rbsegment_relax¶
Bindings for protocols::rbsegment_relax namespace
- class pyrosetta.rosetta.protocols.rbsegment_relax.AutoRBMover¶
Bases:
Mover
- apply(self: pyrosetta.rosetta.protocols.rbsegment_relax.AutoRBMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::rbsegment_relax::AutoRBMover::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.rbsegment_relax.AutoRBMover, : pyrosetta.rosetta.protocols.rbsegment_relax.AutoRBMover) pyrosetta.rosetta.protocols.rbsegment_relax.AutoRBMover ¶
C++: protocols::rbsegment_relax::AutoRBMover::operator=(const class protocols::rbsegment_relax::AutoRBMover &) –> class protocols::rbsegment_relax::AutoRBMover &
- 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>
- 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.rbsegment_relax.AutoRBMover) str ¶
C++: protocols::rbsegment_relax::AutoRBMover::get_name() const –> std::string
- get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose ¶
C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>
- get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>
- get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t ¶
C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>
- get_type(self: pyrosetta.rosetta.protocols.moves.Mover) str ¶
C++: protocols::moves::Mover::get_type() const –> std::string
- info(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.list_std_string_t ¶
non-const accessor
C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &
- last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) float ¶
C++: protocols::moves::Mover::last_proposal_density_ratio() –> double
- static name() str ¶
C++: protocols::moves::Mover::name() –> std::string
- parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None ¶
Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.
C++: protocols::moves::Mover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None ¶
- Provide citations to the passed CitationCollectionList
Subclasses should add the info for themselves and any other classes they use.
The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.
C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void
- static register_options() None ¶
Overload this static method if you access options within the mover.
These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.
C++: protocols::moves::Mover::register_options() –> void
- reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) bool ¶
- Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on
each use.
C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool
- reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) bool ¶
- Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input
pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).
C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool
- reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) None ¶
resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.
C++: protocols::moves::Mover::reset_status() –> void
- set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) None ¶
C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void
- set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) None ¶
C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void
- set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
setter for poses contained for rms
C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void
- set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe
C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void
- set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) None ¶
Set the ‘type’ string
C++: protocols::moves::Mover::set_type(const std::string &) –> void
- setup_topology(self: pyrosetta.rosetta.protocols.rbsegment_relax.AutoRBMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::rbsegment_relax::AutoRBMover::setup_topology(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 &
- class pyrosetta.rosetta.protocols.rbsegment_relax.ConfChangeMover¶
Bases:
CartesianHybridize
- add_dihedral_csts(self: pyrosetta.rosetta.protocols.rbsegment_relax.ConfChangeMover, pose: pyrosetta.rosetta.core.pose.Pose, original_pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::rbsegment_relax::ConfChangeMover::add_dihedral_csts(class core::pose::Pose &, const class core::pose::Pose &) –> void
- add_dihedral_csts_to_rb(self: pyrosetta.rosetta.protocols.rbsegment_relax.ConfChangeMover, pose: pyrosetta.rosetta.core.pose.Pose, original_pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::rbsegment_relax::ConfChangeMover::add_dihedral_csts_to_rb(class core::pose::Pose &, const class core::pose::Pose &) –> void
- apply(self: pyrosetta.rosetta.protocols.rbsegment_relax.ConfChangeMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::rbsegment_relax::ConfChangeMover::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.hybridization.CartesianHybridize, : pyrosetta.rosetta.protocols.hybridization.CartesianHybridize) pyrosetta.rosetta.protocols.hybridization.CartesianHybridize ¶
C++: protocols::hybridization::CartesianHybridize::operator=(const class protocols::hybridization::CartesianHybridize &) –> class protocols::hybridization::CartesianHybridize &
- check_gaps(self: pyrosetta.rosetta.protocols.rbsegment_relax.ConfChangeMover, pose: pyrosetta.rosetta.core.pose.Pose) bool ¶
C++: protocols::rbsegment_relax::ConfChangeMover::check_gaps(class core::pose::Pose &) –> bool
- check_or_create_fragments(self: pyrosetta.rosetta.protocols.rbsegment_relax.ConfChangeMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::rbsegment_relax::ConfChangeMover::check_or_create_fragments(class core::pose::Pose &) –> 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.rbsegment_relax.ConfChangeMover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::rbsegment_relax::ConfChangeMover::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.hybridization.CartesianHybridize) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::hybridization::CartesianHybridize::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>
- get_additional_output(self: pyrosetta.rosetta.protocols.rbsegment_relax.ConfChangeMover) pyrosetta.rosetta.core.pose.Pose ¶
C++: protocols::rbsegment_relax::ConfChangeMover::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.hybridization.CartesianHybridize) str ¶
C++: protocols::hybridization::CartesianHybridize::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_residues_in_rbsegment(self: pyrosetta.rosetta.protocols.rbsegment_relax.ConfChangeMover, rbseg: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment) pyrosetta.rosetta.std.set_unsigned_long_t ¶
C++: protocols::rbsegment_relax::ConfChangeMover::get_residues_in_rbsegment(const class protocols::rbsegment_relax::RBSegment &) const –> class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> >
- get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>
- get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t ¶
C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>
- get_type(self: pyrosetta.rosetta.protocols.moves.Mover) str ¶
C++: protocols::moves::Mover::get_type() const –> std::string
- info(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.list_std_string_t ¶
non-const accessor
C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &
- init(self: pyrosetta.rosetta.protocols.hybridization.CartesianHybridize) None ¶
C++: protocols::hybridization::CartesianHybridize::init() –> void
- 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::rbsegment_relax::ConfChangeMover::mover_name() –> std::string
- multi_rb(self: pyrosetta.rosetta.protocols.rbsegment_relax.ConfChangeMover, pose: pyrosetta.rosetta.core.pose.Pose, multiple_sses: bool) pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment ¶
C++: protocols::rbsegment_relax::ConfChangeMover::multi_rb(class core::pose::Pose &, const bool &) –> class protocols::rbsegment_relax::RBSegment
- 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::rbsegment_relax::ConfChangeMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void
- recursive_residues_from_rbsegs(self: pyrosetta.rosetta.protocols.rbsegment_relax.ConfChangeMover, rbseg: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment, residues: pyrosetta.rosetta.std.set_unsigned_long_t) None ¶
C++: protocols::rbsegment_relax::ConfChangeMover::recursive_residues_from_rbsegs(const class protocols::rbsegment_relax::RBSegment &, class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> > &) 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_cartfrag_overlap(self: pyrosetta.rosetta.protocols.hybridization.CartesianHybridize, cartfrag_overlap_in: int) None ¶
C++: protocols::hybridization::CartesianHybridize::set_cartfrag_overlap(unsigned long) –> void
- set_cenrot(self: pyrosetta.rosetta.protocols.hybridization.CartesianHybridize, cenrot_in: bool) None ¶
C++: protocols::hybridization::CartesianHybridize::set_cenrot(bool) –> 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_fragment_probs(self: pyrosetta.rosetta.protocols.hybridization.CartesianHybridize, prob: float, randprob: float) None ¶
C++: protocols::hybridization::CartesianHybridize::set_fragment_probs(double, double) –> void
- set_increase_cycles(self: pyrosetta.rosetta.protocols.hybridization.CartesianHybridize, increase_cycles_in: float) None ¶
C++: protocols::hybridization::CartesianHybridize::set_increase_cycles(double) –> 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_linmin_only(self: pyrosetta.rosetta.protocols.hybridization.CartesianHybridize, linmin_only_in: bool) None ¶
C++: protocols::hybridization::CartesianHybridize::set_linmin_only(bool) –> void
- set_max_insertion(self: pyrosetta.rosetta.protocols.hybridization.CartesianHybridize, max_in: int) None ¶
C++: protocols::hybridization::CartesianHybridize::set_max_insertion(int) –> void
- set_min_scorefunction(self: pyrosetta.rosetta.protocols.hybridization.CartesianHybridize, scorefxn_in: pyrosetta.rosetta.core.scoring.ScoreFunction) None ¶
C++: protocols::hybridization::CartesianHybridize::set_min_scorefunction(class std::shared_ptr<class core::scoring::ScoreFunction>) –> 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_no_global_frame(self: pyrosetta.rosetta.protocols.hybridization.CartesianHybridize, no_global_frame_in: bool) None ¶
C++: protocols::hybridization::CartesianHybridize::set_no_global_frame(bool) –> void
- set_pack_scorefunction(self: pyrosetta.rosetta.protocols.hybridization.CartesianHybridize, scorefxn_in: pyrosetta.rosetta.core.scoring.ScoreFunction) None ¶
C++: protocols::hybridization::CartesianHybridize::set_pack_scorefunction(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void
- set_per_residue_controls(self: pyrosetta.rosetta.protocols.hybridization.CartesianHybridize, residue_sample_template_in: pyrosetta.rosetta.utility.vector1_bool, residue_sample_abinitio_in: pyrosetta.rosetta.utility.vector1_bool) None ¶
C++: protocols::hybridization::CartesianHybridize::set_per_residue_controls(const class utility::vector1<bool, class std::allocator<bool> > &, const class utility::vector1<bool, class std::allocator<bool> > &) –> void
- set_scorefunction(self: pyrosetta.rosetta.protocols.hybridization.CartesianHybridize, scorefxn_in: pyrosetta.rosetta.core.scoring.ScoreFunction) None ¶
C++: protocols::hybridization::CartesianHybridize::set_scorefunction(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void
- set_seqfrags_only(self: pyrosetta.rosetta.protocols.hybridization.CartesianHybridize, seqfrags_only_in: bool) None ¶
C++: protocols::hybridization::CartesianHybridize::set_seqfrags_only(bool) –> void
- set_skip_long_min(self: pyrosetta.rosetta.protocols.hybridization.CartesianHybridize, skip_long_min_in: bool) None ¶
C++: protocols::hybridization::CartesianHybridize::set_skip_long_min(bool) –> void
- set_temperature(self: pyrosetta.rosetta.protocols.hybridization.CartesianHybridize, temp_in: float) None ¶
C++: protocols::hybridization::CartesianHybridize::set_temperature(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
- 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
- sse_contact_strength(self: pyrosetta.rosetta.protocols.rbsegment_relax.ConfChangeMover, pose: pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t ¶
C++: protocols::rbsegment_relax::ConfChangeMover::sse_contact_strength(class core::pose::Pose &) const –> class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > >
- stage1(self: pyrosetta.rosetta.protocols.rbsegment_relax.ConfChangeMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::rbsegment_relax::ConfChangeMover::stage1(class core::pose::Pose &) –> void
- stage1_pose_setup(self: pyrosetta.rosetta.protocols.rbsegment_relax.ConfChangeMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::rbsegment_relax::ConfChangeMover::stage1_pose_setup(class core::pose::Pose &) –> void
- stage2(self: pyrosetta.rosetta.protocols.rbsegment_relax.ConfChangeMover, pose: pyrosetta.rosetta.core.pose.Pose, original_pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::rbsegment_relax::ConfChangeMover::stage2(class core::pose::Pose &, const class core::pose::Pose &) –> 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.rbsegment_relax.ConfChangeMoverCreator¶
Bases:
MoverCreator
- assign(self: pyrosetta.rosetta.protocols.rbsegment_relax.ConfChangeMoverCreator, : pyrosetta.rosetta.protocols.rbsegment_relax.ConfChangeMoverCreator) pyrosetta.rosetta.protocols.rbsegment_relax.ConfChangeMoverCreator ¶
C++: protocols::rbsegment_relax::ConfChangeMoverCreator::operator=(const class protocols::rbsegment_relax::ConfChangeMoverCreator &) –> class protocols::rbsegment_relax::ConfChangeMoverCreator &
- create_mover(self: pyrosetta.rosetta.protocols.rbsegment_relax.ConfChangeMoverCreator) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::rbsegment_relax::ConfChangeMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>
- keyname(self: pyrosetta.rosetta.protocols.rbsegment_relax.ConfChangeMoverCreator) str ¶
C++: protocols::rbsegment_relax::ConfChangeMoverCreator::keyname() const –> std::string
- class pyrosetta.rosetta.protocols.rbsegment_relax.FragInsertAndAlignMover¶
Bases:
Mover
- Performs a rigid-body movement on a segment of a protein
Derived classes must implement ‘getCoordinateTransform’ and ‘apply’
- apply(*args, **kwargs)¶
Overloaded function.
apply(self: pyrosetta.rosetta.protocols.rbsegment_relax.FragInsertAndAlignMover, pose: pyrosetta.rosetta.core.pose.Pose) -> None
insert one RB fragment + realign
C++: protocols::rbsegment_relax::FragInsertAndAlignMover::apply(class core::pose::Pose &) –> void
apply(self: pyrosetta.rosetta.protocols.rbsegment_relax.FragInsertAndAlignMover, pose: pyrosetta.rosetta.core.pose.Pose, idx: int) -> None
apply(self: pyrosetta.rosetta.protocols.rbsegment_relax.FragInsertAndAlignMover, pose: pyrosetta.rosetta.core.pose.Pose, idx: int, idealize: bool) -> None
insert one RB fragment + realign
C++: protocols::rbsegment_relax::FragInsertAndAlignMover::apply(class core::pose::Pose &, int, bool) –> void
- assign(self: pyrosetta.rosetta.protocols.rbsegment_relax.FragInsertAndAlignMover, : pyrosetta.rosetta.protocols.rbsegment_relax.FragInsertAndAlignMover) pyrosetta.rosetta.protocols.rbsegment_relax.FragInsertAndAlignMover ¶
C++: protocols::rbsegment_relax::FragInsertAndAlignMover::operator=(const class protocols::rbsegment_relax::FragInsertAndAlignMover &) –> class protocols::rbsegment_relax::FragInsertAndAlignMover &
- bootstrapCATrace(self: pyrosetta.rosetta.protocols.rbsegment_relax.FragInsertAndAlignMover, start_pose: pyrosetta.rosetta.core.pose.Pose) None ¶
take a CA-only pose and insert idealized fragments close to the trace
C++: protocols::rbsegment_relax::FragInsertAndAlignMover::bootstrapCATrace(class core::pose::Pose &) –> 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.rbsegment_relax.FragInsertAndAlignMover) pyrosetta.rosetta.protocols.moves.Mover ¶
clone this object
C++: protocols::rbsegment_relax::FragInsertAndAlignMover::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.rbsegment_relax.FragInsertAndAlignMover) str ¶
C++: protocols::rbsegment_relax::FragInsertAndAlignMover::get_name() const –> std::string
- get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose ¶
C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>
- get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>
- get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t ¶
C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>
- get_type(self: pyrosetta.rosetta.protocols.moves.Mover) str ¶
C++: protocols::moves::Mover::get_type() const –> std::string
- info(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.list_std_string_t ¶
non-const accessor
C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &
- last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) float ¶
C++: protocols::moves::Mover::last_proposal_density_ratio() –> double
- static name() str ¶
C++: protocols::moves::Mover::name() –> std::string
- parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None ¶
Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.
C++: protocols::moves::Mover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None ¶
- Provide citations to the passed CitationCollectionList
Subclasses should add the info for themselves and any other classes they use.
The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.
C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void
- static register_options() None ¶
Overload this static method if you access options within the mover.
These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.
C++: protocols::moves::Mover::register_options() –> void
- reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) bool ¶
- Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on
each use.
C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool
- reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) bool ¶
- Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input
pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).
C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool
- reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) None ¶
resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.
C++: protocols::moves::Mover::reset_status() –> void
- set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) None ¶
C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void
- set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) None ¶
C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void
- set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
setter for poses contained for rms
C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void
- set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe
C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void
- set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) None ¶
Set the ‘type’ string
C++: protocols::moves::Mover::set_type(const std::string &) –> void
- show(*args, **kwargs)¶
Overloaded function.
show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None
Outputs details about the Mover, including current settings.
C++: protocols::moves::Mover::show(std::ostream &) const –> void
- test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
- : Unit test support function. Apply one move to a given pose.
Allows extra test specific functions to be called before applying
C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void
- type(*args, **kwargs)¶
Overloaded function.
type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None
Set the ‘type’ string
C++: protocols::moves::Mover::type(const std::string &) –> void
type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str
Get the set ‘type’ string
C++: protocols::moves::Mover::type() const –> const std::string &
- class pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover¶
Bases:
RBSegmentMover
Generic random segment mover
- apply(self: pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
Randomly perturb the segment
C++: protocols::rbsegment_relax::GaussianRBSegmentMover::apply(class core::pose::Pose &) –> void
- applyRotation(*args, **kwargs)¶
Overloaded function.
applyRotation(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover, pose: pyrosetta.rosetta.core.pose.Pose, alpha: float, beta: float, gamma: float) -> None
Apply an arbitrary rotation specified by Euler angles (in degrees!)
C++: protocols::rbsegment_relax::RBSegmentMover::applyRotation(class core::pose::Pose &, double, double, double) –> void
applyRotation(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover, pose: pyrosetta.rosetta.core.pose.Pose, rotation: pyrosetta.rosetta.numeric.xyzMatrix_double_t) -> None
Apply an arbitrary rotation specified by a rotation matrix
C++: protocols::rbsegment_relax::RBSegmentMover::applyRotation(class core::pose::Pose &, class numeric::xyzMatrix<double>) –> void
- applySpin(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover, pose: pyrosetta.rosetta.core.pose.Pose, rotationAxis: pyrosetta.rosetta.numeric.xyzVector_double_t, degrees: float) None ¶
Apply a spin of the specified angle (in degrees) about arbitrary axis
C++: protocols::rbsegment_relax::RBSegmentMover::applySpin(class core::pose::Pose &, class numeric::xyzVector<double>, double) –> void
- applyTransformation(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover, pose: pyrosetta.rosetta.core.pose.Pose, rotation: pyrosetta.rosetta.numeric.xyzMatrix_double_t, translation: pyrosetta.rosetta.numeric.xyzVector_double_t) None ¶
Apply a rotation followed by a translation (does not recompute coordinate transformation between the two!)
C++: protocols::rbsegment_relax::RBSegmentMover::applyTransformation(class core::pose::Pose &, class numeric::xyzMatrix<double>, class numeric::xyzVector<double>) –> void
- applyTranslation(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover, pose: pyrosetta.rosetta.core.pose.Pose, translation: pyrosetta.rosetta.numeric.xyzVector_double_t) None ¶
Apply an arbitrary translation
C++: protocols::rbsegment_relax::RBSegmentMover::applyTranslation(class core::pose::Pose &, class numeric::xyzVector<double>) –> void
- assign(self: pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover, : pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover) pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover ¶
C++: protocols::rbsegment_relax::GaussianRBSegmentMover::operator=(const class protocols::rbsegment_relax::GaussianRBSegmentMover &) –> class protocols::rbsegment_relax::GaussianRBSegmentMover &
- 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.rbsegment_relax.GaussianRBSegmentMover) pyrosetta.rosetta.protocols.moves.Mover ¶
clone this object
C++: protocols::rbsegment_relax::GaussianRBSegmentMover::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>
- getCoordinateTransformation(self: pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover, pose: pyrosetta.rosetta.core.pose.Pose, rotationCenter: pyrosetta.rosetta.numeric.xyzVector_double_t, coordinateTransform: pyrosetta.rosetta.numeric.xyzMatrix_double_t) None ¶
- Get the fragment center / matrix that rotates global coordinates into local fragment coordinates.
Defined such that +z points to the C-terminal end of the helix axis, +x from the helix axis to the N-terminal residue
C++: protocols::rbsegment_relax::GaussianRBSegmentMover::getCoordinateTransformation(const class core::pose::Pose &, class numeric::xyzVector<double> &, class numeric::xyzMatrix<double> &) –> void
- getResidueRange(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover) pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment ¶
Get the the starting and ending residues of transform
C++: protocols::rbsegment_relax::RBSegmentMover::getResidueRange() –> const class protocols::rbsegment_relax::RBSegment &
- 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.rbsegment_relax.GaussianRBSegmentMover) str ¶
C++: protocols::rbsegment_relax::GaussianRBSegmentMover::get_name() const –> std::string
- get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose ¶
C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>
- get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>
- get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t ¶
C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>
- get_type(self: pyrosetta.rosetta.protocols.moves.Mover) str ¶
C++: protocols::moves::Mover::get_type() const –> std::string
- info(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.list_std_string_t ¶
non-const accessor
C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &
- last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) float ¶
C++: protocols::moves::Mover::last_proposal_density_ratio() –> double
- static name() str ¶
C++: protocols::moves::Mover::name() –> std::string
- parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None ¶
Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.
C++: protocols::moves::Mover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- print(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover) None ¶
Print debugging info
C++: protocols::rbsegment_relax::RBSegmentMover::print() –> 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
- setResidueRange(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover, seg: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment) None ¶
(re)set the starting and ending residues of this transform
C++: protocols::rbsegment_relax::RBSegmentMover::setResidueRange(const class protocols::rbsegment_relax::RBSegment &) –> 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_movement(*args, **kwargs)¶
Overloaded function.
set_movement(self: pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover) -> None
set_movement(self: pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover, sigAxisR: float) -> None
set_movement(self: pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover, sigAxisR: float, sigAxisT: float) -> None
set_movement(self: pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover, sigAxisR: float, sigAxisT: float, sigOffAxisR: float) -> None
set_movement(self: pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover, sigAxisR: float, sigAxisT: float, sigOffAxisR: float, sigOffAxisT: float) -> None
set movement parameters
sigR: the stdev of rotation
sigT: the stdev of movement
C++: protocols::rbsegment_relax::GaussianRBSegmentMover::set_movement(double, double, double, 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_segment(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover, seg: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment) None ¶
Set the segment this mover is working on
C++: protocols::rbsegment_relax::RBSegmentMover::set_segment(const class protocols::rbsegment_relax::RBSegment &) –> 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.rbsegment_relax.HelicalGaussianMover¶
Bases:
RBSegmentMover
Random movements wrt the helical axis
- apply(self: pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
Apply a +1 or -1 residue “shift” to this helix
C++: protocols::rbsegment_relax::HelicalGaussianMover::apply(class core::pose::Pose &) –> void
- applyRotation(*args, **kwargs)¶
Overloaded function.
applyRotation(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover, pose: pyrosetta.rosetta.core.pose.Pose, alpha: float, beta: float, gamma: float) -> None
Apply an arbitrary rotation specified by Euler angles (in degrees!)
C++: protocols::rbsegment_relax::RBSegmentMover::applyRotation(class core::pose::Pose &, double, double, double) –> void
applyRotation(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover, pose: pyrosetta.rosetta.core.pose.Pose, rotation: pyrosetta.rosetta.numeric.xyzMatrix_double_t) -> None
Apply an arbitrary rotation specified by a rotation matrix
C++: protocols::rbsegment_relax::RBSegmentMover::applyRotation(class core::pose::Pose &, class numeric::xyzMatrix<double>) –> void
- applySpin(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover, pose: pyrosetta.rosetta.core.pose.Pose, rotationAxis: pyrosetta.rosetta.numeric.xyzVector_double_t, degrees: float) None ¶
Apply a spin of the specified angle (in degrees) about arbitrary axis
C++: protocols::rbsegment_relax::RBSegmentMover::applySpin(class core::pose::Pose &, class numeric::xyzVector<double>, double) –> void
- applyTransformation(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover, pose: pyrosetta.rosetta.core.pose.Pose, rotation: pyrosetta.rosetta.numeric.xyzMatrix_double_t, translation: pyrosetta.rosetta.numeric.xyzVector_double_t) None ¶
Apply a rotation followed by a translation (does not recompute coordinate transformation between the two!)
C++: protocols::rbsegment_relax::RBSegmentMover::applyTransformation(class core::pose::Pose &, class numeric::xyzMatrix<double>, class numeric::xyzVector<double>) –> void
- applyTranslation(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover, pose: pyrosetta.rosetta.core.pose.Pose, translation: pyrosetta.rosetta.numeric.xyzVector_double_t) None ¶
Apply an arbitrary translation
C++: protocols::rbsegment_relax::RBSegmentMover::applyTranslation(class core::pose::Pose &, class numeric::xyzVector<double>) –> void
- assign(self: pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover, : pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover) pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover ¶
C++: protocols::rbsegment_relax::HelicalGaussianMover::operator=(const class protocols::rbsegment_relax::HelicalGaussianMover &) –> class protocols::rbsegment_relax::HelicalGaussianMover &
- 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.rbsegment_relax.HelicalGaussianMover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::rbsegment_relax::HelicalGaussianMover::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>
- getCoordinateTransformation(self: pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover, pose: pyrosetta.rosetta.core.pose.Pose, rotationCenter: pyrosetta.rosetta.numeric.xyzVector_double_t, coordinateTransform: pyrosetta.rosetta.numeric.xyzMatrix_double_t) None ¶
- Get the fragment center / matrix that rotates global coordinates into local fragment coordinates.
Defined such that +z points to the C-terminal end of the helix axis, +x from the helix axis to the N-terminal residue
C++: protocols::rbsegment_relax::HelicalGaussianMover::getCoordinateTransformation(const class core::pose::Pose &, class numeric::xyzVector<double> &, class numeric::xyzMatrix<double> &) –> void
- getResidueRange(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover) pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment ¶
Get the the starting and ending residues of transform
C++: protocols::rbsegment_relax::RBSegmentMover::getResidueRange() –> const class protocols::rbsegment_relax::RBSegment &
- 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.rbsegment_relax.HelicalGaussianMover) str ¶
C++: protocols::rbsegment_relax::HelicalGaussianMover::get_name() const –> std::string
- get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose ¶
C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>
- get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>
- get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t ¶
C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>
- get_type(self: pyrosetta.rosetta.protocols.moves.Mover) str ¶
C++: protocols::moves::Mover::get_type() const –> std::string
- info(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.list_std_string_t ¶
non-const accessor
C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &
- last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) float ¶
C++: protocols::moves::Mover::last_proposal_density_ratio() –> double
- static name() str ¶
C++: protocols::moves::Mover::name() –> std::string
- parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None ¶
Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.
C++: protocols::moves::Mover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- print(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover) None ¶
Print debugging info
C++: protocols::rbsegment_relax::RBSegmentMover::print() –> 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
- setResidueRange(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover, seg: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment) None ¶
(re)set the starting and ending residues of this transform
C++: protocols::rbsegment_relax::RBSegmentMover::setResidueRange(const class protocols::rbsegment_relax::RBSegment &) –> 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_movement(*args, **kwargs)¶
Overloaded function.
set_movement(self: pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover) -> None
set_movement(self: pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover, sigAxisR: float) -> None
set_movement(self: pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover, sigAxisR: float, sigAxisT: float) -> None
set_movement(self: pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover, sigAxisR: float, sigAxisT: float, sigOffAxisR: float) -> None
set_movement(self: pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover, sigAxisR: float, sigAxisT: float, sigOffAxisR: float, sigOffAxisT: float) -> None
set movement parameters
sigAxisR: the stdev of rotation along the helical axis
sigAxisT: the stdev of movement along the helical axis
sigOffAxisR: the stdev of rotation normal to the helical axis
sigOffAxisT: the stdev of movement normal to the helical axis
C++: protocols::rbsegment_relax::HelicalGaussianMover::set_movement(double, double, double, 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_segment(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover, seg: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment) None ¶
Set the segment this mover is working on
C++: protocols::rbsegment_relax::RBSegmentMover::set_segment(const class protocols::rbsegment_relax::RBSegment &) –> 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.rbsegment_relax.IdealizeHelicesMover¶
Bases:
Mover
- apply(self: pyrosetta.rosetta.protocols.rbsegment_relax.IdealizeHelicesMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::rbsegment_relax::IdealizeHelicesMover::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.rbsegment_relax.IdealizeHelicesMover, : pyrosetta.rosetta.protocols.rbsegment_relax.IdealizeHelicesMover) pyrosetta.rosetta.protocols.rbsegment_relax.IdealizeHelicesMover ¶
C++: protocols::rbsegment_relax::IdealizeHelicesMover::operator=(const class protocols::rbsegment_relax::IdealizeHelicesMover &) –> class protocols::rbsegment_relax::IdealizeHelicesMover &
- 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.rbsegment_relax.IdealizeHelicesMover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::rbsegment_relax::IdealizeHelicesMover::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.rbsegment_relax.IdealizeHelicesMover) str ¶
C++: protocols::rbsegment_relax::IdealizeHelicesMover::get_name() const –> std::string
- get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose ¶
C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>
- get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>
- get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t ¶
C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>
- get_type(self: pyrosetta.rosetta.protocols.moves.Mover) str ¶
C++: protocols::moves::Mover::get_type() const –> std::string
- info(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.list_std_string_t ¶
non-const accessor
C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &
- last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) float ¶
C++: protocols::moves::Mover::last_proposal_density_ratio() –> double
- static mover_name() str ¶
C++: protocols::rbsegment_relax::IdealizeHelicesMover::mover_name() –> std::string
- static name() str ¶
C++: protocols::moves::Mover::name() –> std::string
- parse_my_tag(self: pyrosetta.rosetta.protocols.rbsegment_relax.IdealizeHelicesMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None ¶
C++: protocols::rbsegment_relax::IdealizeHelicesMover::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::rbsegment_relax::IdealizeHelicesMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void
- static register_options() None ¶
Overload this static method if you access options within the mover.
These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.
C++: protocols::moves::Mover::register_options() –> void
- reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) bool ¶
- Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on
each use.
C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool
- reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) bool ¶
- Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input
pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).
C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool
- reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) None ¶
resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.
C++: protocols::moves::Mover::reset_status() –> void
- set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) None ¶
C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void
- set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) None ¶
C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void
- set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
setter for poses contained for rms
C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void
- set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe
C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void
- set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) None ¶
Set the ‘type’ string
C++: protocols::moves::Mover::set_type(const std::string &) –> void
- show(*args, **kwargs)¶
Overloaded function.
show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None
Outputs details about the Mover, including current settings.
C++: protocols::moves::Mover::show(std::ostream &) const –> void
- test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
- : Unit test support function. Apply one move to a given pose.
Allows extra test specific functions to be called before applying
C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void
- type(*args, **kwargs)¶
Overloaded function.
type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None
Set the ‘type’ string
C++: protocols::moves::Mover::type(const std::string &) –> void
type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str
Get the set ‘type’ string
C++: protocols::moves::Mover::type() const –> const std::string &
- class pyrosetta.rosetta.protocols.rbsegment_relax.IdealizeHelicesMoverCreator¶
Bases:
MoverCreator
- assign(self: pyrosetta.rosetta.protocols.rbsegment_relax.IdealizeHelicesMoverCreator, : pyrosetta.rosetta.protocols.rbsegment_relax.IdealizeHelicesMoverCreator) pyrosetta.rosetta.protocols.rbsegment_relax.IdealizeHelicesMoverCreator ¶
C++: protocols::rbsegment_relax::IdealizeHelicesMoverCreator::operator=(const class protocols::rbsegment_relax::IdealizeHelicesMoverCreator &) –> class protocols::rbsegment_relax::IdealizeHelicesMoverCreator &
- create_mover(self: pyrosetta.rosetta.protocols.rbsegment_relax.IdealizeHelicesMoverCreator) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::rbsegment_relax::IdealizeHelicesMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>
- keyname(self: pyrosetta.rosetta.protocols.rbsegment_relax.IdealizeHelicesMoverCreator) str ¶
C++: protocols::rbsegment_relax::IdealizeHelicesMoverCreator::keyname() const –> std::string
- class pyrosetta.rosetta.protocols.rbsegment_relax.MakeStarTopologyMover¶
Bases:
Mover
- apply(self: pyrosetta.rosetta.protocols.rbsegment_relax.MakeStarTopologyMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::rbsegment_relax::MakeStarTopologyMover::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.rbsegment_relax.MakeStarTopologyMover, : pyrosetta.rosetta.protocols.rbsegment_relax.MakeStarTopologyMover) pyrosetta.rosetta.protocols.rbsegment_relax.MakeStarTopologyMover ¶
C++: protocols::rbsegment_relax::MakeStarTopologyMover::operator=(const class protocols::rbsegment_relax::MakeStarTopologyMover &) –> class protocols::rbsegment_relax::MakeStarTopologyMover &
- 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.rbsegment_relax.MakeStarTopologyMover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::rbsegment_relax::MakeStarTopologyMover::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.rbsegment_relax.MakeStarTopologyMover) str ¶
C++: protocols::rbsegment_relax::MakeStarTopologyMover::get_name() const –> std::string
- get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose ¶
C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>
- get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>
- get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t ¶
C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>
- get_type(self: pyrosetta.rosetta.protocols.moves.Mover) str ¶
C++: protocols::moves::Mover::get_type() const –> std::string
- info(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.list_std_string_t ¶
non-const accessor
C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &
- last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) float ¶
C++: protocols::moves::Mover::last_proposal_density_ratio() –> double
- static mover_name() str ¶
C++: protocols::rbsegment_relax::MakeStarTopologyMover::mover_name() –> std::string
- static name() str ¶
C++: protocols::moves::Mover::name() –> std::string
- parse_my_tag(self: pyrosetta.rosetta.protocols.rbsegment_relax.MakeStarTopologyMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None ¶
C++: protocols::rbsegment_relax::MakeStarTopologyMover::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::rbsegment_relax::MakeStarTopologyMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void
- static register_options() None ¶
Overload this static method if you access options within the mover.
These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.
C++: protocols::moves::Mover::register_options() –> void
- reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) bool ¶
- Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on
each use.
C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool
- reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) bool ¶
- Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input
pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).
C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool
- reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) None ¶
resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.
C++: protocols::moves::Mover::reset_status() –> void
- set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) None ¶
C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void
- set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) None ¶
C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void
- set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
setter for poses contained for rms
C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void
- set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe
C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void
- set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) None ¶
Set the ‘type’ string
C++: protocols::moves::Mover::set_type(const std::string &) –> void
- show(*args, **kwargs)¶
Overloaded function.
show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None
Outputs details about the Mover, including current settings.
C++: protocols::moves::Mover::show(std::ostream &) const –> void
- test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
- : Unit test support function. Apply one move to a given pose.
Allows extra test specific functions to be called before applying
C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void
- type(*args, **kwargs)¶
Overloaded function.
type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None
Set the ‘type’ string
C++: protocols::moves::Mover::type(const std::string &) –> void
type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str
Get the set ‘type’ string
C++: protocols::moves::Mover::type() const –> const std::string &
- class pyrosetta.rosetta.protocols.rbsegment_relax.MakeStarTopologyMoverCreator¶
Bases:
MoverCreator
- assign(self: pyrosetta.rosetta.protocols.rbsegment_relax.MakeStarTopologyMoverCreator, : pyrosetta.rosetta.protocols.rbsegment_relax.MakeStarTopologyMoverCreator) pyrosetta.rosetta.protocols.rbsegment_relax.MakeStarTopologyMoverCreator ¶
C++: protocols::rbsegment_relax::MakeStarTopologyMoverCreator::operator=(const class protocols::rbsegment_relax::MakeStarTopologyMoverCreator &) –> class protocols::rbsegment_relax::MakeStarTopologyMoverCreator &
- create_mover(self: pyrosetta.rosetta.protocols.rbsegment_relax.MakeStarTopologyMoverCreator) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::rbsegment_relax::MakeStarTopologyMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>
- keyname(self: pyrosetta.rosetta.protocols.rbsegment_relax.MakeStarTopologyMoverCreator) str ¶
C++: protocols::rbsegment_relax::MakeStarTopologyMoverCreator::keyname() const –> std::string
- class pyrosetta.rosetta.protocols.rbsegment_relax.OptimizeThreadingMover¶
Bases:
Mover
- apply(self: pyrosetta.rosetta.protocols.rbsegment_relax.OptimizeThreadingMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::rbsegment_relax::OptimizeThreadingMover::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.rbsegment_relax.OptimizeThreadingMover, : pyrosetta.rosetta.protocols.rbsegment_relax.OptimizeThreadingMover) pyrosetta.rosetta.protocols.rbsegment_relax.OptimizeThreadingMover ¶
C++: protocols::rbsegment_relax::OptimizeThreadingMover::operator=(const class protocols::rbsegment_relax::OptimizeThreadingMover &) –> class protocols::rbsegment_relax::OptimizeThreadingMover &
- 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.rbsegment_relax.OptimizeThreadingMover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::rbsegment_relax::OptimizeThreadingMover::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.rbsegment_relax.OptimizeThreadingMover) str ¶
C++: protocols::rbsegment_relax::OptimizeThreadingMover::get_name() const –> std::string
- get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose ¶
C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>
- get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>
- get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t ¶
C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>
- get_type(self: pyrosetta.rosetta.protocols.moves.Mover) str ¶
C++: protocols::moves::Mover::get_type() const –> std::string
- info(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.list_std_string_t ¶
non-const accessor
C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &
- last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) float ¶
C++: protocols::moves::Mover::last_proposal_density_ratio() –> double
- static mover_name() str ¶
C++: protocols::rbsegment_relax::OptimizeThreadingMover::mover_name() –> std::string
- static name() str ¶
C++: protocols::moves::Mover::name() –> std::string
- parse_my_tag(self: pyrosetta.rosetta.protocols.rbsegment_relax.OptimizeThreadingMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None ¶
C++: protocols::rbsegment_relax::OptimizeThreadingMover::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::rbsegment_relax::OptimizeThreadingMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void
- static register_options() None ¶
Overload this static method if you access options within the mover.
These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.
C++: protocols::moves::Mover::register_options() –> void
- reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) bool ¶
- Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on
each use.
C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool
- reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) bool ¶
- Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input
pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).
C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool
- reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) None ¶
resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.
C++: protocols::moves::Mover::reset_status() –> void
- set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) None ¶
C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void
- set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) None ¶
C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void
- set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
setter for poses contained for rms
C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void
- set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe
C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void
- set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) None ¶
Set the ‘type’ string
C++: protocols::moves::Mover::set_type(const std::string &) –> void
- show(*args, **kwargs)¶
Overloaded function.
show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None
Outputs details about the Mover, including current settings.
C++: protocols::moves::Mover::show(std::ostream &) const –> void
- test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
- : Unit test support function. Apply one move to a given pose.
Allows extra test specific functions to be called before applying
C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void
- type(*args, **kwargs)¶
Overloaded function.
type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None
Set the ‘type’ string
C++: protocols::moves::Mover::type(const std::string &) –> void
type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str
Get the set ‘type’ string
C++: protocols::moves::Mover::type() const –> const std::string &
- class pyrosetta.rosetta.protocols.rbsegment_relax.OptimizeThreadingMoverCreator¶
Bases:
MoverCreator
- assign(self: pyrosetta.rosetta.protocols.rbsegment_relax.OptimizeThreadingMoverCreator, : pyrosetta.rosetta.protocols.rbsegment_relax.OptimizeThreadingMoverCreator) pyrosetta.rosetta.protocols.rbsegment_relax.OptimizeThreadingMoverCreator ¶
C++: protocols::rbsegment_relax::OptimizeThreadingMoverCreator::operator=(const class protocols::rbsegment_relax::OptimizeThreadingMoverCreator &) –> class protocols::rbsegment_relax::OptimizeThreadingMoverCreator &
- create_mover(self: pyrosetta.rosetta.protocols.rbsegment_relax.OptimizeThreadingMoverCreator) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::rbsegment_relax::OptimizeThreadingMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>
- keyname(self: pyrosetta.rosetta.protocols.rbsegment_relax.OptimizeThreadingMoverCreator) str ¶
C++: protocols::rbsegment_relax::OptimizeThreadingMoverCreator::keyname() const –> std::string
- class pyrosetta.rosetta.protocols.rbsegment_relax.RBResidueRange¶
Bases:
pybind11_object
RB residue range
- char_type(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBResidueRange) str ¶
C++: protocols::rbsegment_relax::RBResidueRange::char_type() const –> char
- end(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBResidueRange) int ¶
C++: protocols::rbsegment_relax::RBResidueRange::end() const –> unsigned long
- length(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBResidueRange) int ¶
C++: protocols::rbsegment_relax::RBResidueRange::length() const –> unsigned long
- set_end(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBResidueRange, E: int) None ¶
C++: protocols::rbsegment_relax::RBResidueRange::set_end(unsigned long) –> void
- set_start(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBResidueRange, S: int) None ¶
C++: protocols::rbsegment_relax::RBResidueRange::set_start(unsigned long) –> void
- start(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBResidueRange) int ¶
C++: protocols::rbsegment_relax::RBResidueRange::start() const –> unsigned long
- type(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBResidueRange) pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentType ¶
C++: protocols::rbsegment_relax::RBResidueRange::type() const –> enum protocols::rbsegment_relax::RBSegmentType
- class pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment¶
Bases:
pybind11_object
Rigid-body segments in a protein
- assign(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment, : pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment) pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment ¶
C++: protocols::rbsegment_relax::RBSegment::operator=(const class protocols::rbsegment_relax::RBSegment &) –> class protocols::rbsegment_relax::RBSegment &
- getSigAxisR(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment) float ¶
C++: protocols::rbsegment_relax::RBSegment::getSigAxisR() const –> double
- getSigAxisT(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment) float ¶
C++: protocols::rbsegment_relax::RBSegment::getSigAxisT() const –> double
- getSigOffAxisR(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment) float ¶
C++: protocols::rbsegment_relax::RBSegment::getSigOffAxisR() const –> double
- getSigOffAxisT(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment) float ¶
C++: protocols::rbsegment_relax::RBSegment::getSigOffAxisT() const –> double
- get_movement(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment, sigAxisR: float, sigAxisT: float, sigOffAxisR: float, sigOffAxisT: float) None ¶
C++: protocols::rbsegment_relax::RBSegment::get_movement(double &, double &, double &, double &) const –> void
- initialized(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment) bool ¶
C++: protocols::rbsegment_relax::RBSegment::initialized() const –> bool
- isCompound(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment) bool ¶
C++: protocols::rbsegment_relax::RBSegment::isCompound() const –> bool
- isEmpty(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment) bool ¶
C++: protocols::rbsegment_relax::RBSegment::isEmpty() const –> bool
- isGenericRB(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment) bool ¶
C++: protocols::rbsegment_relax::RBSegment::isGenericRB() const –> bool
- isHelix(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment) bool ¶
C++: protocols::rbsegment_relax::RBSegment::isHelix() const –> bool
- isSheet(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment) bool ¶
C++: protocols::rbsegment_relax::RBSegment::isSheet() const –> bool
- isSimple(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment) bool ¶
C++: protocols::rbsegment_relax::RBSegment::isSimple() const –> bool
- nContinuousSegments(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment) int ¶
C++: protocols::rbsegment_relax::RBSegment::nContinuousSegments() const –> unsigned long
- remap(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment, mapping: pyrosetta.rosetta.core.id.SequenceMapping) pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment ¶
C++: protocols::rbsegment_relax::RBSegment::remap(const class core::id::SequenceMapping &) const –> class protocols::rbsegment_relax::RBSegment
- set_movement(*args, **kwargs)¶
Overloaded function.
set_movement(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment, sigAxisR: float, sigAxisT: float) -> None
set_movement(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment, sigAxisR: float, sigAxisT: float, sigOffAxisR: float) -> None
set_movement(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment, sigAxisR: float, sigAxisT: float, sigOffAxisR: float, sigOffAxisT: float) -> None
C++: protocols::rbsegment_relax::RBSegment::set_movement(double, double, double, double) –> void
- split(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment) pyrosetta.rosetta.utility.vector1_protocols_rbsegment_relax_RBSegment ¶
split a RBsegment of potentially discontinuous segments in a vector of multiple consecutive RBsegments
C++: protocols::rbsegment_relax::RBSegment::split() const –> class utility::vector1<class protocols::rbsegment_relax::RBSegment, class std::allocator<class protocols::rbsegment_relax::RBSegment> >
- class pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover¶
Bases:
Mover
- Performs a rigid-body movement on a segment of a protein
Derived classes must implement ‘getCoordinateTransform’ and ‘apply’
- apply(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
Apply the rigid-body fragment mover to a pose. Must be defined by derived classes.
C++: protocols::rbsegment_relax::RBSegmentMover::apply(class core::pose::Pose &) –> void
- applyRotation(*args, **kwargs)¶
Overloaded function.
applyRotation(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover, pose: pyrosetta.rosetta.core.pose.Pose, alpha: float, beta: float, gamma: float) -> None
Apply an arbitrary rotation specified by Euler angles (in degrees!)
C++: protocols::rbsegment_relax::RBSegmentMover::applyRotation(class core::pose::Pose &, double, double, double) –> void
applyRotation(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover, pose: pyrosetta.rosetta.core.pose.Pose, rotation: pyrosetta.rosetta.numeric.xyzMatrix_double_t) -> None
Apply an arbitrary rotation specified by a rotation matrix
C++: protocols::rbsegment_relax::RBSegmentMover::applyRotation(class core::pose::Pose &, class numeric::xyzMatrix<double>) –> void
- applySpin(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover, pose: pyrosetta.rosetta.core.pose.Pose, rotationAxis: pyrosetta.rosetta.numeric.xyzVector_double_t, degrees: float) None ¶
Apply a spin of the specified angle (in degrees) about arbitrary axis
C++: protocols::rbsegment_relax::RBSegmentMover::applySpin(class core::pose::Pose &, class numeric::xyzVector<double>, double) –> void
- applyTransformation(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover, pose: pyrosetta.rosetta.core.pose.Pose, rotation: pyrosetta.rosetta.numeric.xyzMatrix_double_t, translation: pyrosetta.rosetta.numeric.xyzVector_double_t) None ¶
Apply a rotation followed by a translation (does not recompute coordinate transformation between the two!)
C++: protocols::rbsegment_relax::RBSegmentMover::applyTransformation(class core::pose::Pose &, class numeric::xyzMatrix<double>, class numeric::xyzVector<double>) –> void
- applyTranslation(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover, pose: pyrosetta.rosetta.core.pose.Pose, translation: pyrosetta.rosetta.numeric.xyzVector_double_t) None ¶
Apply an arbitrary translation
C++: protocols::rbsegment_relax::RBSegmentMover::applyTranslation(class core::pose::Pose &, class numeric::xyzVector<double>) –> void
- assign(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover, : pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover) pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover ¶
C++: protocols::rbsegment_relax::RBSegmentMover::operator=(const class protocols::rbsegment_relax::RBSegmentMover &) –> class protocols::rbsegment_relax::RBSegmentMover &
- 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>
- 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>
- getCoordinateTransformation(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover, : pyrosetta.rosetta.core.pose.Pose, rotationCenter: pyrosetta.rosetta.numeric.xyzVector_double_t, coordinateTransform: pyrosetta.rosetta.numeric.xyzMatrix_double_t) None ¶
- Returns: (a) the matrix that rotates global coordinates into local fragment coordinates and
(b) the center of rotation of the fragment. Default implementation sets them to global coords
C++: protocols::rbsegment_relax::RBSegmentMover::getCoordinateTransformation(const class core::pose::Pose &, class numeric::xyzVector<double> &, class numeric::xyzMatrix<double> &) –> void
- getResidueRange(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover) pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment ¶
Get the the starting and ending residues of transform
C++: protocols::rbsegment_relax::RBSegmentMover::getResidueRange() –> const class protocols::rbsegment_relax::RBSegment &
- 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.rbsegment_relax.RBSegmentMover) str ¶
C++: protocols::rbsegment_relax::RBSegmentMover::get_name() const –> std::string
- get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose ¶
C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>
- get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>
- get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t ¶
C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>
- get_type(self: pyrosetta.rosetta.protocols.moves.Mover) str ¶
C++: protocols::moves::Mover::get_type() const –> std::string
- info(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.list_std_string_t ¶
non-const accessor
C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &
- last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) float ¶
C++: protocols::moves::Mover::last_proposal_density_ratio() –> double
- static name() str ¶
C++: protocols::moves::Mover::name() –> std::string
- parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None ¶
Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.
C++: protocols::moves::Mover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- print(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover) None ¶
Print debugging info
C++: protocols::rbsegment_relax::RBSegmentMover::print() –> 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
- setResidueRange(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover, seg: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment) None ¶
(re)set the starting and ending residues of this transform
C++: protocols::rbsegment_relax::RBSegmentMover::setResidueRange(const class protocols::rbsegment_relax::RBSegment &) –> 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_movement(*args, **kwargs)¶
Overloaded function.
set_movement(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover) -> None
set_movement(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover, p1: float) -> None
set_movement(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover, p1: float, p2: float) -> None
set_movement(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover, p1: float, p2: float, p3: float) -> None
set_movement(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover, p1: float, p2: float, p3: float, p4: float) -> None
Set mover-specific movement parameters. Do nothing by default.
C++: protocols::rbsegment_relax::RBSegmentMover::set_movement(double, double, double, double) –> void
set_movement(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover, rb: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment) -> None
steal movement params from a segment definition
C++: protocols::rbsegment_relax::RBSegmentMover::set_movement(const class protocols::rbsegment_relax::RBSegment &) –> 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_segment(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover, seg: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment) None ¶
Set the segment this mover is working on
C++: protocols::rbsegment_relax::RBSegmentMover::set_segment(const class protocols::rbsegment_relax::RBSegment &) –> 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.rbsegment_relax.RBSegmentRelax¶
Bases:
Mover
- add_compositeSegmentMover(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentRelax, newMover: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover) None ¶
C++: protocols::rbsegment_relax::RBSegmentRelax::add_compositeSegmentMover(class std::shared_ptr<class protocols::rbsegment_relax::RBSegmentMover>) –> void
- add_genericRBMover(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentRelax, newMover: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover) None ¶
C++: protocols::rbsegment_relax::RBSegmentRelax::add_genericRBMover(class std::shared_ptr<class protocols::rbsegment_relax::RBSegmentMover>) –> void
- add_helixMover(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentRelax, newMover: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover) None ¶
C++: protocols::rbsegment_relax::RBSegmentRelax::add_helixMover(class std::shared_ptr<class protocols::rbsegment_relax::RBSegmentMover>) –> void
- add_strandMover(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentRelax, newMover: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover) None ¶
C++: protocols::rbsegment_relax::RBSegmentRelax::add_strandMover(class std::shared_ptr<class protocols::rbsegment_relax::RBSegmentMover>) –> void
- add_wholeStructureMover(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentRelax, newMover: pyrosetta.rosetta.protocols.moves.Mover) None ¶
C++: protocols::rbsegment_relax::RBSegmentRelax::add_wholeStructureMover(class std::shared_ptr<class protocols::moves::Mover>) –> void
- apply(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentRelax, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::rbsegment_relax::RBSegmentRelax::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentRelax, : pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentRelax) pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentRelax ¶
C++: protocols::rbsegment_relax::RBSegmentRelax::operator=(const class protocols::rbsegment_relax::RBSegmentRelax &) –> class protocols::rbsegment_relax::RBSegmentRelax &
- 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_movesets(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentRelax) None ¶
C++: protocols::rbsegment_relax::RBSegmentRelax::clear_movesets() –> 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_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.rbsegment_relax.RBSegmentRelax) str ¶
C++: protocols::rbsegment_relax::RBSegmentRelax::get_name() const –> std::string
- get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose ¶
C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>
- get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>
- get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t ¶
C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>
- get_type(self: pyrosetta.rosetta.protocols.moves.Mover) str ¶
C++: protocols::moves::Mover::get_type() const –> std::string
- info(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.list_std_string_t ¶
non-const accessor
C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &
- initialize(*args, **kwargs)¶
Overloaded function.
initialize(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentRelax, frag_libs: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_fragment_FragSet_t) -> None
initialize(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentRelax, frag_libs: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_fragment_FragSet_t, rnd: float) -> None
C++: protocols::rbsegment_relax::RBSegmentRelax::initialize(const class utility::vector1<class std::shared_ptr<class core::fragment::FragSet>, class std::allocator<class std::shared_ptr<class core::fragment::FragSet> > > &, double) –> void
- 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_bootstrap(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentRelax, boot: bool) None ¶
C++: protocols::rbsegment_relax::RBSegmentRelax::set_bootstrap(bool) –> void
- set_cst_weight(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentRelax, wt: float) None ¶
C++: protocols::rbsegment_relax::RBSegmentRelax::set_cst_weight(double) –> void
- set_cst_width(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentRelax, width: float) None ¶
C++: protocols::rbsegment_relax::RBSegmentRelax::set_cst_width(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_fix_ligands(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentRelax, fix: bool) None ¶
C++: protocols::rbsegment_relax::RBSegmentRelax::set_fix_ligands(bool) –> void
- set_genericRBMoveStepsize(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentRelax, trans: float, rot: float) None ¶
C++: protocols::rbsegment_relax::RBSegmentRelax::set_genericRBMoveStepsize(double, double) –> void
- set_helicalMoveStepsize(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentRelax, onAxisTrans: float, onAxisRot: float, offAxisTrans: float, offAxisRot: float) None ¶
C++: protocols::rbsegment_relax::RBSegmentRelax::set_helicalMoveStepsize(double, double, double, double) –> 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_ncycles(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentRelax, ncycles: int) None ¶
C++: protocols::rbsegment_relax::RBSegmentRelax::set_ncycles(int) –> void
- set_randomize(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentRelax, rand: int) None ¶
C++: protocols::rbsegment_relax::RBSegmentRelax::set_randomize(unsigned long) –> void
- set_skip_lr(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentRelax, skip: bool) None ¶
C++: protocols::rbsegment_relax::RBSegmentRelax::set_skip_lr(bool) –> void
- set_temperature(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentRelax, start: float, final: float) None ¶
C++: protocols::rbsegment_relax::RBSegmentRelax::set_temperature(double, 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
- 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.rbsegment_relax.RBSegmentType¶
Bases:
pybind11_object
Enumeration of RB types
Members:
RB_HELIX
RB_SHEET
RB_DEFAULT
- RB_DEFAULT = <RBSegmentType.RB_DEFAULT: 3>¶
- RB_HELIX = <RBSegmentType.RB_HELIX: 1>¶
- RB_SHEET = <RBSegmentType.RB_SHEET: 2>¶
- property name¶
- property value¶
- class pyrosetta.rosetta.protocols.rbsegment_relax.RB_lt¶
Bases:
pybind11_object
- class pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover¶
Bases:
RBSegmentMover
“Register shift” a segment by one amino-acid Works in both centroid and all-atom
- apply(*args, **kwargs)¶
Overloaded function.
apply(self: pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover, pose: pyrosetta.rosetta.core.pose.Pose) -> None
Apply a + or - residue “shift” to this helix
C++: protocols::rbsegment_relax::SequenceShiftMover::apply(class core::pose::Pose &) –> void
apply(self: pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover, pose: pyrosetta.rosetta.core.pose.Pose, shift: int) -> None
Apply a + or - residue “shift” to this helix
C++: protocols::rbsegment_relax::SequenceShiftMover::apply(class core::pose::Pose &, int) –> void
- applyRotation(*args, **kwargs)¶
Overloaded function.
applyRotation(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover, pose: pyrosetta.rosetta.core.pose.Pose, alpha: float, beta: float, gamma: float) -> None
Apply an arbitrary rotation specified by Euler angles (in degrees!)
C++: protocols::rbsegment_relax::RBSegmentMover::applyRotation(class core::pose::Pose &, double, double, double) –> void
applyRotation(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover, pose: pyrosetta.rosetta.core.pose.Pose, rotation: pyrosetta.rosetta.numeric.xyzMatrix_double_t) -> None
Apply an arbitrary rotation specified by a rotation matrix
C++: protocols::rbsegment_relax::RBSegmentMover::applyRotation(class core::pose::Pose &, class numeric::xyzMatrix<double>) –> void
- applySpin(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover, pose: pyrosetta.rosetta.core.pose.Pose, rotationAxis: pyrosetta.rosetta.numeric.xyzVector_double_t, degrees: float) None ¶
Apply a spin of the specified angle (in degrees) about arbitrary axis
C++: protocols::rbsegment_relax::RBSegmentMover::applySpin(class core::pose::Pose &, class numeric::xyzVector<double>, double) –> void
- applyTransformation(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover, pose: pyrosetta.rosetta.core.pose.Pose, rotation: pyrosetta.rosetta.numeric.xyzMatrix_double_t, translation: pyrosetta.rosetta.numeric.xyzVector_double_t) None ¶
Apply a rotation followed by a translation (does not recompute coordinate transformation between the two!)
C++: protocols::rbsegment_relax::RBSegmentMover::applyTransformation(class core::pose::Pose &, class numeric::xyzMatrix<double>, class numeric::xyzVector<double>) –> void
- applyTranslation(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover, pose: pyrosetta.rosetta.core.pose.Pose, translation: pyrosetta.rosetta.numeric.xyzVector_double_t) None ¶
Apply an arbitrary translation
C++: protocols::rbsegment_relax::RBSegmentMover::applyTranslation(class core::pose::Pose &, class numeric::xyzVector<double>) –> void
- assign(self: pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover, : pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover) pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover ¶
C++: protocols::rbsegment_relax::SequenceShiftMover::operator=(const class protocols::rbsegment_relax::SequenceShiftMover &) –> class protocols::rbsegment_relax::SequenceShiftMover &
- 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.rbsegment_relax.SequenceShiftMover) pyrosetta.rosetta.protocols.moves.Mover ¶
clone this object
C++: protocols::rbsegment_relax::SequenceShiftMover::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>
- getCoordinateTransformation(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover, : pyrosetta.rosetta.core.pose.Pose, rotationCenter: pyrosetta.rosetta.numeric.xyzVector_double_t, coordinateTransform: pyrosetta.rosetta.numeric.xyzMatrix_double_t) None ¶
- Returns: (a) the matrix that rotates global coordinates into local fragment coordinates and
(b) the center of rotation of the fragment. Default implementation sets them to global coords
C++: protocols::rbsegment_relax::RBSegmentMover::getCoordinateTransformation(const class core::pose::Pose &, class numeric::xyzVector<double> &, class numeric::xyzMatrix<double> &) –> void
- getResidueRange(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover) pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment ¶
Get the the starting and ending residues of transform
C++: protocols::rbsegment_relax::RBSegmentMover::getResidueRange() –> const class protocols::rbsegment_relax::RBSegment &
- 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.rbsegment_relax.RBSegmentMover) str ¶
C++: protocols::rbsegment_relax::RBSegmentMover::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_residues_to_rebuild(self: pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover) pyrosetta.rosetta.protocols.loops.Loops ¶
IF ref_pose is given, get a list of residues to rebuild via fragment insertion
C++: protocols::rbsegment_relax::SequenceShiftMover::get_residues_to_rebuild() –> class std::shared_ptr<class protocols::loops::Loops>
- get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>
- get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t ¶
C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>
- get_type(self: pyrosetta.rosetta.protocols.moves.Mover) str ¶
C++: protocols::moves::Mover::get_type() const –> std::string
- info(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.list_std_string_t ¶
non-const accessor
C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &
- last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) float ¶
C++: protocols::moves::Mover::last_proposal_density_ratio() –> double
- static name() str ¶
C++: protocols::moves::Mover::name() –> std::string
- parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None ¶
Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.
C++: protocols::moves::Mover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- print(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover) None ¶
Print debugging info
C++: protocols::rbsegment_relax::RBSegmentMover::print() –> 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
- score(*args, **kwargs)¶
Overloaded function.
score(self: pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover) -> int
score(self: pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover, step_fn: bool) -> int
Return a score: the minimum number of block shifts accumulated
C++: protocols::rbsegment_relax::SequenceShiftMover::score(bool) –> int
- setResidueRange(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover, seg: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment) None ¶
(re)set the starting and ending residues of this transform
C++: protocols::rbsegment_relax::RBSegmentMover::setResidueRange(const class protocols::rbsegment_relax::RBSegment &) –> 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_extra_penalty(self: pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover, penalty_res: pyrosetta.rosetta.utility.vector1_bool) None ¶
Set an extra block-shift penalty at certain residues
C++: protocols::rbsegment_relax::SequenceShiftMover::set_extra_penalty(const class utility::vector1<bool, class std::allocator<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_movement(self: pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover, : float, : float, : float, : float) None ¶
set movement parameters. ignore all input args
C++: protocols::rbsegment_relax::SequenceShiftMover::set_movement(double, double, double, 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_segment(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover, seg: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment) None ¶
Set the segment this mover is working on
C++: protocols::rbsegment_relax::RBSegmentMover::set_segment(const class protocols::rbsegment_relax::RBSegment &) –> 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_verbose(self: pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover, inval: bool) None ¶
C++: protocols::rbsegment_relax::SequenceShiftMover::set_verbose(bool) –> 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
- trigger_accept(self: pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover) None ¶
Last move accepted; update offsets_
C++: protocols::rbsegment_relax::SequenceShiftMover::trigger_accept() –> 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.rbsegment_relax.StrandTwistingMover¶
Bases:
RBSegmentMover
Strand Twisting
- apply(self: pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
Apply a +1 or -1 residue “shift” to this helix
C++: protocols::rbsegment_relax::StrandTwistingMover::apply(class core::pose::Pose &) –> void
- applyRotation(*args, **kwargs)¶
Overloaded function.
applyRotation(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover, pose: pyrosetta.rosetta.core.pose.Pose, alpha: float, beta: float, gamma: float) -> None
Apply an arbitrary rotation specified by Euler angles (in degrees!)
C++: protocols::rbsegment_relax::RBSegmentMover::applyRotation(class core::pose::Pose &, double, double, double) –> void
applyRotation(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover, pose: pyrosetta.rosetta.core.pose.Pose, rotation: pyrosetta.rosetta.numeric.xyzMatrix_double_t) -> None
Apply an arbitrary rotation specified by a rotation matrix
C++: protocols::rbsegment_relax::RBSegmentMover::applyRotation(class core::pose::Pose &, class numeric::xyzMatrix<double>) –> void
- applySpin(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover, pose: pyrosetta.rosetta.core.pose.Pose, rotationAxis: pyrosetta.rosetta.numeric.xyzVector_double_t, degrees: float) None ¶
Apply a spin of the specified angle (in degrees) about arbitrary axis
C++: protocols::rbsegment_relax::RBSegmentMover::applySpin(class core::pose::Pose &, class numeric::xyzVector<double>, double) –> void
- applyTransformation(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover, pose: pyrosetta.rosetta.core.pose.Pose, rotation: pyrosetta.rosetta.numeric.xyzMatrix_double_t, translation: pyrosetta.rosetta.numeric.xyzVector_double_t) None ¶
Apply a rotation followed by a translation (does not recompute coordinate transformation between the two!)
C++: protocols::rbsegment_relax::RBSegmentMover::applyTransformation(class core::pose::Pose &, class numeric::xyzMatrix<double>, class numeric::xyzVector<double>) –> void
- applyTranslation(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover, pose: pyrosetta.rosetta.core.pose.Pose, translation: pyrosetta.rosetta.numeric.xyzVector_double_t) None ¶
Apply an arbitrary translation
C++: protocols::rbsegment_relax::RBSegmentMover::applyTranslation(class core::pose::Pose &, class numeric::xyzVector<double>) –> void
- assign(self: pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover, : pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover) pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover ¶
C++: protocols::rbsegment_relax::StrandTwistingMover::operator=(const class protocols::rbsegment_relax::StrandTwistingMover &) –> class protocols::rbsegment_relax::StrandTwistingMover &
- 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.rbsegment_relax.StrandTwistingMover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::rbsegment_relax::StrandTwistingMover::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>
- getCoordinateTransformation(self: pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover, pose: pyrosetta.rosetta.core.pose.Pose, rotationCenter: pyrosetta.rosetta.numeric.xyzVector_double_t, coordinateTransform: pyrosetta.rosetta.numeric.xyzMatrix_double_t) None ¶
- Get the fragment center / matrix that rotates global coordinates into local fragment coordinates.
Defined such that +z points to the C-terminal end of the helix axis, +x from the helix axis to the N-terminal residue
C++: protocols::rbsegment_relax::StrandTwistingMover::getCoordinateTransformation(const class core::pose::Pose &, class numeric::xyzVector<double> &, class numeric::xyzMatrix<double> &) –> void
- getResidueRange(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover) pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment ¶
Get the the starting and ending residues of transform
C++: protocols::rbsegment_relax::RBSegmentMover::getResidueRange() –> const class protocols::rbsegment_relax::RBSegment &
- 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.rbsegment_relax.StrandTwistingMover) str ¶
C++: protocols::rbsegment_relax::StrandTwistingMover::get_name() const –> std::string
- get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose ¶
C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>
- get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>
- get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t ¶
C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>
- get_type(self: pyrosetta.rosetta.protocols.moves.Mover) str ¶
C++: protocols::moves::Mover::get_type() const –> std::string
- info(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.list_std_string_t ¶
non-const accessor
C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &
- last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) float ¶
C++: protocols::moves::Mover::last_proposal_density_ratio() –> double
- static name() str ¶
C++: protocols::moves::Mover::name() –> std::string
- parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None ¶
Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.
C++: protocols::moves::Mover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- print(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover) None ¶
Print debugging info
C++: protocols::rbsegment_relax::RBSegmentMover::print() –> 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
- setResidueRange(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover, seg: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment) None ¶
(re)set the starting and ending residues of this transform
C++: protocols::rbsegment_relax::RBSegmentMover::setResidueRange(const class protocols::rbsegment_relax::RBSegment &) –> 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_movement(*args, **kwargs)¶
Overloaded function.
set_movement(self: pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover) -> None
set_movement(self: pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover, sigAxisR: float) -> None
set_movement(self: pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover, sigAxisR: float, sigAxisT: float) -> None
set_movement(self: pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover, sigAxisR: float, sigAxisT: float, sigOffAxisR: float) -> None
set_movement(self: pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover, sigAxisR: float, sigAxisT: float, sigOffAxisR: float, sigOffAxisT: float) -> None
set movement parameters
sigAxisR: the stdev of rotation along the helical axis
sigAxisT: the stdev of movement along the helical axis
sigOffAxisR: the stdev of rotation normal to the helical axis
sigOffAxisT: the stdev of movement normal to the helical axis
C++: protocols::rbsegment_relax::StrandTwistingMover::set_movement(double, double, double, 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_segment(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover, seg: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment) None ¶
Set the segment this mover is working on
C++: protocols::rbsegment_relax::RBSegmentMover::set_segment(const class protocols::rbsegment_relax::RBSegment &) –> 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 &
- pyrosetta.rosetta.protocols.rbsegment_relax.guess_rbsegs_from_pose(pose: pyrosetta.rosetta.core.pose.Pose, rigid_segs: pyrosetta.rosetta.utility.vector1_protocols_rbsegment_relax_RBSegment, rb_chunks: pyrosetta.rosetta.utility.vector1_protocols_rbsegment_relax_RBSegment, loops: pyrosetta.rosetta.protocols.loops.Loops) None ¶
use DSSP and simple rules to guess the asignment of rigid-body segments
C++: protocols::rbsegment_relax::guess_rbsegs_from_pose(const class core::pose::Pose &, class utility::vector1<class protocols::rbsegment_relax::RBSegment, class std::allocator<class protocols::rbsegment_relax::RBSegment> > &, class utility::vector1<class protocols::rbsegment_relax::RBSegment, class std::allocator<class protocols::rbsegment_relax::RBSegment> > &, class protocols::loops::Loops &) –> void
- pyrosetta.rosetta.protocols.rbsegment_relax.read_RBSegment_file(*args, **kwargs)¶
Overloaded function.
read_RBSegment_file(rbsegs: pyrosetta.rosetta.utility.vector1_protocols_rbsegment_relax_RBSegment, loops: pyrosetta.rosetta.protocols.loops.Loops, filename: str) -> None
read_RBSegment_file(rbsegs: pyrosetta.rosetta.utility.vector1_protocols_rbsegment_relax_RBSegment, loops: pyrosetta.rosetta.protocols.loops.Loops, filename: str, autoGenerateLoops: bool) -> None
read_RBSegment_file(rbsegs: pyrosetta.rosetta.utility.vector1_protocols_rbsegment_relax_RBSegment, loops: pyrosetta.rosetta.protocols.loops.Loops, filename: str, autoGenerateLoops: bool, nres: int) -> None
read_RBSegment_file(rbsegs: pyrosetta.rosetta.utility.vector1_protocols_rbsegment_relax_RBSegment, loops: pyrosetta.rosetta.protocols.loops.Loops, filename: str, autoGenerateLoops: bool, nres: int, cutpts: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None
Parses an RB segment file into a vector of RBsegments
C++: protocols::rbsegment_relax::read_RBSegment_file(class utility::vector1<class protocols::rbsegment_relax::RBSegment, class std::allocator<class protocols::rbsegment_relax::RBSegment> > &, class protocols::loops::Loops &, std::string, bool, int, class utility::vector1<unsigned long, class std::allocator<unsigned long> >) –> void
- pyrosetta.rosetta.protocols.rbsegment_relax.remap_rb_segments(rbsegs: pyrosetta.rosetta.utility.vector1_protocols_rbsegment_relax_RBSegment, rbsegs_remap: pyrosetta.rosetta.utility.vector1_protocols_rbsegment_relax_RBSegment, resmap: pyrosetta.rosetta.core.id.SequenceMapping) None ¶
res mapping to rbsegments
C++: protocols::rbsegment_relax::remap_rb_segments(const class utility::vector1<class protocols::rbsegment_relax::RBSegment, class std::allocator<class protocols::rbsegment_relax::RBSegment> > &, class utility::vector1<class protocols::rbsegment_relax::RBSegment, class std::allocator<class protocols::rbsegment_relax::RBSegment> > &, const class core::id::SequenceMapping &) –> void
- pyrosetta.rosetta.protocols.rbsegment_relax.restore_pose_from_rbsegs(rbsegs: pyrosetta.rosetta.utility.vector1_protocols_rbsegment_relax_RBSegment, pose_in: pyrosetta.rosetta.core.pose.Pose, pose_out: pyrosetta.rosetta.core.pose.Pose) None ¶
restore loops from pose
C++: protocols::rbsegment_relax::restore_pose_from_rbsegs(const class utility::vector1<class protocols::rbsegment_relax::RBSegment, class std::allocator<class protocols::rbsegment_relax::RBSegment> > &, const class core::pose::Pose &, class core::pose::Pose &) –> void
- pyrosetta.rosetta.protocols.rbsegment_relax.select_RBsegments(rbsegs_in: pyrosetta.rosetta.utility.vector1_protocols_rbsegment_relax_RBSegment, loops_in: pyrosetta.rosetta.protocols.loops.Loops, rbsegs_selected: pyrosetta.rosetta.utility.vector1_protocols_rbsegment_relax_RBSegment, loops_selected: pyrosetta.rosetta.protocols.loops.Loops) None ¶
C++: protocols::rbsegment_relax::select_RBsegments(const class utility::vector1<class protocols::rbsegment_relax::RBSegment, class std::allocator<class protocols::rbsegment_relax::RBSegment> > &, const class protocols::loops::Loops &, class utility::vector1<class protocols::rbsegment_relax::RBSegment, class std::allocator<class protocols::rbsegment_relax::RBSegment> > &, class protocols::loops::Loops &) –> void
- pyrosetta.rosetta.protocols.rbsegment_relax.set_constraints(pose: pyrosetta.rosetta.core.pose.Pose, cst_pose: pyrosetta.rosetta.core.pose.Pose, cst_width: float, cst_stdev: float, cst_seqwidth: int) None ¶
set up constraints accounting for missing density in start pose
C++: protocols::rbsegment_relax::set_constraints(class core::pose::Pose &, const class core::pose::Pose &, double, double, unsigned long) –> void
- pyrosetta.rosetta.protocols.rbsegment_relax.set_rb_constraints(pose: pyrosetta.rosetta.core.pose.Pose, cst_pose: pyrosetta.rosetta.core.pose.Pose, rbsegs: pyrosetta.rosetta.utility.vector1_protocols_rbsegment_relax_RBSegment, resmap: pyrosetta.rosetta.core.id.SequenceMapping, cst_width: float, cst_stdev: float, cst_seqwidth: int) None ¶
set up constraints over RB segments only; allow ambiguity in sequence threading
C++: protocols::rbsegment_relax::set_rb_constraints(class core::pose::Pose &, const class core::pose::Pose &, const class utility::vector1<class protocols::rbsegment_relax::RBSegment, class std::allocator<class protocols::rbsegment_relax::RBSegment> > &, const class core::id::SequenceMapping &, double, double, unsigned long) –> void
- pyrosetta.rosetta.protocols.rbsegment_relax.setup_disconnected(pose: pyrosetta.rosetta.core.pose.Pose) None ¶
build a pose where every residue is connected by jumps to vrt
C++: protocols::rbsegment_relax::setup_disconnected(class core::pose::Pose &) –> void
- pyrosetta.rosetta.protocols.rbsegment_relax.setup_pose_from_rbsegs(*args, **kwargs)¶
Overloaded function.
setup_pose_from_rbsegs(rbsegs: pyrosetta.rosetta.utility.vector1_protocols_rbsegment_relax_RBSegment, pose_in: pyrosetta.rosetta.core.pose.Pose, pose_out: pyrosetta.rosetta.core.pose.Pose, resmap: pyrosetta.rosetta.core.id.SequenceMapping, mm: pyrosetta.rosetta.core.kinematics.MoveMap) -> None
setup_pose_from_rbsegs(rbsegs: pyrosetta.rosetta.utility.vector1_protocols_rbsegment_relax_RBSegment, pose_in: pyrosetta.rosetta.core.pose.Pose, pose_out: pyrosetta.rosetta.core.pose.Pose, resmap: pyrosetta.rosetta.core.id.SequenceMapping, mm: pyrosetta.rosetta.core.kinematics.MoveMap, fixligs: bool) -> None
remove loops from pose
C++: protocols::rbsegment_relax::setup_pose_from_rbsegs(const class utility::vector1<class protocols::rbsegment_relax::RBSegment, class std::allocator<class protocols::rbsegment_relax::RBSegment> > &, const class core::pose::Pose &, class core::pose::Pose &, class core::id::SequenceMapping &, class core::kinematics::MoveMap &, bool) –> void
- pyrosetta.rosetta.protocols.rbsegment_relax.setup_pose_rbsegs_keep_loops(pose: pyrosetta.rosetta.core.pose.Pose, rbsegs: pyrosetta.rosetta.utility.vector1_protocols_rbsegment_relax_RBSegment, loops: pyrosetta.rosetta.protocols.loops.Loops, mm: pyrosetta.rosetta.core.kinematics.MoveMap) pyrosetta.rosetta.utility.vector1_unsigned_long ¶
C++: protocols::rbsegment_relax::setup_pose_rbsegs_keep_loops(class core::pose::Pose &, const class utility::vector1<class protocols::rbsegment_relax::RBSegment, class std::allocator<class protocols::rbsegment_relax::RBSegment> > &, const class protocols::loops::Loops &, class std::shared_ptr<class core::kinematics::MoveMap>) –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >
- pyrosetta.rosetta.protocols.rbsegment_relax.setup_star_topology(pose: pyrosetta.rosetta.core.pose.Pose) None ¶
setup star-topology fold tree
C++: protocols::rbsegment_relax::setup_star_topology(class core::pose::Pose &) –> void