idealize

Bindings for protocols::idealize namespace

class pyrosetta.rosetta.protocols.idealize.IdealizeMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

Mover class for transforming a Pose to ideal bonds of the given Pose. The idea is that this Mover stochastically picks a move-able position, forces that position into ideal geometry, and tries to use minimization to bring the coordinates back to very near their starting points.

apply(self: pyrosetta.rosetta.protocols.idealize.IdealizeMover, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::idealize::IdealizeMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.idealize.IdealizeMover, : pyrosetta.rosetta.protocols.idealize.IdealizeMover) pyrosetta.rosetta.protocols.idealize.IdealizeMover

C++: protocols::idealize::IdealizeMover::operator=(const class protocols::idealize::IdealizeMover &) –> class protocols::idealize::IdealizeMover &

atom_pair_constraint_weight(self: pyrosetta.rosetta.protocols.idealize.IdealizeMover, setting: float) pyrosetta.rosetta.protocols.idealize.IdealizeMover

C++: protocols::idealize::IdealizeMover::atom_pair_constraint_weight(const double) –> class protocols::idealize::IdealizeMover &

chainbreaks(self: pyrosetta.rosetta.protocols.idealize.IdealizeMover, setting: bool) pyrosetta.rosetta.protocols.idealize.IdealizeMover

C++: protocols::idealize::IdealizeMover::chainbreaks(const bool) –> class protocols::idealize::IdealizeMover &

cis_omega(self: pyrosetta.rosetta.protocols.idealize.IdealizeMover, setting: bool) pyrosetta.rosetta.protocols.idealize.IdealizeMover

C++: protocols::idealize::IdealizeMover::cis_omega(const bool) –> class protocols::idealize::IdealizeMover &

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.idealize.IdealizeMover) pyrosetta.rosetta.protocols.moves.Mover

clone has to be overridden only if clone invocation is expected.

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

constraints_only(*args, **kwargs)

Overloaded function.

  1. constraints_only(self: pyrosetta.rosetta.protocols.idealize.IdealizeMover) -> bool

C++: protocols::idealize::IdealizeMover::constraints_only() const –> bool

  1. constraints_only(self: pyrosetta.rosetta.protocols.idealize.IdealizeMover, c: bool) -> None

C++: protocols::idealize::IdealizeMover::constraints_only(const bool) –> void

coordinate_constraint_weight(self: pyrosetta.rosetta.protocols.idealize.IdealizeMover, setting: float) pyrosetta.rosetta.protocols.idealize.IdealizeMover

C++: protocols::idealize::IdealizeMover::coordinate_constraint_weight(const double) –> class protocols::idealize::IdealizeMover &

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>

fast(self: pyrosetta.rosetta.protocols.idealize.IdealizeMover, setting: bool) pyrosetta.rosetta.protocols.idealize.IdealizeMover

C++: protocols::idealize::IdealizeMover::fast(const bool) –> class protocols::idealize::IdealizeMover &

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

C++: protocols::idealize::IdealizeMover::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.idealize.IdealizeMover) str

C++: protocols::idealize::IdealizeMover::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

ignore_residues_in_csts(*args, **kwargs)

Overloaded function.

  1. ignore_residues_in_csts(self: pyrosetta.rosetta.protocols.idealize.IdealizeMover) -> pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

C++: protocols::idealize::IdealizeMover::ignore_residues_in_csts() const –> class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>

  1. ignore_residues_in_csts(self: pyrosetta.rosetta.protocols.idealize.IdealizeMover, i: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) -> None

C++: protocols::idealize::IdealizeMover::ignore_residues_in_csts(const class std::shared_ptr<const class core::select::residue_selector::ResidueSelector> &) –> void

impose_constraints(*args, **kwargs)

Overloaded function.

  1. impose_constraints(self: pyrosetta.rosetta.protocols.idealize.IdealizeMover, i: bool) -> None

C++: protocols::idealize::IdealizeMover::impose_constraints(const bool) –> void

  1. impose_constraints(self: pyrosetta.rosetta.protocols.idealize.IdealizeMover) -> bool

C++: protocols::idealize::IdealizeMover::impose_constraints() const –> bool

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::idealize::IdealizeMover::mover_name() –> std::string

static name() str

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

parse_my_tag(self: pyrosetta.rosetta.protocols.idealize.IdealizeMover, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None

C++: protocols::idealize::IdealizeMover::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::idealize::IdealizeMover::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

report_CA_rmsd(self: pyrosetta.rosetta.protocols.idealize.IdealizeMover, setting: bool) pyrosetta.rosetta.protocols.idealize.IdealizeMover

C++: protocols::idealize::IdealizeMover::report_CA_rmsd(const bool) –> class protocols::idealize::IdealizeMover &

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_pos_list(self: pyrosetta.rosetta.protocols.idealize.IdealizeMover, pos_list: pyrosetta.rosetta.utility.vector1_unsigned_long) None

Sets the list of residue positions to idealize.

C++: protocols::idealize::IdealizeMover::set_pos_list(class utility::vector1<unsigned long, class std::allocator<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.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.idealize.IdealizeMoverCreator

Bases: pyrosetta.rosetta.protocols.moves.MoverCreator

assign(self: pyrosetta.rosetta.protocols.idealize.IdealizeMoverCreator, : pyrosetta.rosetta.protocols.idealize.IdealizeMoverCreator) pyrosetta.rosetta.protocols.idealize.IdealizeMoverCreator

C++: protocols::idealize::IdealizeMoverCreator::operator=(const class protocols::idealize::IdealizeMoverCreator &) –> class protocols::idealize::IdealizeMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.idealize.IdealizeMoverCreator) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::idealize::IdealizeMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.idealize.IdealizeMoverCreator) str

C++: protocols::idealize::IdealizeMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.idealize.IdealizeMoverCreator, xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::idealize::IdealizeMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

pyrosetta.rosetta.protocols.idealize.basic_idealize(*args, **kwargs)

Overloaded function.

  1. basic_idealize(pose: pyrosetta.rosetta.core.pose.Pose, pos_list: pyrosetta.rosetta.utility.vector1_unsigned_long, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, fast: bool) -> None

  2. basic_idealize(pose: pyrosetta.rosetta.core.pose.Pose, pos_list: pyrosetta.rosetta.utility.vector1_unsigned_long, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, fast: bool, chainbreaks: bool) -> None

  3. basic_idealize(pose: pyrosetta.rosetta.core.pose.Pose, pos_list: pyrosetta.rosetta.utility.vector1_unsigned_long, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, fast: bool, chainbreaks: bool, cis_omega: bool) -> None

C++: protocols::idealize::basic_idealize(class core::pose::Pose &, class utility::vector1<unsigned long, class std::allocator<unsigned long> >, const class core::scoring::ScoreFunction &, const bool, const bool, const bool) –> void

pyrosetta.rosetta.protocols.idealize.dihedral_distance(pose1: pyrosetta.rosetta.core.pose.Pose, pose2: pyrosetta.rosetta.core.pose.Pose, use_pos: pyrosetta.rosetta.utility.vector1_bool, avg_bb_angle_dev: float, max_bb_angle_dev: float, avg_chi_angle_dev: float, max_chi_angle_dev: float) None

C++: protocols::idealize::dihedral_distance(const class core::pose::Pose &, const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, double &, double &, double &, double &) –> void