simple_moves

Bindings for protocols::simple_moves namespace

class pyrosetta.rosetta.protocols.simple_moves.AddCavitiesMover

Bases: pyrosetta.rosetta.protocols.moves.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_std_allocator_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.

  1. show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None

  2. 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.

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

Set the ‘type’ string

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

  1. 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: pyrosetta.rosetta.protocols.moves.Mover

add_new_chain(self: pyrosetta.rosetta.protocols.simple_moves.AddChainMover, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::simple_moves::AddChainMover::add_new_chain(class core::pose::Pose &) const –> void

apply(self: pyrosetta.rosetta.protocols.simple_moves.AddChainMover, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::simple_moves::AddChainMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.AddChainMover, : pyrosetta.rosetta.protocols.simple_moves.AddChainMover) pyrosetta.rosetta.protocols.simple_moves.AddChainMover

C++: protocols::simple_moves::AddChainMover::operator=(const class protocols::simple_moves::AddChainMover &) –> class protocols::simple_moves::AddChainMover &

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

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

clear_info is called by jd2 before calling apply

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

clone(self: pyrosetta.rosetta.protocols.simple_moves.AddChainMover) pyrosetta.rosetta.protocols.moves.Mover

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

create(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

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

fname(*args, **kwargs)

Overloaded function.

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

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

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

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

fresh_instance(self: pyrosetta.rosetta.protocols.simple_moves.AddChainMover) pyrosetta.rosetta.protocols.moves.Mover

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

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

fpd

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

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

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

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) protocols::jobdist::BasicJob

C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) str
A tag is a unique identifier used to identify structures produced

by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

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

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

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

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

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

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

get_name(self: pyrosetta.rosetta.protocols.simple_moves.AddChainMover) str

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

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

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

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

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

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t

C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) str

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

info(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.list_std_string_std_allocator_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.

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

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

  1. 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: utility::tag::XMLSchemaDefinition) None

C++: protocols::simple_moves::AddChainMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

random_access(*args, **kwargs)

Overloaded function.

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

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

  1. 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.

  1. 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

  1. 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.

  1. show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None

  2. 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.

  1. 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

  1. 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.

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

Set the ‘type’ string

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

  1. 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.

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

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

  1. 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: pyrosetta.rosetta.protocols.moves.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: 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: pyrosetta.rosetta.protocols.moves.Mover

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

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

apply(self: pyrosetta.rosetta.protocols.simple_moves.AddJobPairData, : pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::simple_moves::AddJobPairData::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.AddJobPairData, : pyrosetta.rosetta.protocols.simple_moves.AddJobPairData) pyrosetta.rosetta.protocols.simple_moves.AddJobPairData

C++: protocols::simple_moves::AddJobPairData::operator=(const class protocols::simple_moves::AddJobPairData &) –> class protocols::simple_moves::AddJobPairData &

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

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

clear_info is called by jd2 before calling apply

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

clone(self: pyrosetta.rosetta.protocols.simple_moves.AddJobPairData) pyrosetta.rosetta.protocols.moves.Mover

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

create(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

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

fresh_instance(self: pyrosetta.rosetta.protocols.simple_moves.AddJobPairData) pyrosetta.rosetta.protocols.moves.Mover

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

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

fpd

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

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

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

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) protocols::jobdist::BasicJob

C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) str
A tag is a unique identifier used to identify structures produced

by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

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

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

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

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

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

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

get_name(self: pyrosetta.rosetta.protocols.simple_moves.AddJobPairData) str

C++: protocols::simple_moves::AddJobPairData::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

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

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

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

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t

C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) str

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

info(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.list_std_string_std_allocator_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: 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.

  1. show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None

  2. 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.

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

Set the ‘type’ string

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

  1. 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: pyrosetta.rosetta.protocols.moves.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: 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: pyrosetta.rosetta.protocols.moves.Mover

apply(self: pyrosetta.rosetta.protocols.simple_moves.AddPDBInfoMover, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::simple_moves::AddPDBInfoMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.AddPDBInfoMover, : pyrosetta.rosetta.protocols.simple_moves.AddPDBInfoMover) pyrosetta.rosetta.protocols.simple_moves.AddPDBInfoMover

C++: protocols::simple_moves::AddPDBInfoMover::operator=(const class protocols::simple_moves::AddPDBInfoMover &) –> class protocols::simple_moves::AddPDBInfoMover &

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

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

clear_info is called by jd2 before calling apply

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

clone(self: pyrosetta.rosetta.protocols.simple_moves.AddPDBInfoMover) pyrosetta.rosetta.protocols.moves.Mover

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

create(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

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

fresh_instance(self: pyrosetta.rosetta.protocols.simple_moves.AddPDBInfoMover) pyrosetta.rosetta.protocols.moves.Mover

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

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

fpd

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

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

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

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) protocols::jobdist::BasicJob

C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) str
A tag is a unique identifier used to identify structures produced

by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

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

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

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

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

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

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

get_name(self: pyrosetta.rosetta.protocols.simple_moves.AddPDBInfoMover) str

C++: protocols::simple_moves::AddPDBInfoMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

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

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

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

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t

C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) str

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

info(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.list_std_string_std_allocator_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: 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.

  1. show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None

  2. 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.

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

Set the ‘type’ string

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

  1. 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: pyrosetta.rosetta.protocols.moves.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: 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: pyrosetta.rosetta.protocols.moves.Mover

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

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

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

apply(self: pyrosetta.rosetta.protocols.simple_moves.AddResidueCouplingConstraint, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::simple_moves::AddResidueCouplingConstraint::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.AddResidueCouplingConstraint, : pyrosetta.rosetta.protocols.simple_moves.AddResidueCouplingConstraint) pyrosetta.rosetta.protocols.simple_moves.AddResidueCouplingConstraint

C++: protocols::simple_moves::AddResidueCouplingConstraint::operator=(const class protocols::simple_moves::AddResidueCouplingConstraint &) –> class protocols::simple_moves::AddResidueCouplingConstraint &

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

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

clear_info is called by jd2 before calling apply

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

clone(self: pyrosetta.rosetta.protocols.simple_moves.AddResidueCouplingConstraint) pyrosetta.rosetta.protocols.moves.Mover

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

create(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

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

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

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

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

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

fpd

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

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

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

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) protocols::jobdist::BasicJob

C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) str
A tag is a unique identifier used to identify structures produced

by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

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

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

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

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

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

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

get_name(self: pyrosetta.rosetta.protocols.simple_moves.AddResidueCouplingConstraint) str

C++: protocols::simple_moves::AddResidueCouplingConstraint::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

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

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

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

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t

C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) str

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

info(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.list_std_string_std_allocator_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: 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.

  1. show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None

  2. 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.

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

Set the ‘type’ string

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

  1. 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: pyrosetta.rosetta.protocols.moves.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: 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: pyrosetta.rosetta.protocols.moves.Mover

apply(self: pyrosetta.rosetta.protocols.simple_moves.AddResidueLabelMover, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::simple_moves::AddResidueLabelMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.AddResidueLabelMover, : pyrosetta.rosetta.protocols.simple_moves.AddResidueLabelMover) pyrosetta.rosetta.protocols.simple_moves.AddResidueLabelMover

C++: protocols::simple_moves::AddResidueLabelMover::operator=(const class protocols::simple_moves::AddResidueLabelMover &) –> class protocols::simple_moves::AddResidueLabelMover &

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

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

clear_info is called by jd2 before calling apply

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

clone(self: pyrosetta.rosetta.protocols.simple_moves.AddResidueLabelMover) pyrosetta.rosetta.protocols.moves.Mover

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

create(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

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

fresh_instance(self: pyrosetta.rosetta.protocols.simple_moves.AddResidueLabelMover) pyrosetta.rosetta.protocols.moves.Mover

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

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

fpd

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

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

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

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) protocols::jobdist::BasicJob

C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) str
A tag is a unique identifier used to identify structures produced

by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

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

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

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

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

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

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

get_name(self: pyrosetta.rosetta.protocols.simple_moves.AddResidueLabelMover) str

C++: protocols::simple_moves::AddResidueLabelMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

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

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

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

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t

C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) str

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

info(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.list_std_string_std_allocator_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.

  1. show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None

  2. 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.

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

Set the ‘type’ string

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

  1. 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: pyrosetta.rosetta.protocols.moves.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: 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: pyrosetta.rosetta.protocols.moves.Mover

Adds variant types to selected residues

apply(self: pyrosetta.rosetta.protocols.simple_moves.AddSapConstraintMover, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::simple_moves::AddSapConstraintMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.AddSapConstraintMover, ot: pyrosetta.rosetta.protocols.simple_moves.AddSapConstraintMover) pyrosetta.rosetta.protocols.simple_moves.AddSapConstraintMover

C++: protocols::simple_moves::AddSapConstraintMover::operator=(const class protocols::simple_moves::AddSapConstraintMover &) –> class protocols::simple_moves::AddSapConstraintMover &

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

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

clear_info is called by jd2 before calling apply

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

clone(self: pyrosetta.rosetta.protocols.simple_moves.AddSapConstraintMover) pyrosetta.rosetta.protocols.moves.Mover

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

create(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

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

fresh_instance(self: pyrosetta.rosetta.protocols.simple_moves.AddSapConstraintMover) pyrosetta.rosetta.protocols.moves.Mover

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

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

fpd

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

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

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

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) protocols::jobdist::BasicJob

C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) str
A tag is a unique identifier used to identify structures produced

by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

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

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

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

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

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

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

get_name(self: pyrosetta.rosetta.protocols.simple_moves.AddSapConstraintMover) str

C++: protocols::simple_moves::AddSapConstraintMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

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

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

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

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t

C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) str

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

info(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.list_std_string_std_allocator_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: 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.

  1. show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None

  2. 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.

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

Set the ‘type’ string

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

  1. 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: pyrosetta.rosetta.protocols.moves.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: 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: pyrosetta.rosetta.protocols.moves.Mover

Adds variant types to selected residues

add_constraint(self: pyrosetta.rosetta.protocols.simple_moves.AddSapMathConstraintMover, weight: float, name: str) None

C++: protocols::simple_moves::AddSapMathConstraintMover::add_constraint(double, const std::string &) –> void

apply(self: pyrosetta.rosetta.protocols.simple_moves.AddSapMathConstraintMover, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::simple_moves::AddSapMathConstraintMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.AddSapMathConstraintMover, ot: pyrosetta.rosetta.protocols.simple_moves.AddSapMathConstraintMover) pyrosetta.rosetta.protocols.simple_moves.AddSapMathConstraintMover

C++: protocols::simple_moves::AddSapMathConstraintMover::operator=(const class protocols::simple_moves::AddSapMathConstraintMover &) –> class protocols::simple_moves::AddSapMathConstraintMover &

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

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

clear_info is called by jd2 before calling apply

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

clone(self: pyrosetta.rosetta.protocols.simple_moves.AddSapMathConstraintMover) pyrosetta.rosetta.protocols.moves.Mover

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

create(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

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

fresh_instance(self: pyrosetta.rosetta.protocols.simple_moves.AddSapMathConstraintMover) pyrosetta.rosetta.protocols.moves.Mover

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

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

fpd

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

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

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

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) protocols::jobdist::BasicJob

C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) str
A tag is a unique identifier used to identify structures produced

by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

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

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

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

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

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

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

get_name(self: pyrosetta.rosetta.protocols.simple_moves.AddSapMathConstraintMover) str

C++: protocols::simple_moves::AddSapMathConstraintMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

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

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

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

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t

C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) str

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

info(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.list_std_string_std_allocator_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: 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.

  1. show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None

  2. 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.

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

Set the ‘type’ string

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

  1. 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: pyrosetta.rosetta.protocols.moves.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: 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: pyrosetta.rosetta.protocols.moves.Mover

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

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

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

C++: protocols::simple_moves::AlignChainMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.AlignChainMover, : pyrosetta.rosetta.protocols.simple_moves.AlignChainMover) pyrosetta.rosetta.protocols.simple_moves.AlignChainMover

C++: protocols::simple_moves::AlignChainMover::operator=(const class protocols::simple_moves::AlignChainMover &) –> class protocols::simple_moves::AlignChainMover &

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

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

clear_info is called by jd2 before calling apply

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

clone(self: pyrosetta.rosetta.protocols.simple_moves.AlignChainMover) pyrosetta.rosetta.protocols.moves.Mover

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

create(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

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

fresh_instance(self: pyrosetta.rosetta.protocols.simple_moves.AlignChainMover) pyrosetta.rosetta.protocols.moves.Mover

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

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

fpd

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

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

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

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) protocols::jobdist::BasicJob

C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) str
A tag is a unique identifier used to identify structures produced

by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

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

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

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

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

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

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

get_name(self: pyrosetta.rosetta.protocols.simple_moves.AlignChainMover) str

C++: protocols::simple_moves::AlignChainMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

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

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

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

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t

C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) str

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

info(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.list_std_string_std_allocator_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.

  1. 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>

  1. 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: 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.

  1. show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None

  2. 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.

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

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

  1. 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.

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

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

  1. 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.

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

Set the ‘type’ string

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

  1. 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: pyrosetta.rosetta.protocols.moves.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: 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_builtins.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_builtins.pybind11_object

property idx
property residx
property xyz
class pyrosetta.rosetta.protocols.simple_moves.BBConRotMover

Bases: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover

apply(self: pyrosetta.rosetta.protocols.simple_moves.BBConRotMover, : pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::simple_moves::BBConRotMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.BBConRotMover, : pyrosetta.rosetta.protocols.simple_moves.BBConRotMover) pyrosetta.rosetta.protocols.simple_moves.BBConRotMover

C++: protocols::simple_moves::BBConRotMover::operator=(const class protocols::simple_moves::BBConRotMover &) –> class protocols::simple_moves::BBConRotMover &

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

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

clear_info is called by jd2 before calling apply

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

clone(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover) pyrosetta.rosetta.protocols.moves.Mover

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

create(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

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

factorA(self: pyrosetta.rosetta.protocols.simple_moves.BBConRotMover, fA: float) None

C++: protocols::simple_moves::BBConRotMover::factorA(const double) –> void

factorB(self: pyrosetta.rosetta.protocols.simple_moves.BBConRotMover, fB: float) None

C++: protocols::simple_moves::BBConRotMover::factorB(const double) –> void

factorC(self: pyrosetta.rosetta.protocols.simple_moves.BBConRotMover, fC: float) None

C++: protocols::simple_moves::BBConRotMover::factorC(const double) –> void

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

Callback executed after all Monte Carlo trials are completed.

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

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

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

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

get_A(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover) None

C++: protocols::simple_moves::BBGaussianMover::get_A() –> void

get_G(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover) None

C++: protocols::simple_moves::BBGaussianMover::get_G() –> void

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

calculate L matrix and update pose

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

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

calculate L’, update last_proposal_density

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

get_VdRdPhi(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, : pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::simple_moves::BBGaussianMover::get_VdRdPhi(const class core::pose::Pose &) –> void

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

fpd

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

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

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

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) protocols::jobdist::BasicJob

C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) str
A tag is a unique identifier used to identify structures produced

by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

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

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

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

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

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

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

get_name(self: pyrosetta.rosetta.protocols.simple_moves.BBConRotMover) str

C++: protocols::simple_moves::BBConRotMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

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

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

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

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t

C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) str

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

info(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.list_std_string_std_allocator_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.

  1. 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>

  1. 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: 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.

  1. show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None

  2. 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.

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

Set the ‘type’ string

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

  1. 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: pyrosetta.rosetta.protocols.moves.Mover

Mover interface to BBDihedralSampler ( 1D ). Samples using BBDihedralSamplers randomly using residues set in the movemap. If multiple samplers are given, will randomly sample on them.

add_sampler(self: pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover, sampler: protocols::simple_moves::bb_sampler::BBDihedralSampler) None

Add a sampler to this mover.

C++: protocols::simple_moves::BBDihedralSamplerMover::add_sampler(class std::shared_ptr<class protocols::simple_moves::bb_sampler::BBDihedralSampler>) –> void

apply(self: pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::simple_moves::BBDihedralSamplerMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover, : pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover) pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover

C++: protocols::simple_moves::BBDihedralSamplerMover::operator=(const class protocols::simple_moves::BBDihedralSamplerMover &) –> class protocols::simple_moves::BBDihedralSamplerMover &

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

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

clear_info is called by jd2 before calling apply

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

clone(self: pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover) pyrosetta.rosetta.protocols.moves.Mover

required in the context of the parser/scripting scheme

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

create(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

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

fresh_instance(self: pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover) pyrosetta.rosetta.protocols.moves.Mover

required in the context of the parser/scripting scheme

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

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

fpd

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

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

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

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) protocols::jobdist::BasicJob

C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) str
A tag is a unique identifier used to identify structures produced

by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

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

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

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

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

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

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

get_name(self: pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover) str

C++: protocols::simple_moves::BBDihedralSamplerMover::get_name() const –> std::string

get_name_of_last_sampler_used(self: pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover) str

Return the name of the last sampler used during the last apply

C++: protocols::simple_moves::BBDihedralSamplerMover::get_name_of_last_sampler_used() –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

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

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

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

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t

C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) str

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

info(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.list_std_string_std_allocator_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) 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.

  1. show(self: pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover) -> None

  2. 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.

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

Set the ‘type’ string

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

  1. 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: pyrosetta.rosetta.protocols.moves.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: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover

a particular gaussian mover from the original paper

using 8 torsion angles as DOF, 3 atoms (Ca,C,O) as end

apply(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::simple_moves::BBGaussianMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover, : pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover) pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover

C++: protocols::simple_moves::BBG8T3AMover::operator=(const class protocols::simple_moves::BBG8T3AMover &) –> class protocols::simple_moves::BBG8T3AMover &

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

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

clear_info is called by jd2 before calling apply

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

clone(self: pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::simple_moves::BBG8T3AMover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

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

factorA(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, fA: float) None

C++: protocols::simple_moves::BBGaussianMover::factorA(const double) –> void

factorB(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, fB: float) None

C++: protocols::simple_moves::BBGaussianMover::factorB(const double) –> void

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

Callback executed after all Monte Carlo trials are completed.

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

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

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

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

get_A(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover) None

C++: protocols::simple_moves::BBGaussianMover::get_A() –> void

get_G(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover) None

C++: protocols::simple_moves::BBGaussianMover::get_G() –> void

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

calculate L matrix and update pose

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

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

calculate L’, update last_proposal_density

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

get_VdRdPhi(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, : pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::simple_moves::BBGaussianMover::get_VdRdPhi(const class core::pose::Pose &) –> void

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

fpd

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

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

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

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) protocols::jobdist::BasicJob

C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) str
A tag is a unique identifier used to identify structures produced

by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

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

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

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

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

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

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

get_name(self: pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover) str

C++: protocols::simple_moves::BBG8T3AMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

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

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

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

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t

C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) str

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

info(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.list_std_string_std_allocator_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.

  1. 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>

  1. 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: 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.

  1. show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None

  2. 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.

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

Set the ‘type’ string

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

  1. 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: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover

the basic class for implementing Gaussian Perturbation of bb

“Monte Carlo update for chain molecules: Biased Gaussian steps in torsional space” “The Journal of Chemical Physics, Vol. 114, No. 18. (2001), pp. 8154-8158.” Two steps for perturbing the backbone and keeping the geometry constrain Step 1: Gaussian Biased steps in torsional space: the end atoms of the moving segment should be choosen by user and to keep the geometry constrain(6), the DOF of the moving segment > 6 Step 2: “pivot” update the bb conformation, or followed by a chainclosure method (BBConRot)

apply(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::simple_moves::BBGaussianMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, : pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover) pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover

C++: protocols::simple_moves::BBGaussianMover::operator=(const class protocols::simple_moves::BBGaussianMover &) –> class protocols::simple_moves::BBGaussianMover &

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

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

clear_info is called by jd2 before calling apply

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

clone(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover) pyrosetta.rosetta.protocols.moves.Mover

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

create(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

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

factorA(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, fA: float) None

C++: protocols::simple_moves::BBGaussianMover::factorA(const double) –> void

factorB(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, fB: float) None

C++: protocols::simple_moves::BBGaussianMover::factorB(const double) –> void

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

Callback executed after all Monte Carlo trials are completed.

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

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

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

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

get_A(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover) None

C++: protocols::simple_moves::BBGaussianMover::get_A() –> void

get_G(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover) None

C++: protocols::simple_moves::BBGaussianMover::get_G() –> void

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

calculate L matrix and update pose

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

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

calculate L’, update last_proposal_density

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

get_VdRdPhi(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, : pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::simple_moves::BBGaussianMover::get_VdRdPhi(const class core::pose::Pose &) –> void

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

fpd

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

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

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

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) protocols::jobdist::BasicJob

C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) str
A tag is a unique identifier used to identify structures produced

by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

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

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

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

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

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

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

get_name(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover) str

C++: protocols::simple_moves::BBGaussianMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

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

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

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

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t

C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) str

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

info(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.list_std_string_std_allocator_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.

  1. 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>

  1. 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: 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.

  1. show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None

  2. 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.

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

Set the ‘type’ string

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

  1. 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: pyrosetta.rosetta.protocols.moves.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: 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: pyrosetta.rosetta.protocols.canonical_sampling.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.

  1. 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

  1. 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

  1. angle_max(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, angle_max_in: pyrosetta.rosetta.std.map_char_double) -> None

Sets the max angle of perturbation, for secondary structures

‘H’, ‘E’, and ‘L’. new_angle = old_angle +/- ( angle_max/2 )

C++: protocols::simple_moves::BackboneMover::angle_max(class std::map<char, double, struct std::less<char>, class std::allocator<struct std::pair<const char, double> > >) –> void

apply(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, : pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::simple_moves::BackboneMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, : pyrosetta.rosetta.protocols.simple_moves.BackboneMover) pyrosetta.rosetta.protocols.simple_moves.BackboneMover

C++: protocols::simple_moves::BackboneMover::operator=(const class protocols::simple_moves::BackboneMover &) –> class protocols::simple_moves::BackboneMover &

static backbone_mover_complex_type_namer(tag_name: str) str

C++: protocols::simple_moves::BackboneMover::backbone_mover_complex_type_namer(std::string) –> std::string

check_rama(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover) bool

C++: protocols::simple_moves::BackboneMover::check_rama() –> bool

clear(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover) None

C++: protocols::simple_moves::BackboneMover::clear() –> void

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

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

clear_info is called by jd2 before calling apply

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

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

Return a clone of the Mover object.

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

static complex_type_generator_for_backbone_mover(xsd: utility::tag::XMLSchemaDefinition) utility::tag::XMLSchemaComplexTypeGenerator

C++: protocols::simple_moves::BackboneMover::complex_type_generator_for_backbone_mover(class utility::tag::XMLSchemaDefinition &) –> class std::shared_ptr<class utility::tag::XMLSchemaComplexTypeGenerator>

create(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

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

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

Callback executed after all Monte Carlo trials are completed.

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

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

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

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

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

fpd

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

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

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

get_angle_max(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, type: str) float
Gets the max angle of perturbation for residues with <type>

secondary structure. (<type> must be ‘H’, ‘E’, or ‘L’.)

Example:

bbmover.angle_max(‘H’)

See also:

ShearMover SmallMover

C++: protocols::simple_moves::BackboneMover::get_angle_max(const char) const –> double

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) protocols::jobdist::BasicJob

C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) str
A tag is a unique identifier used to identify structures produced

by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

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

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

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

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

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

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

get_name(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover) str

C++: protocols::simple_moves::BackboneMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

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

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

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

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t

C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) str

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

info(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.list_std_string_std_allocator_std_string_t

non-const accessor

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

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

Callback executed before any Monte Carlo trials are attempted.

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

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

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

last_inner_score_delta_over_temperature()

metropolis_hastings_mover()

set_metropolis_hastings_mover()

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

last_inner_score_delta_over_temperature(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) float
If this is a multi-trial move, return the change in internal

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

is_multi_trial()

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

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) float

Return the proposal density ratio for last apply method.

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

make_move(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, : pyrosetta.rosetta.core.pose.Pose) bool

C++: protocols::simple_moves::BackboneMover::make_move(class core::pose::Pose &) –> bool

metropolis_hastings_mover(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) pyrosetta.rosetta.std.weak_ptr_protocols_canonical_sampling_MetropolisHastingsMover_t
If this is a multi-trial move, return the MetropolisHastingsMover

being used internally.

is_multi_trial()

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

move_with_rama(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, pose: pyrosetta.rosetta.core.pose.Pose) bool

C++: protocols::simple_moves::BackboneMover::move_with_rama(class core::pose::Pose &) –> bool

move_with_scorefxn(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, pose: pyrosetta.rosetta.core.pose.Pose) bool

C++: protocols::simple_moves::BackboneMover::move_with_scorefxn(class core::pose::Pose &) –> bool

movemap(*args, **kwargs)

Overloaded function.

  1. 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

  1. 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.

  1. nmoves(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, nmoves_in: int) -> None

C++: protocols::simple_moves::BackboneMover::nmoves(const unsigned long) –> void

  1. 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.

  1. 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>

  1. 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.

  1. 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>

  1. selector(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) -> None

C++: protocols::simple_moves::BackboneMover::selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

set_angles(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, : float) None

C++: protocols::simple_moves::BackboneMover::set_angles(double) –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) None

C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) None

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

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

setter for poses contained for rms

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

set_metropolis_hastings_mover(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, metropolis_hastings_mover: pyrosetta.rosetta.std.weak_ptr_protocols_canonical_sampling_MetropolisHastingsMover_t) None
If this is a multi-trial move, set the MetropolisHastingsMover to

be used internally.

is_multi_trial()

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

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

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

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

set_preserve_detailed_balance(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, preserve_detailed_balance: bool) None

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

C++: protocols::simple_moves::BackboneMover::set_preserve_detailed_balance(bool) –> void

set_residue_selector(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) None

Set the ResidueSelector that this mover will use.

Clones the input.

C++: protocols::simple_moves::BackboneMover::set_residue_selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

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

Set the ‘type’ string

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

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.

  1. show(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover) -> None

  2. 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.

  1. temperature(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, temperature_in: float) -> None

C++: protocols::simple_moves::BackboneMover::temperature(const double) –> void

  1. 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.

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

Set the ‘type’ string

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

  1. 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: pyrosetta.rosetta.protocols.moves.Mover

ChainSplitMover splits a pose into two chains given a cutpoint. This may be necessary for evaluating a domain interface using classes such as the InterfaceAnalyzerMover

apply(self: pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::simple_moves::ChainSplitMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover, : pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover) pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover

C++: protocols::simple_moves::ChainSplitMover::operator=(const class protocols::simple_moves::ChainSplitMover &) –> class protocols::simple_moves::ChainSplitMover &

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

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

clear_info is called by jd2 before calling apply

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

clone(self: pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover) pyrosetta.rosetta.protocols.moves.Mover

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

create(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

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

fresh_instance(self: pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover) pyrosetta.rosetta.protocols.moves.Mover

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

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

fpd

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

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

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

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) protocols::jobdist::BasicJob

C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) str
A tag is a unique identifier used to identify structures produced

by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

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

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

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

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

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

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

get_name(self: pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover) str

C++: protocols::simple_moves::ChainSplitMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

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

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

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

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t

C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) str

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

info(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.list_std_string_std_allocator_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.

  1. show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None

  2. 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.

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

Set the ‘type’ string

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

  1. 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: pyrosetta.rosetta.protocols.moves.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.

  1. Holds the Pose’s original FoldTree

  2. Applies its ChangeFoldTreeMover

  3. Applies its Main mover

  4. Returns the Pose’s original FoldTree

apply(self: pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover, pose: pyrosetta.rosetta.core.pose.Pose) None
  1. Holds the Pose’s original FoldTree

  1. Applies the ChangeFoldTreeMover

  2. Applies the Main mover

  3. Returns the Pose’s original FoldTree

C++: protocols::simple_moves::ChangeAndResetFoldTreeMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover, : pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover) pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover

C++: protocols::simple_moves::ChangeAndResetFoldTreeMover::operator=(const class protocols::simple_moves::ChangeAndResetFoldTreeMover &) –> class protocols::simple_moves::ChangeAndResetFoldTreeMover &

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

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

clear_info is called by jd2 before calling apply

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

clone(self: pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover) pyrosetta.rosetta.protocols.moves.Mover

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

create(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

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

fresh_instance(self: pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover) pyrosetta.rosetta.protocols.moves.Mover

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

ft_mover(self: pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover) pyrosetta.rosetta.protocols.moves.ChangeFoldTreeMover

Get the ChangeFoldTreeMover

C++: protocols::simple_moves::ChangeAndResetFoldTreeMover::ft_mover() const –> class std::shared_ptr<class protocols::moves::ChangeFoldTreeMover>

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

fpd

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

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

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

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) protocols::jobdist::BasicJob

C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) str
A tag is a unique identifier used to identify structures produced

by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

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

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

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

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

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

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

get_name(self: pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover) str

C++: protocols::simple_moves::ChangeAndResetFoldTreeMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

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

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

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

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t

C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) str

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

info(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.list_std_string_std_allocator_std_string_t

non-const accessor

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

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) float

C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

mover(self: pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover) pyrosetta.rosetta.protocols.moves.Mover

Get the main mover

C++: protocols::simple_moves::ChangeAndResetFoldTreeMover::mover() const –> class std::shared_ptr<class protocols::moves::Mover>

static mover_name() str

C++: protocols::simple_moves::ChangeAndResetFoldTreeMover::mover_name() –> std::string

static name() str

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

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

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

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

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None
Provide citations to the passed CitationCollectionList

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

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

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

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::simple_moves::ChangeAndResetFoldTreeMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() None

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

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

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

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) bool
Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on

each use.

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

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) bool
Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input

pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

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

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

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

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

scorefxn(self: pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover) pyrosetta.rosetta.core.scoring.ScoreFunction

Get the set ScoreFunction

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

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) None

C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) None

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

set_ft_mover(self: pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover, ft_mover: pyrosetta.rosetta.protocols.moves.ChangeFoldTreeMover) None

Set the ChangeFoldTreeMover

C++: protocols::simple_moves::ChangeAndResetFoldTreeMover::set_ft_mover(class std::shared_ptr<class protocols::moves::ChangeFoldTreeMover>) –> void

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

setter for poses contained for rms

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

set_mover(self: pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover, main_mover: pyrosetta.rosetta.protocols.moves.Mover) None

Set the main mover to apply

C++: protocols::simple_moves::ChangeAndResetFoldTreeMover::set_mover(class std::shared_ptr<class protocols::moves::Mover>) –> void

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

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

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

set_scorefxn(self: pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) None
Set the ScoreFunction.

Used ONLY for printing score information before and after the move!!

C++: protocols::simple_moves::ChangeAndResetFoldTreeMover::set_scorefxn(class std::shared_ptr<const class core::scoring::ScoreFunction>) –> void

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

Set the ‘type’ string

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

show(*args, **kwargs)

Overloaded function.

  1. show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None

  2. 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.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMoverCreator

Bases: pyrosetta.rosetta.protocols.moves.MoverCreator

assign(self: pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMoverCreator, : pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMoverCreator) pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMoverCreator

C++: protocols::simple_moves::ChangeAndResetFoldTreeMoverCreator::operator=(const class protocols::simple_moves::ChangeAndResetFoldTreeMoverCreator &) –> class protocols::simple_moves::ChangeAndResetFoldTreeMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMoverCreator) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::simple_moves::ChangeAndResetFoldTreeMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMoverCreator) str

C++: protocols::simple_moves::ChangeAndResetFoldTreeMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMoverCreator, xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::simple_moves::ChangeAndResetFoldTreeMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover

Bases: pyrosetta.rosetta.protocols.simple_moves.FragmentMover

A FragmentMover that applies uniform sampling of fragments

apply(*args, **kwargs)

Overloaded function.

  1. apply(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, : pyrosetta.rosetta.core.pose.Pose, pos: int) -> bool

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

Applies classic fragment insertion based on a FragSet

example:

mover_3mer.apply(pose)

See also:

ClassicFragmentMover Pose ConstantLengthFragSet

C++: protocols::simple_moves::ClassicFragmentMover::apply(class core::pose::Pose &) –> void

apply_at_all_positions(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover, : pyrosetta.rosetta.core.pose.Pose) int

apply at all movemable positions — honors movemap

C++: protocols::simple_moves::FragmentMover::apply_at_all_positions(class core::pose::Pose &) const –> unsigned long

apply_fragment(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, frame: pyrosetta.rosetta.core.fragment.Frame, frag_num: int, movemap: pyrosetta.rosetta.core.kinematics.MoveMap, pose: pyrosetta.rosetta.core.pose.Pose) bool

apply the chosen fragment,

this can be overloaded to change action, e.,g., WobbleMover introduces chain-break before fragment insertion and does ccd-loop closure afterwards

C++: protocols::simple_moves::ClassicFragmentMover::apply_fragment(const class core::fragment::Frame &, unsigned long, const class core::kinematics::MoveMap &, class core::pose::Pose &) const –> bool

assign(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, : pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover) pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover

C++: protocols::simple_moves::ClassicFragmentMover::operator=(const class protocols::simple_moves::ClassicFragmentMover &) –> class protocols::simple_moves::ClassicFragmentMover &

check_ss(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover) bool

accessor

C++: protocols::simple_moves::ClassicFragmentMover::check_ss() const –> bool

choose_fragment(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, : pyrosetta.rosetta.core.fragment.FrameList, : pyrosetta.rosetta.core.pose.Pose, frame_num: int, frag_num: int) bool
given FrameList and pose, this method yields a fragment ( frame_num/ frag_num);

return false if nothing suitable is found

C++: protocols::simple_moves::ClassicFragmentMover::choose_fragment(const class core::fragment::FrameList &, const class core::pose::Pose &, unsigned long &, unsigned long &) const –> bool

choose_window_length(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, : pyrosetta.rosetta.core.pose.Pose, window_length: int) bool
yields a length (window_length) of the fragment window to sample from

( return false, if no suitable length is found )

C++: protocols::simple_moves::ClassicFragmentMover::choose_window_length(const class core::pose::Pose &, unsigned long &) const –> bool

choose_window_start(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, : pyrosetta.rosetta.core.pose.Pose, window_length: int, window_start: int) bool
yields a start position (window_start) for fragment window to sample from

( return false, if nothing suitable is found )

C++: protocols::simple_moves::ClassicFragmentMover::choose_window_start(const class core::pose::Pose &, unsigned long, unsigned long &) const –> bool

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

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

clear_info is called by jd2 before calling apply

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

clone(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover) pyrosetta.rosetta.protocols.moves.Mover

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

create(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

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

define_start_window(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, window_start: int) None

apply fragment at predefined position

C++: protocols::simple_moves::ClassicFragmentMover::define_start_window(unsigned long) –> void

enable_end_bias_check(*args, **kwargs)

Overloaded function.

  1. enable_end_bias_check(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover) -> None

  2. enable_end_bias_check(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, setting: bool) -> None

C++: protocols::simple_moves::ClassicFragmentMover::enable_end_bias_check(bool) –> void

end_bias(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover) float

C++: protocols::simple_moves::ClassicFragmentMover::end_bias() const –> double

end_bias_check(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, : pyrosetta.rosetta.core.pose.Pose, window_start: int) bool

C++: protocols::simple_moves::ClassicFragmentMover::end_bias_check(const class core::pose::Pose &, unsigned long) const –> bool

end_bias_check_enabled(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover) bool

C++: protocols::simple_moves::ClassicFragmentMover::end_bias_check_enabled() const –> bool

fragments(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover) pyrosetta.rosetta.core.fragment.FragSet

accessor to the fragment set

C++: protocols::simple_moves::FragmentMover::fragments() const –> class std::shared_ptr<const class core::fragment::FragSet>

fresh_instance(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover) pyrosetta.rosetta.protocols.moves.Mover

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

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

fpd

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

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

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

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) protocols::jobdist::BasicJob

C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) str
A tag is a unique identifier used to identify structures produced

by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

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

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

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

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

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

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

get_name(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover) str

C++: protocols::simple_moves::ClassicFragmentMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

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

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

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

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t

C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) str

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

info(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.list_std_string_std_allocator_std_string_t

non-const accessor

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

initialize(self: pyrosetta.rosetta.protocols.moves.MoveMapMover, : pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::moves::MoveMapMover::initialize(class core::pose::Pose &) –> void

insert_map(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover) pyrosetta.rosetta.utility.vector1_unsigned_long

C++: protocols::simple_moves::FragmentMover::insert_map() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

insert_size(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover) pyrosetta.rosetta.utility.vector1_unsigned_long

C++: protocols::simple_moves::FragmentMover::insert_size() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) float

C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

movemap(*args, **kwargs)

Overloaded function.

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

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

  1. movemap(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover) -> pyrosetta.rosetta.core.kinematics.MoveMap

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

static name() str

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

on_new_fragments(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover) None

is called from set_fragments()

C++: protocols::simple_moves::ClassicFragmentMover::on_new_fragments() –> void

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

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

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

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None
Provide citations to the passed CitationCollectionList

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

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

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

static register_options() None

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

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

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

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) bool
Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on

each use.

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

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) bool
Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input

pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

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

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

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

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

set_check_ss(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, setting: bool) None

check_ss controls whether fragment insertions are rejected that create short helices (<3) or strands (<2)

C++: protocols::simple_moves::ClassicFragmentMover::set_check_ss(bool) –> void

set_current_job