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¶

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¶

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¶

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¶

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¶

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¶

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¶

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¶

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¶

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¶

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¶

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¶

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¶

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¶

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¶

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¶

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¶

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¶

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¶

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¶

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¶

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

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¶

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

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

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

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¶

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

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¶

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

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

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

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¶

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>

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¶

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 > > &

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

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¶

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¶

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¶

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¶

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¶