idealize¶
Bindings for protocols::idealize namespace
- class pyrosetta.rosetta.protocols.idealize.IdealizeMover¶
Bases:
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.
constraints_only(self: pyrosetta.rosetta.protocols.idealize.IdealizeMover) -> bool
C++: protocols::idealize::IdealizeMover::constraints_only() const –> bool
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.
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>
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.
impose_constraints(self: pyrosetta.rosetta.protocols.idealize.IdealizeMover, i: bool) -> None
C++: protocols::idealize::IdealizeMover::impose_constraints(const bool) –> void
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_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.
show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None
Outputs details about the Mover, including current settings.
C++: protocols::moves::Mover::show(std::ostream &) const –> void
- test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
- : Unit test support function. Apply one move to a given pose.
Allows extra test specific functions to be called before applying
C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void
- type(*args, **kwargs)¶
Overloaded function.
type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None
Set the ‘type’ string
C++: protocols::moves::Mover::type(const std::string &) –> void
type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str
Get the set ‘type’ string
C++: protocols::moves::Mover::type() const –> const std::string &
- class pyrosetta.rosetta.protocols.idealize.IdealizeMoverCreator¶
Bases:
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
- pyrosetta.rosetta.protocols.idealize.basic_idealize(*args, **kwargs)¶
Overloaded function.
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
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
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