsigned long) –> void

set_movemap(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover, movemap: pyrosetta.rosetta.core.kinematics.MoveMap) → None¶

setter for the movemap

C++: protocols::simple_moves::FragmentMover::set_movemap(class std::shared_ptr<const class core::kinematics::MoveMap>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

shared_from_this(self: pyrosetta.rosetta.protocols.simple_moves.SmoothFragmentMover) → pyrosetta.rosetta.protocols.simple_moves.SmoothFragmentMover¶: C++: protocols::simple_moves::SmoothFragmentMover::shared_from_this() –> class std::shared_ptr<class protocols::simple_moves::SmoothFragmentMover>

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover) -> None
show(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, output: pyrosetta.rosetta.std.ostream) -> None

C++: protocols::simple_moves::ClassicFragmentMover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

valid_ss(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, new_ss: str) → bool¶

returns true if the ss string is acceptable

C++: protocols::simple_moves::ClassicFragmentMover::valid_ss(const std::string &) const –> bool

class pyrosetta.rosetta.protocols.simple_moves.WriteFiltersToPose¶

Bases: Mover

Writes the results from all filters to the pose file.

This mover goes through all filters in the RosettaScripts file and writes their user-defined name, (optionally) their filter type, and their numerical result to the output .pdb file. The include_type option writes the filter type. The user can also specify a prefix to append before the user-defined filter name; for instance, let’s say there is a PackStat filter, as well as several movers like fastdesign and docking. The “prefix” option allows the user to have several versions of WriteFiltersToPose which take the filter results from different steps in the process. If the RosettaScripts XML file has these instances of WriteFiltersToPose:

<WriteFiltersToPose name=”writer1” prefix=”post_fastdesign_”/> <WriteFiltersToPose name=”writer2” prefix=”post_docking_” include_type=”true”/>

If the only filter is a PackStat filter named “packing”, the output pdb will have two lines at the end that look something like this:

post_docking_packing PackStat 0.6794 post_fastdesign_packing 0.6751

If there are multiple filters, each instance of this mover will write all filters to the pose.

Note: If you would like to only write a single filter result to your pose, use FilterReportAsPoseExtraScoresMover

apply(self: pyrosetta.rosetta.protocols.simple_moves.WriteFiltersToPose, : pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::simple_moves::WriteFiltersToPose::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.WriteFiltersToPose, : pyrosetta.rosetta.protocols.simple_moves.WriteFiltersToPose) → pyrosetta.rosetta.protocols.simple_moves.WriteFiltersToPose¶: C++: protocols::simple_moves::WriteFiltersToPose::operator=(const class protocols::simple_moves::WriteFiltersToPose &) –> class protocols::simple_moves::WriteFiltersToPose &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.simple_moves.WriteFiltersToPose) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::WriteFiltersToPose::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.simple_moves.WriteFiltersToPose) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::WriteFiltersToPose::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.simple_moves.WriteFiltersToPose) → str¶: C++: protocols::simple_moves::WriteFiltersToPose::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static mover_name() → str¶: C++: protocols::simple_moves::WriteFiltersToPose::mover_name() –> std::string

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.simple_moves.WriteFiltersToPose, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::simple_moves::WriteFiltersToPose::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::WriteFiltersToPose::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.simple_moves.WriteFiltersToPoseCreator¶

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.simple_moves.WriteFiltersToPoseCreator, : pyrosetta.rosetta.protocols.simple_moves.WriteFiltersToPoseCreator) → pyrosetta.rosetta.protocols.simple_moves.WriteFiltersToPoseCreator¶: C++: protocols::simple_moves::WriteFiltersToPoseCreator::operator=(const class protocols::simple_moves::WriteFiltersToPoseCreator &) –> class protocols::simple_moves::WriteFiltersToPoseCreator &

create_mover(self: pyrosetta.rosetta.protocols.simple_moves.WriteFiltersToPoseCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::WriteFiltersToPoseCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.simple_moves.WriteFiltersToPoseCreator) → str¶: C++: protocols::simple_moves::WriteFiltersToPoseCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.simple_moves.WriteFiltersToPoseCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::WriteFiltersToPoseCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.simple_moves.WriteSSEMover¶

Bases: Mover

Writes SSE assignation from DSSP or prediction from PSIPRED as REMARK.

apply(self: pyrosetta.rosetta.protocols.simple_moves.WriteSSEMover, : pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::simple_moves::WriteSSEMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.WriteSSEMover, : pyrosetta.rosetta.protocols.simple_moves.WriteSSEMover) → pyrosetta.rosetta.protocols.simple_moves.WriteSSEMover¶: C++: protocols::simple_moves::WriteSSEMover::operator=(const class protocols::simple_moves::WriteSSEMover &) –> class protocols::simple_moves::WriteSSEMover &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.simple_moves.WriteSSEMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::WriteSSEMover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

cmd(self: pyrosetta.rosetta.protocols.simple_moves.WriteSSEMover, cmd: str) → None¶: C++: protocols::simple_moves::WriteSSEMover::cmd(const std::string &) –> void

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

dssp(self: pyrosetta.rosetta.protocols.simple_moves.WriteSSEMover, pick: bool) → None¶: C++: protocols::simple_moves::WriteSSEMover::dssp(bool) –> void

fresh_instance(self: pyrosetta.rosetta.protocols.simple_moves.WriteSSEMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::WriteSSEMover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.simple_moves.WriteSSEMover) → str¶: C++: protocols::simple_moves::WriteSSEMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static mover_name() → str¶: C++: protocols::simple_moves::WriteSSEMover::mover_name() –> std::string

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.simple_moves.WriteSSEMover, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::simple_moves::WriteSSEMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::WriteSSEMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

write_phipsi(self: pyrosetta.rosetta.protocols.simple_moves.WriteSSEMover, pick: bool) → None¶: C++: protocols::simple_moves::WriteSSEMover::write_phipsi(bool) –> void

class pyrosetta.rosetta.protocols.simple_moves.WriteSSEMoverCreator¶

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.simple_moves.WriteSSEMoverCreator, : pyrosetta.rosetta.protocols.simple_moves.WriteSSEMoverCreator) → pyrosetta.rosetta.protocols.simple_moves.WriteSSEMoverCreator¶: C++: protocols::simple_moves::WriteSSEMoverCreator::operator=(const class protocols::simple_moves::WriteSSEMoverCreator &) –> class protocols::simple_moves::WriteSSEMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.simple_moves.WriteSSEMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::simple_moves::WriteSSEMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.simple_moves.WriteSSEMoverCreator) → str¶: C++: protocols::simple_moves::WriteSSEMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.simple_moves.WriteSSEMoverCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::simple_moves::WriteSSEMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

pyrosetta.rosetta.protocols.simple_moves.setup_vary_polar_hydrogen_geometry(mm: pyrosetta.rosetta.core.kinematics.MoveMap, pose: pyrosetta.rosetta.core.pose.Pose, atom_level_domain_map: pyrosetta.rosetta.core.pose.toolbox.AtomLevelDomainMap) → None¶: C++: protocols::simple_moves::setup_vary_polar_hydrogen_geometry(class core::kinematics::MoveMap &, class core::pose::Pose &, class std::shared_ptr<const class core::pose::toolbox::AtomLevelDomainMap>) –> void

pyrosetta.rosetta.protocols.simple_moves.setup_vary_rna_bond_geometry(*args, **kwargs)¶

Overloaded function.

setup_vary_rna_bond_geometry(mm: pyrosetta.rosetta.core.kinematics.MoveMap, pose: pyrosetta.rosetta.core.pose.Pose, atom_level_domain_map: pyrosetta.rosetta.core.pose.toolbox.AtomLevelDomainMap) -> None
setup_vary_rna_bond_geometry(mm: pyrosetta.rosetta.core.kinematics.MoveMap, pose: pyrosetta.rosetta.core.pose.Pose, atom_level_domain_map: pyrosetta.rosetta.core.pose.toolbox.AtomLevelDomainMap, score_type: pyrosetta.rosetta.core.scoring.ScoreType) -> None

C++: protocols::simple_moves::setup_vary_rna_bond_geometry(class core::kinematics::MoveMap &, class core::pose::Pose &, class std::shared_ptr<const class core::pose::toolbox::AtomLevelDomainMap>, enum core::scoring::ScoreType) –> void

pyrosetta.rosetta.protocols.simple_moves.uniform_dof_distribution(dof_type: pyrosetta.rosetta.core.id.DOF_Type, num_bins: int, min: float, max: float) → pyrosetta.rosetta.utility.vector1_double¶: C++: protocols::simple_moves::uniform_dof_distribution(enum core::id::DOF_Type, unsigned long, double, double) –> class utility::vector1<double, class std::allocator<double> >