coupled_moves¶

Bindings for protocols::coupled_moves namespace

class pyrosetta.rosetta.protocols.coupled_moves.CoupledMovesProtocol¶

Bases: Mover

Protocol that combines backbone moves and sidechain moves in a single Monte Carlo step.

CoupledMoves protocol makes use of the simple mover CoupledMover. The CoupledMover apply function makes a single coupled move as follows: (1) Backbone move – As of March 2018, there are three options: backrub, kinematic closure with walking perturber, or kinematic closure with fragment perturber. (2) Side chain move – The three residues at the center of the perturbed backbone are sampled by BoltzmannRotamerMover. (3) Repack – 10A shell around the residues from step 2 is repacked.

CoupledMoves will also move a ligand.

Assumptions: - If there is a ligand, it should be the last residue in the pdb.

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

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

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

compute_ligand_score_bonus(self: pyrosetta.rosetta.protocols.coupled_moves.CoupledMovesProtocol, pose: pyrosetta.rosetta.core.pose.Pose) → float¶: C++: protocols::coupled_moves::CoupledMovesProtocol::compute_ligand_score_bonus(class std::shared_ptr<class core::pose::Pose>) –> double

configure_score_fxn(self: pyrosetta.rosetta.protocols.coupled_moves.CoupledMovesProtocol) → None¶

adds terms for the backrub step to the scorefunction. Used by ctor; also useful when using set_score_fxn

C++: protocols::coupled_moves::CoupledMovesProtocol::configure_score_fxn() –> void

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

exclude_nonclashing_positions(self: pyrosetta.rosetta.protocols.coupled_moves.CoupledMovesProtocol, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::coupled_moves::CoupledMovesProtocol::exclude_nonclashing_positions(class std::shared_ptr<class core::pose::Pose>) –> void

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

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

fpd

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

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

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

get_backbone_mover(self: pyrosetta.rosetta.protocols.coupled_moves.CoupledMovesProtocol) → str¶: C++: protocols::coupled_moves::CoupledMovesProtocol::get_backbone_mover() const –> std::string

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

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

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

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

get_design_positions(self: pyrosetta.rosetta.protocols.coupled_moves.CoupledMovesProtocol) → pyrosetta.rosetta.utility.vector1_unsigned_long¶: C++: protocols::coupled_moves::CoupledMovesProtocol::get_design_positions() const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

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

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

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

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

get_ligand_mode(self: pyrosetta.rosetta.protocols.coupled_moves.CoupledMovesProtocol) → bool¶: C++: protocols::coupled_moves::CoupledMovesProtocol::get_ligand_mode() const –> bool

get_ligand_prob(self: pyrosetta.rosetta.protocols.coupled_moves.CoupledMovesProtocol) → float¶: C++: protocols::coupled_moves::CoupledMovesProtocol::get_ligand_prob() const –> double

get_ligand_resnums(self: pyrosetta.rosetta.protocols.coupled_moves.CoupledMovesProtocol) → pyrosetta.rosetta.utility.vector1_unsigned_long¶: C++: protocols::coupled_moves::CoupledMovesProtocol::get_ligand_resnums() const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

get_ligand_weight(self: pyrosetta.rosetta.protocols.coupled_moves.CoupledMovesProtocol) → float¶: C++: protocols::coupled_moves::CoupledMovesProtocol::get_ligand_weight() const –> double

get_loop_size(self: pyrosetta.rosetta.protocols.coupled_moves.CoupledMovesProtocol) → int¶: C++: protocols::coupled_moves::CoupledMovesProtocol::get_loop_size() const –> unsigned long

get_move_positions(self: pyrosetta.rosetta.protocols.coupled_moves.CoupledMovesProtocol) → pyrosetta.rosetta.utility.vector1_unsigned_long¶: C++: protocols::coupled_moves::CoupledMovesProtocol::get_move_positions() const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

get_move_type(self: pyrosetta.rosetta.protocols.coupled_moves.CoupledMovesProtocol) → str¶: C++: protocols::coupled_moves::CoupledMovesProtocol::get_move_type() const –> std::string

get_name(self: pyrosetta.rosetta.protocols.coupled_moves.CoupledMovesProtocol) → str¶: C++: protocols::coupled_moves::CoupledMovesProtocol::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_ntrials(self: pyrosetta.rosetta.protocols.coupled_moves.CoupledMovesProtocol) → int¶: C++: protocols::coupled_moves::CoupledMovesProtocol::get_ntrials() –> unsigned long

get_number_ligands(self: pyrosetta.rosetta.protocols.coupled_moves.CoupledMovesProtocol) → int¶: C++: protocols::coupled_moves::CoupledMovesProtocol::get_number_ligands() const –> unsigned long

get_perturber(self: pyrosetta.rosetta.protocols.coupled_moves.CoupledMovesProtocol) → protocols::kinematic_closure::perturbers::Perturber¶: C++: protocols::coupled_moves::CoupledMovesProtocol::get_perturber() const –> class std::shared_ptr<class protocols::kinematic_closure::perturbers::Perturber>

get_repack_neighborhood(self: pyrosetta.rosetta.protocols.coupled_moves.CoupledMovesProtocol) → bool¶: C++: protocols::coupled_moves::CoupledMovesProtocol::get_repack_neighborhood() const –> const bool &

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

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

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

get_unique_sequences(self: pyrosetta.rosetta.protocols.coupled_moves.CoupledMovesProtocol) → pyrosetta.rosetta.std.map_std_string_double¶: C++: protocols::coupled_moves::CoupledMovesProtocol::get_unique_sequences() const –> class std::map<std::string, double, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, double> > >

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

non-const accessor

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

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

static mover_name() → str¶: C++: protocols::coupled_moves::CoupledMovesProtocol::mover_name() –> std::string

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

parse_my_tag(self: pyrosetta.rosetta.protocols.coupled_moves.CoupledMovesProtocol, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶

parse_my_tag

C++: protocols::coupled_moves::CoupledMovesProtocol::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::coupled_moves::CoupledMovesProtocol::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None¶

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

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

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

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

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

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

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

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

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

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

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

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

set_backbone_mover(self: pyrosetta.rosetta.protocols.coupled_moves.CoupledMovesProtocol, backbone_mover: str) → None¶: C++: protocols::coupled_moves::CoupledMovesProtocol::set_backbone_mover(const std::string &) –> void

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

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

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

setter for poses contained for rms

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

set_ligand_mode(self: pyrosetta.rosetta.protocols.coupled_moves.CoupledMovesProtocol, ligand_mode: bool) → None¶: C++: protocols::coupled_moves::CoupledMovesProtocol::set_ligand_mode(const bool) –> void

set_ligand_prob(self: pyrosetta.rosetta.protocols.coupled_moves.CoupledMovesProtocol, ligand_prob: float) → None¶: C++: protocols::coupled_moves::CoupledMovesProtocol::set_ligand_prob(const double) –> void

set_ligand_weight(self: pyrosetta.rosetta.protocols.coupled_moves.CoupledMovesProtocol, ligand_weight: float) → None¶: C++: protocols::coupled_moves::CoupledMovesProtocol::set_ligand_weight(const double) –> void

set_loop_size(self: pyrosetta.rosetta.protocols.coupled_moves.CoupledMovesProtocol, loop_size: int) → None¶: C++: protocols::coupled_moves::CoupledMovesProtocol::set_loop_size(unsigned long) –> void

set_main_task_factory(self: pyrosetta.rosetta.protocols.coupled_moves.CoupledMovesProtocol, tf: pyrosetta.rosetta.core.pack.task.TaskFactory) → None¶

set the task factory. Note that the ctor sets InitializeFromCommandline plus either ReadResfile or RestrictToRepacking.

C++: protocols::coupled_moves::CoupledMovesProtocol::set_main_task_factory(const class std::shared_ptr<class core::pack::task::TaskFactory>) –> 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_ntrials(self: pyrosetta.rosetta.protocols.coupled_moves.CoupledMovesProtocol, ntrials: int) → None¶: C++: protocols::coupled_moves::CoupledMovesProtocol::set_ntrials(unsigned long) –> void

set_number_ligands(self: pyrosetta.rosetta.protocols.coupled_moves.CoupledMovesProtocol, number_ligands: int) → None¶: C++: protocols::coupled_moves::CoupledMovesProtocol::set_number_ligands(const unsigned long) –> void

set_perturber(self: pyrosetta.rosetta.protocols.coupled_moves.CoupledMovesProtocol, perturber: protocols::kinematic_closure::perturbers::Perturber) → None¶: C++: protocols::coupled_moves::CoupledMovesProtocol::set_perturber(class std::shared_ptr<class protocols::kinematic_closure::perturbers::Perturber>) –> void

set_repack_neighborhood(self: pyrosetta.rosetta.protocols.coupled_moves.CoupledMovesProtocol, repack_neighborhood: bool) → None¶: C++: protocols::coupled_moves::CoupledMovesProtocol::set_repack_neighborhood(bool) –> void

set_score_fxn(self: pyrosetta.rosetta.protocols.coupled_moves.CoupledMovesProtocol, sf: pyrosetta.rosetta.core.scoring.ScoreFunction) → None¶

set the score function. NOTICE: you will want to also use the companion configure_score_fxn afterwards to add backrub terms to the SF, if you did not do so yourself!

C++: protocols::coupled_moves::CoupledMovesProtocol::set_score_fxn(const class std::shared_ptr<class core::scoring::ScoreFunction>) –> void

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

Set the ‘type’ string

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

setup_coupled_mover(self: pyrosetta.rosetta.protocols.coupled_moves.CoupledMovesProtocol, task: pyrosetta.rosetta.core.pack.task.PackerTask, pose_copy: pyrosetta.rosetta.core.pose.Pose, coupled_mover: protocols::simple_moves::CoupledMover) → protocols::simple_moves::CoupledMover¶: C++: protocols::coupled_moves::CoupledMovesProtocol::setup_coupled_mover(class std::shared_ptr<class core::pack::task::PackerTask>, class std::shared_ptr<class core::pose::Pose>, class std::shared_ptr<class protocols::simple_moves::CoupledMover>) –> class std::shared_ptr<class protocols::simple_moves::CoupledMover>

setup_coupled_mover_for_ligand(self: pyrosetta.rosetta.protocols.coupled_moves.CoupledMovesProtocol, pose_copy: pyrosetta.rosetta.core.pose.Pose, task: pyrosetta.rosetta.core.pack.task.PackerTask, coupled_mover: protocols::simple_moves::CoupledMover) → protocols::simple_moves::CoupledMover¶: C++: protocols::coupled_moves::CoupledMovesProtocol::setup_coupled_mover_for_ligand(class std::shared_ptr<class core::pose::Pose>, class std::shared_ptr<class core::pack::task::PackerTask>, class std::shared_ptr<class protocols::simple_moves::CoupledMover>) –> class std::shared_ptr<class protocols::simple_moves::CoupledMover>

setup_move_and_design_positions(self: pyrosetta.rosetta.protocols.coupled_moves.CoupledMovesProtocol, task: pyrosetta.rosetta.core.pack.task.PackerTask, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::coupled_moves::CoupledMovesProtocol::setup_move_and_design_positions(class std::shared_ptr<const class core::pack::task::PackerTask>, class std::shared_ptr<const class core::pose::Pose>) –> void

setup_move_type(self: pyrosetta.rosetta.protocols.coupled_moves.CoupledMovesProtocol, move_prob: float) → None¶: C++: protocols::coupled_moves::CoupledMovesProtocol::setup_move_type(const double) –> void

setup_resnum(self: pyrosetta.rosetta.protocols.coupled_moves.CoupledMovesProtocol, move_prob: float, coupled_mover: protocols::simple_moves::CoupledMover, pose_copy: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::coupled_moves::CoupledMovesProtocol::setup_resnum(const double, class std::shared_ptr<class protocols::simple_moves::CoupledMover>, class std::shared_ptr<class core::pose::Pose>) –> void

show(*args, **kwargs)¶

Overloaded function.

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

Outputs details about the Mover, including current settings.

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

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

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

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

type(*args, **kwargs)¶

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

write_info_to_log(self: pyrosetta.rosetta.protocols.coupled_moves.CoupledMovesProtocol, pose_copy: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::coupled_moves::CoupledMovesProtocol::write_info_to_log(class std::shared_ptr<class core::pose::Pose>) –> void

class pyrosetta.rosetta.protocols.coupled_moves.CoupledMovesProtocolCreator¶

Bases: MoverCreator

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

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

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

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