minimization_packing¶
Bindings for protocols::minimization_packing namespace
- class pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMover¶
Bases:
Mover
- apply(self: pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::minimization_packing::BoltzmannRotamerMover::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMover, : pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMover) pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMover ¶
C++: protocols::minimization_packing::BoltzmannRotamerMover::operator=(const class protocols::minimization_packing::BoltzmannRotamerMover &) –> class protocols::minimization_packing::BoltzmannRotamerMover &
- 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.minimization_packing.BoltzmannRotamerMover) pyrosetta.rosetta.protocols.moves.Mover ¶
clone this object
C++: protocols::minimization_packing::BoltzmannRotamerMover::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.minimization_packing.BoltzmannRotamerMover) pyrosetta.rosetta.protocols.moves.Mover ¶
create this type of object
C++: protocols::minimization_packing::BoltzmannRotamerMover::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_bias_sampling(self: pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMover) bool ¶
C++: protocols::minimization_packing::BoltzmannRotamerMover::get_bias_sampling() const –> bool
- get_bump_check(self: pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMover) bool ¶
C++: protocols::minimization_packing::BoltzmannRotamerMover::get_bump_check() const –> bool
- 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_ligand_resnum(self: pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMover) int ¶
C++: protocols::minimization_packing::BoltzmannRotamerMover::get_ligand_resnum() const –> unsigned long
- get_ligand_weight(self: pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMover) float ¶
C++: protocols::minimization_packing::BoltzmannRotamerMover::get_ligand_weight() const –> double
- get_name(self: pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMover) str ¶
C++: protocols::minimization_packing::BoltzmannRotamerMover::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_randomize_resnum(self: pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMover) bool ¶
C++: protocols::minimization_packing::BoltzmannRotamerMover::get_randomize_resnum() const –> bool
- get_resnum(self: pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMover) int ¶
C++: protocols::minimization_packing::BoltzmannRotamerMover::get_resnum() const –> unsigned long
- get_scorefxn(self: pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMover) pyrosetta.rosetta.core.scoring.ScoreFunction ¶
C++: protocols::minimization_packing::BoltzmannRotamerMover::get_scorefxn() const –> class std::shared_ptr<const class core::scoring::ScoreFunction>
- 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_task(self: pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMover) pyrosetta.rosetta.core.pack.task.PackerTask ¶
C++: protocols::minimization_packing::BoltzmannRotamerMover::get_task() const –> class std::shared_ptr<class core::pack::task::PackerTask>
- get_temperature(self: pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMover) float ¶
C++: protocols::minimization_packing::BoltzmannRotamerMover::get_temperature() const –> double
- 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::minimization_packing::BoltzmannRotamerMover::mover_name() –> std::string
- static name() str ¶
C++: protocols::moves::Mover::name() –> std::string
- parse_my_tag(self: pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None ¶
C++: protocols::minimization_packing::BoltzmannRotamerMover::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::minimization_packing::BoltzmannRotamerMover::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
- select_rotamer(self: pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMover, boltzmann_factors: pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_double_t, partition_function: float) int ¶
C++: protocols::minimization_packing::BoltzmannRotamerMover::select_rotamer(const class utility::vector1<struct std::pair<unsigned long, double>, class std::allocator<struct std::pair<unsigned long, double> > > &, const double &) –> unsigned long
- set_bias_sampling(self: pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMover, bias_sampling: bool) None ¶
C++: protocols::minimization_packing::BoltzmannRotamerMover::set_bias_sampling(bool) –> void
- set_bump_check(self: pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMover, bump_check: bool) None ¶
C++: protocols::minimization_packing::BoltzmannRotamerMover::set_bump_check(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_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
setter for poses contained for rms
C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void
- set_ligand_resnum(self: pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMover, ligand_resnum: int) None ¶
C++: protocols::minimization_packing::BoltzmannRotamerMover::set_ligand_resnum(unsigned long) –> void
- set_ligand_weight(self: pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMover, ligand_weight: float) None ¶
C++: protocols::minimization_packing::BoltzmannRotamerMover::set_ligand_weight(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_randomize_resnum(self: pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMover, randomize_resnum: bool) None ¶
C++: protocols::minimization_packing::BoltzmannRotamerMover::set_randomize_resnum(bool) –> void
- set_resnum(self: pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMover, resnum: int) None ¶
C++: protocols::minimization_packing::BoltzmannRotamerMover::set_resnum(unsigned long) –> void
- set_score_function(self: pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMover, sf: pyrosetta.rosetta.core.scoring.ScoreFunction) None ¶
C++: protocols::minimization_packing::BoltzmannRotamerMover::set_score_function(class std::shared_ptr<const class core::scoring::ScoreFunction>) –> void
- set_scorefxn(self: pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMover, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) None ¶
C++: protocols::minimization_packing::BoltzmannRotamerMover::set_scorefxn(class std::shared_ptr<const class core::scoring::ScoreFunction>) –> void
- set_task(self: pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMover, task: pyrosetta.rosetta.core.pack.task.PackerTask) None ¶
C++: protocols::minimization_packing::BoltzmannRotamerMover::set_task(class std::shared_ptr<class core::pack::task::PackerTask>) –> void
- set_task_factory(self: pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMover, tf: pyrosetta.rosetta.core.pack.task.TaskFactory) None ¶
C++: protocols::minimization_packing::BoltzmannRotamerMover::set_task_factory(class std::shared_ptr<const class core::pack::task::TaskFactory>) –> void
- set_temperature(self: pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMover, temperature: float) None ¶
C++: protocols::minimization_packing::BoltzmannRotamerMover::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.minimization_packing.BoltzmannRotamerMover) -> None
show(self: pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMover, output: pyrosetta.rosetta.std.ostream) -> None
C++: protocols::minimization_packing::BoltzmannRotamerMover::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.minimization_packing.BoltzmannRotamerMoverCreator¶
Bases:
MoverCreator
- assign(self: pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMoverCreator, : pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMoverCreator) pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMoverCreator ¶
C++: protocols::minimization_packing::BoltzmannRotamerMoverCreator::operator=(const class protocols::minimization_packing::BoltzmannRotamerMoverCreator &) –> class protocols::minimization_packing::BoltzmannRotamerMoverCreator &
- create_mover(self: pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMoverCreator) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::minimization_packing::BoltzmannRotamerMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>
- keyname(self: pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMoverCreator) str ¶
C++: protocols::minimization_packing::BoltzmannRotamerMoverCreator::keyname() const –> std::string
- class pyrosetta.rosetta.protocols.minimization_packing.ChainGroupDiscriminator¶
Bases:
GroupDiscriminator
- assign(self: pyrosetta.rosetta.protocols.minimization_packing.ChainGroupDiscriminator, : pyrosetta.rosetta.protocols.minimization_packing.ChainGroupDiscriminator) pyrosetta.rosetta.protocols.minimization_packing.ChainGroupDiscriminator ¶
C++: protocols::minimization_packing::ChainGroupDiscriminator::operator=(const class protocols::minimization_packing::ChainGroupDiscriminator &) –> class protocols::minimization_packing::ChainGroupDiscriminator &
- clone(self: pyrosetta.rosetta.protocols.minimization_packing.ChainGroupDiscriminator) pyrosetta.rosetta.protocols.minimization_packing.GroupDiscriminator ¶
C++: protocols::minimization_packing::ChainGroupDiscriminator::clone() const –> class std::shared_ptr<class protocols::minimization_packing::GroupDiscriminator>
- group_id(self: pyrosetta.rosetta.protocols.minimization_packing.ChainGroupDiscriminator, pose: pyrosetta.rosetta.core.pose.Pose, seqpos: int) int ¶
C++: protocols::minimization_packing::ChainGroupDiscriminator::group_id(const class core::pose::Pose &, unsigned long) const –> unsigned long
- class pyrosetta.rosetta.protocols.minimization_packing.DisulfideOptimizationMover¶
Bases:
Mover
A Mover to jointly optimize the geometry of a pair of disulfide-bonded residues.
- apply(self: pyrosetta.rosetta.protocols.minimization_packing.DisulfideOptimizationMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
Apply the mover
C++: protocols::minimization_packing::DisulfideOptimizationMover::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.minimization_packing.DisulfideOptimizationMover, : pyrosetta.rosetta.protocols.minimization_packing.DisulfideOptimizationMover) pyrosetta.rosetta.protocols.minimization_packing.DisulfideOptimizationMover ¶
C++: protocols::minimization_packing::DisulfideOptimizationMover::operator=(const class protocols::minimization_packing::DisulfideOptimizationMover &) –> class protocols::minimization_packing::DisulfideOptimizationMover &
- 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.minimization_packing.DisulfideOptimizationMover) pyrosetta.rosetta.protocols.moves.Mover ¶
required in the context of the parser/scripting scheme
C++: protocols::minimization_packing::DisulfideOptimizationMover::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.minimization_packing.DisulfideOptimizationMover) pyrosetta.rosetta.protocols.moves.Mover ¶
required in the context of the parser/scripting scheme
C++: protocols::minimization_packing::DisulfideOptimizationMover::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.minimization_packing.DisulfideOptimizationMover) str ¶
C++: protocols::minimization_packing::DisulfideOptimizationMover::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 > > &
- interaction_graph_threads(self: pyrosetta.rosetta.protocols.minimization_packing.DisulfideOptimizationMover) int ¶
Set threads to request for packing.
Vikram K. Mulligan (vmulligan.org).
C++: protocols::minimization_packing::DisulfideOptimizationMover::interaction_graph_threads() const –> unsigned long
- 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::minimization_packing::DisulfideOptimizationMover::mover_name() –> std::string
- static name() str ¶
C++: protocols::moves::Mover::name() –> std::string
- parse_my_tag(self: pyrosetta.rosetta.protocols.minimization_packing.DisulfideOptimizationMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None ¶
parse XML tag (to use this Mover in Rosetta Scripts)
C++: protocols::minimization_packing::DisulfideOptimizationMover::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::minimization_packing::DisulfideOptimizationMover::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_final_optimization_n_iter(self: pyrosetta.rosetta.protocols.minimization_packing.DisulfideOptimizationMover, final_optimization_n_iter: int) None ¶
C++: protocols::minimization_packing::DisulfideOptimizationMover::set_final_optimization_n_iter(const unsigned long) –> void
- set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
setter for poses contained for rms
C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void
- set_interaction_graph_threads(self: pyrosetta.rosetta.protocols.minimization_packing.DisulfideOptimizationMover, setting: int) None ¶
Set threads to request for packing.
Vikram K. Mulligan (vmulligan.org).
C++: protocols::minimization_packing::DisulfideOptimizationMover::set_interaction_graph_threads(const unsigned long) –> 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_score_function(self: pyrosetta.rosetta.protocols.minimization_packing.DisulfideOptimizationMover, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) None ¶
C++: protocols::minimization_packing::DisulfideOptimizationMover::set_score_function(const class std::shared_ptr<const class core::scoring::ScoreFunction> &) –> void
- set_selector(self: pyrosetta.rosetta.protocols.minimization_packing.DisulfideOptimizationMover, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) None ¶
C++: protocols::minimization_packing::DisulfideOptimizationMover::set_selector(const class std::shared_ptr<const class core::select::residue_selector::ResidueSelector> &) –> void
- set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) None ¶
Set the ‘type’ string
C++: protocols::moves::Mover::set_type(const std::string &) –> void
- show(*args, **kwargs)¶
Overloaded function.
show(self: pyrosetta.rosetta.protocols.minimization_packing.DisulfideOptimizationMover) -> None
show(self: pyrosetta.rosetta.protocols.minimization_packing.DisulfideOptimizationMover, output: pyrosetta.rosetta.std.ostream) -> None
C++: protocols::minimization_packing::DisulfideOptimizationMover::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.minimization_packing.DisulfideOptimizationMoverCreator¶
Bases:
MoverCreator
- assign(self: pyrosetta.rosetta.protocols.minimization_packing.DisulfideOptimizationMoverCreator, : pyrosetta.rosetta.protocols.minimization_packing.DisulfideOptimizationMoverCreator) pyrosetta.rosetta.protocols.minimization_packing.DisulfideOptimizationMoverCreator ¶
C++: protocols::minimization_packing::DisulfideOptimizationMoverCreator::operator=(const class protocols::minimization_packing::DisulfideOptimizationMoverCreator &) –> class protocols::minimization_packing::DisulfideOptimizationMoverCreator &
- create_mover(self: pyrosetta.rosetta.protocols.minimization_packing.DisulfideOptimizationMoverCreator) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::minimization_packing::DisulfideOptimizationMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>
- keyname(self: pyrosetta.rosetta.protocols.minimization_packing.DisulfideOptimizationMoverCreator) str ¶
C++: protocols::minimization_packing::DisulfideOptimizationMoverCreator::keyname() const –> std::string
- provide_xml_schema(self: pyrosetta.rosetta.protocols.minimization_packing.DisulfideOptimizationMoverCreator, xsd: utility::tag::XMLSchemaDefinition) None ¶
C++: protocols::minimization_packing::DisulfideOptimizationMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void
- class pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMinMover¶
Bases:
RotamerTrialsMinMover
Wrapper for Rotamer Trials with Minimization, which modifies only rotamers whose energy changed by a given constant
- apply(self: pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMinMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
apply this mover to a pose
C++: protocols::minimization_packing::EnergyCutRotamerTrialsMinMover::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMinMover, : pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMinMover) pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMinMover ¶
C++: protocols::minimization_packing::EnergyCutRotamerTrialsMinMover::operator=(const class protocols::minimization_packing::EnergyCutRotamerTrialsMinMover &) –> class protocols::minimization_packing::EnergyCutRotamerTrialsMinMover &
- 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.minimization_packing.RotamerTrialsMinMover) pyrosetta.rosetta.protocols.moves.Mover ¶
Return a copy of this mover instance (for RosettaScripts)
C++: protocols::minimization_packing::RotamerTrialsMinMover::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.minimization_packing.RotamerTrialsMinMover) pyrosetta.rosetta.protocols.moves.Mover ¶
Return a new mover instance (for RosettaScripts)
C++: protocols::minimization_packing::RotamerTrialsMinMover::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.minimization_packing.EnergyCutRotamerTrialsMinMover) str ¶
C++: protocols::minimization_packing::EnergyCutRotamerTrialsMinMover::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 > > &
- init(self: pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMinMover) None ¶
C++: protocols::minimization_packing::RotamerTrialsMinMover::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::minimization_packing::RotamerTrialsMinMover::mover_name() –> std::string
- static name() str ¶
C++: protocols::moves::Mover::name() –> std::string
- parse_my_tag(self: pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMinMover, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None ¶
Parse XML for RosettaScripts
C++: protocols::minimization_packing::RotamerTrialsMinMover::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::minimization_packing::RotamerTrialsMinMover::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
- score_function(self: pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMinMover, sf: pyrosetta.rosetta.core.scoring.ScoreFunction) None ¶
C++: protocols::minimization_packing::RotamerTrialsMinMover::score_function(class std::shared_ptr<const class core::scoring::ScoreFunction>) –> 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.minimization_packing.RotamerTrialsMinMover) -> None
show(self: pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMinMover, output: pyrosetta.rosetta.std.ostream) -> None
C++: protocols::minimization_packing::RotamerTrialsMinMover::show(std::ostream &) const –> void
- task_factory(self: pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMinMover, tf: pyrosetta.rosetta.core.pack.task.TaskFactory) None ¶
C++: protocols::minimization_packing::RotamerTrialsMinMover::task_factory(class std::shared_ptr<const class core::pack::task::TaskFactory>) –> 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.minimization_packing.EnergyCutRotamerTrialsMover¶
Bases:
RotamerTrialsMover
- apply(self: pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
apply this mover to a pose
C++: protocols::minimization_packing::EnergyCutRotamerTrialsMover::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMover, : pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMover) pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMover ¶
C++: protocols::minimization_packing::EnergyCutRotamerTrialsMover::operator=(const class protocols::minimization_packing::EnergyCutRotamerTrialsMover &) –> class protocols::minimization_packing::EnergyCutRotamerTrialsMover &
- 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.minimization_packing.RotamerTrialsMover) pyrosetta.rosetta.protocols.moves.Mover ¶
clone this object
C++: protocols::minimization_packing::RotamerTrialsMover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>
- static complex_type_generator_for_rotamer_trials_mover(xsd: utility::tag::XMLSchemaDefinition) utility::tag::XMLSchemaComplexTypeGenerator ¶
C++: protocols::minimization_packing::RotamerTrialsMover::complex_type_generator_for_rotamer_trials_mover(class utility::tag::XMLSchemaDefinition &) –> class std::shared_ptr<class utility::tag::XMLSchemaComplexTypeGenerator>
- create(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>
- fresh_instance(self: pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMover) pyrosetta.rosetta.protocols.moves.Mover ¶
create this type of object
C++: protocols::minimization_packing::RotamerTrialsMover::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.minimization_packing.EnergyCutRotamerTrialsMover) str ¶
C++: protocols::minimization_packing::EnergyCutRotamerTrialsMover::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::minimization_packing::RotamerTrialsMover::mover_name() –> std::string
- static name() str ¶
C++: protocols::moves::Mover::name() –> std::string
- parse_my_tag(self: pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None ¶
C++: protocols::minimization_packing::RotamerTrialsMover::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::minimization_packing::RotamerTrialsMover::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
- score_function(self: pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMover, sf: pyrosetta.rosetta.core.scoring.ScoreFunction) None ¶
C++: protocols::minimization_packing::RotamerTrialsMover::score_function(class std::shared_ptr<const class core::scoring::ScoreFunction>) –> 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.minimization_packing.RotamerTrialsMover) -> None
show(self: pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMover, output: pyrosetta.rosetta.std.ostream) -> None
C++: protocols::minimization_packing::RotamerTrialsMover::show(std::ostream &) const –> void
- task_factory(self: pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMover, tf: pyrosetta.rosetta.core.pack.task.TaskFactory) None ¶
C++: protocols::minimization_packing::RotamerTrialsMover::task_factory(class std::shared_ptr<const class core::pack::task::TaskFactory>) –> 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.minimization_packing.GreenPacker¶
Bases:
Mover
- apply(self: pyrosetta.rosetta.protocols.minimization_packing.GreenPacker, : pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::minimization_packing::GreenPacker::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.minimization_packing.GreenPacker, : pyrosetta.rosetta.protocols.minimization_packing.GreenPacker) pyrosetta.rosetta.protocols.minimization_packing.GreenPacker ¶
C++: protocols::minimization_packing::GreenPacker::operator=(const class protocols::minimization_packing::GreenPacker &) –> class protocols::minimization_packing::GreenPacker &
- 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.minimization_packing.GreenPacker) str ¶
C++: protocols::minimization_packing::GreenPacker::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_group_discriminator(self: pyrosetta.rosetta.protocols.minimization_packing.GreenPacker, : pyrosetta.rosetta.protocols.minimization_packing.GroupDiscriminator) None ¶
C++: protocols::minimization_packing::GreenPacker::set_group_discriminator(class std::shared_ptr<class protocols::minimization_packing::GroupDiscriminator>) –> 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_reference_round_task_factory(self: pyrosetta.rosetta.protocols.minimization_packing.GreenPacker, : pyrosetta.rosetta.core.pack.task.TaskFactory) None ¶
C++: protocols::minimization_packing::GreenPacker::set_reference_round_task_factory(class std::shared_ptr<class core::pack::task::TaskFactory>) –> void
- set_scorefunction(self: pyrosetta.rosetta.protocols.minimization_packing.GreenPacker, : pyrosetta.rosetta.core.scoring.ScoreFunction) None ¶
C++: protocols::minimization_packing::GreenPacker::set_scorefunction(const class core::scoring::ScoreFunction &) –> void
- set_task_factory(self: pyrosetta.rosetta.protocols.minimization_packing.GreenPacker, : pyrosetta.rosetta.core.pack.task.TaskFactory) None ¶
C++: protocols::minimization_packing::GreenPacker::set_task_factory(class std::shared_ptr<class core::pack::task::TaskFactory>) –> 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.minimization_packing.GroupDiscriminator¶
Bases:
pybind11_object
Interface class used to break a pose down into a set of component “groups” where intra-group rotamer-pair energies are preserved between calls to the GreenPacker. E.g. in rigid-body docking between two proteins, chains 1 and 2 define groups 1 and 2. In rigid-body docking between two domains of the same chain, those residues upstream of jump 1 define group 1, and those downstream of jump 1 define group 2. In loop modelling, the static background is group 1, and the loop itself is group 0, since loop residues will have their bb dofs change regularly between repackings.
- assign(self: pyrosetta.rosetta.protocols.minimization_packing.GroupDiscriminator, : pyrosetta.rosetta.protocols.minimization_packing.GroupDiscriminator) pyrosetta.rosetta.protocols.minimization_packing.GroupDiscriminator ¶
C++: protocols::minimization_packing::GroupDiscriminator::operator=(const class protocols::minimization_packing::GroupDiscriminator &) –> class protocols::minimization_packing::GroupDiscriminator &
- clone(self: pyrosetta.rosetta.protocols.minimization_packing.GroupDiscriminator) pyrosetta.rosetta.protocols.minimization_packing.GroupDiscriminator ¶
C++: protocols::minimization_packing::GroupDiscriminator::clone() const –> class std::shared_ptr<class protocols::minimization_packing::GroupDiscriminator>
- group_id(self: pyrosetta.rosetta.protocols.minimization_packing.GroupDiscriminator, pose: pyrosetta.rosetta.core.pose.Pose, seqpos: int) int ¶
C++: protocols::minimization_packing::GroupDiscriminator::group_id(const class core::pose::Pose &, unsigned long) const –> unsigned long
- class pyrosetta.rosetta.protocols.minimization_packing.MinMover¶
Bases:
MoveMapMover
A protocols::moves::Mover that minimizes a Pose to a local energy minimum by performing energy minimization of a ScoreFunction over the allowable degrees of freedom, defined by a MoveMap. The minimization type, minimization tolerance, and various other options can be also be set.
- Common Methods:
MinMover.apply MinMover.movemap MinMover.score_function
- abs_score_convergence_threshold(*args, **kwargs)¶
Overloaded function.
abs_score_convergence_threshold(self: pyrosetta.rosetta.protocols.minimization_packing.MinMover, newval: float) -> None
C++: protocols::minimization_packing::MinMover::abs_score_convergence_threshold(double) –> void
abs_score_convergence_threshold(self: pyrosetta.rosetta.protocols.minimization_packing.MinMover) -> float
C++: protocols::minimization_packing::MinMover::abs_score_convergence_threshold() const –> double
- abs_score_diff_after_minimization(self: pyrosetta.rosetta.protocols.minimization_packing.MinMover) float ¶
C++: protocols::minimization_packing::MinMover::abs_score_diff_after_minimization() const –> double
- apply(self: pyrosetta.rosetta.protocols.minimization_packing.MinMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
- Minimizes the DOFs of <pose_> specified in the MoveMap
using the ScoreFunction
- example(s):
minmover.apply(pose)
- See also:
MinMover MinMover.movemap MinMover.score_function
C++: protocols::minimization_packing::MinMover::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.minimization_packing.MinMover, : pyrosetta.rosetta.protocols.minimization_packing.MinMover) pyrosetta.rosetta.protocols.minimization_packing.MinMover ¶
C++: protocols::minimization_packing::MinMover::operator=(const class protocols::minimization_packing::MinMover &) –> class protocols::minimization_packing::MinMover &
- cartesian(*args, **kwargs)¶
Overloaded function.
cartesian(self: pyrosetta.rosetta.protocols.minimization_packing.MinMover, newval: bool) -> None
C++: protocols::minimization_packing::MinMover::cartesian(bool) –> void
cartesian(self: pyrosetta.rosetta.protocols.minimization_packing.MinMover) -> bool
C++: protocols::minimization_packing::MinMover::cartesian() const –> bool
- clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) None ¶
Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.
clear_info is called by jd2 before calling apply
C++: protocols::moves::Mover::clear_info() –> void
- clone(self: pyrosetta.rosetta.protocols.minimization_packing.MinMover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::minimization_packing::MinMover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>
- static complex_type_generator_for_min_mover(xsd: utility::tag::XMLSchemaDefinition) utility::tag::XMLSchemaComplexTypeGenerator ¶
C++: protocols::minimization_packing::MinMover::complex_type_generator_for_min_mover(class utility::tag::XMLSchemaDefinition &) –> class std::shared_ptr<class utility::tag::XMLSchemaComplexTypeGenerator>
- create(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>
- deriv_check(*args, **kwargs)¶
Overloaded function.
deriv_check(self: pyrosetta.rosetta.protocols.minimization_packing.MinMover, deriv_check_in: bool) -> None
C++: protocols::minimization_packing::MinMover::deriv_check(bool) –> void
deriv_check(self: pyrosetta.rosetta.protocols.minimization_packing.MinMover) -> bool
C++: protocols::minimization_packing::MinMover::deriv_check() const –> bool
- explicitly_set_movemap(self: pyrosetta.rosetta.protocols.minimization_packing.MinMover) pyrosetta.rosetta.core.kinematics.MoveMap ¶
- Get the explicitly set movemap object, if present, nullptr if not
Will not create a default or look at the MoveMapFactory
C++: protocols::minimization_packing::MinMover::explicitly_set_movemap() const –> class std::shared_ptr<const class core::kinematics::MoveMap>
- fresh_instance(self: pyrosetta.rosetta.protocols.minimization_packing.MinMover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::minimization_packing::MinMover::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.minimization_packing.MinMover) str ¶
C++: protocols::minimization_packing::MinMover::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(self: pyrosetta.rosetta.protocols.moves.MoveMapMover, : pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::moves::MoveMapMover::initialize(class core::pose::Pose &) –> void
- last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) float ¶
C++: protocols::moves::Mover::last_proposal_density_ratio() –> double
- max_iter(self: pyrosetta.rosetta.protocols.minimization_packing.MinMover, max_iter_in: int) None ¶
C++: protocols::minimization_packing::MinMover::max_iter(unsigned long) –> void
- min_options(*args, **kwargs)¶
Overloaded function.
min_options(self: pyrosetta.rosetta.protocols.minimization_packing.MinMover) -> pyrosetta.rosetta.core.optimization.MinimizerOptions
allow non-const access to the internal minimizer options object
C++: protocols::minimization_packing::MinMover::min_options() –> class std::shared_ptr<class core::optimization::MinimizerOptions>
min_options(self: pyrosetta.rosetta.protocols.minimization_packing.MinMover, min_options: pyrosetta.rosetta.core.optimization.MinimizerOptions) -> None
directly set the internal minimizer options object
C++: protocols::minimization_packing::MinMover::min_options(class std::shared_ptr<class core::optimization::MinimizerOptions>) –> void
- min_type(*args, **kwargs)¶
Overloaded function.
min_type(self: pyrosetta.rosetta.protocols.minimization_packing.MinMover, min_type_in: str) -> None
C++: protocols::minimization_packing::MinMover::min_type(std::string) –> void
min_type(self: pyrosetta.rosetta.protocols.minimization_packing.MinMover) -> str
C++: protocols::minimization_packing::MinMover::min_type() const –> std::string
- movemap(*args, **kwargs)¶
Overloaded function.
movemap(self: pyrosetta.rosetta.protocols.minimization_packing.MinMover, movemap_in: pyrosetta.rosetta.core.kinematics.MoveMap) -> None
- Sets the MoveMap to <movemap_in>
determines which DOF to minimize
- example(s):
minmover.movemap(movemap1)
- See also:
MinMover MinMover.apply MinMover.score_function MoveMap
C++: protocols::minimization_packing::MinMover::movemap(class std::shared_ptr<const class core::kinematics::MoveMap>) –> void
movemap(self: pyrosetta.rosetta.protocols.minimization_packing.MinMover, pose: pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.core.kinematics.MoveMap
Get the movemap for the pose
This is the preferred version to call.
C++: protocols::minimization_packing::MinMover::movemap(const class core::pose::Pose &) const –> class std::shared_ptr<const class core::kinematics::MoveMap>
- movemap_factory(self: pyrosetta.rosetta.protocols.minimization_packing.MinMover, mmf: pyrosetta.rosetta.core.select.movemap.MoveMapFactory) None ¶
- Sets the MoveMapFactory
The MoveMapFactory will be used to construct a MoveMap if an explicit one isn’t set
C++: protocols::minimization_packing::MinMover::movemap_factory(class std::shared_ptr<const class core::select::movemap::MoveMapFactory>) –> void
- static mover_name() str ¶
C++: protocols::minimization_packing::MinMover::mover_name() –> std::string
- static name() str ¶
C++: protocols::moves::Mover::name() –> std::string
- nb_list(*args, **kwargs)¶
Overloaded function.
nb_list(self: pyrosetta.rosetta.protocols.minimization_packing.MinMover, nb_list_in: bool) -> None
core::optimization::MinimizerOptions::use_nblist(bool)
C++: protocols::minimization_packing::MinMover::nb_list(bool) –> void
nb_list(self: pyrosetta.rosetta.protocols.minimization_packing.MinMover) -> bool
core::optimization::MinimizerOptions::use_nblist()
C++: protocols::minimization_packing::MinMover::nb_list() const –> bool
- omega(*args, **kwargs)¶
Overloaded function.
omega(self: pyrosetta.rosetta.protocols.minimization_packing.MinMover) -> bool
C++: protocols::minimization_packing::MinMover::omega() const –> bool
omega(self: pyrosetta.rosetta.protocols.minimization_packing.MinMover, b: bool) -> None
C++: protocols::minimization_packing::MinMover::omega(const bool) –> void
- parse_dof_task_type(self: pyrosetta.rosetta.protocols.minimization_packing.MinMover, tag_name: str, dof_type: pyrosetta.rosetta.core.id.DOF_Type, torsion_type: pyrosetta.rosetta.core.id.TorsionType, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None ¶
C++: protocols::minimization_packing::MinMover::parse_dof_task_type(const std::string &, enum core::id::DOF_Type, enum core::id::TorsionType, class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- parse_dof_tasks(self: pyrosetta.rosetta.protocols.minimization_packing.MinMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None ¶
C++: protocols::minimization_packing::MinMover::parse_dof_tasks(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- parse_movemap_factory(self: pyrosetta.rosetta.protocols.minimization_packing.MinMover, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None ¶
C++: protocols::minimization_packing::MinMover::parse_movemap_factory(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- parse_my_tag(self: pyrosetta.rosetta.protocols.minimization_packing.MinMover, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None ¶
Called by protocols::moves::MoverFactory when constructing new protocols::moves::Movers. Takes care of the specific mover’s parsing.
C++: protocols::minimization_packing::MinMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- parse_opts(self: pyrosetta.rosetta.protocols.minimization_packing.MinMover, : pyrosetta.rosetta.utility.tag.Tag, data_map: pyrosetta.rosetta.basic.datacache.DataMap) None ¶
C++: protocols::minimization_packing::MinMover::parse_opts(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::minimization_packing::MinMover::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
- score_diff_after_minimization(self: pyrosetta.rosetta.protocols.minimization_packing.MinMover) float ¶
C++: protocols::minimization_packing::MinMover::score_diff_after_minimization() const –> double
- score_function(*args, **kwargs)¶
Overloaded function.
score_function(self: pyrosetta.rosetta.protocols.minimization_packing.MinMover, scorefxn_in: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None
- Sets the ScoreFunction to <scorefxn_in>
determines which function to minimize
- example(s):
minmover.score_function(scorefxn)
- See also:
MinMover MinMover.apply MinMover.movemap ScoreFunction
C++: protocols::minimization_packing::MinMover::score_function(class std::shared_ptr<const class core::scoring::ScoreFunction>) –> void
score_function(self: pyrosetta.rosetta.protocols.minimization_packing.MinMover) -> pyrosetta.rosetta.core.scoring.ScoreFunction
C++: protocols::minimization_packing::MinMover::score_function() const –> class std::shared_ptr<const class core::scoring::ScoreFunction>
- set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) None ¶
C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void
- set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) None ¶
C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void
- set_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_movemap(self: pyrosetta.rosetta.protocols.minimization_packing.MinMover, movemap_in: pyrosetta.rosetta.core.kinematics.MoveMap) None ¶
C++: protocols::minimization_packing::MinMover::set_movemap(class std::shared_ptr<const class core::kinematics::MoveMap>) –> 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.minimization_packing.MinMover) -> None
show(self: pyrosetta.rosetta.protocols.minimization_packing.MinMover, output: pyrosetta.rosetta.std.ostream) -> None
C++: protocols::minimization_packing::MinMover::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
- tolerance(*args, **kwargs)¶
Overloaded function.
tolerance(self: pyrosetta.rosetta.protocols.minimization_packing.MinMover, tolerance_in: float) -> None
C++: protocols::minimization_packing::MinMover::tolerance(double) –> void
tolerance(self: pyrosetta.rosetta.protocols.minimization_packing.MinMover) -> float
C++: protocols::minimization_packing::MinMover::tolerance() const –> double
- 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.minimization_packing.MinMoverCreator¶
Bases:
MoverCreator
- assign(self: pyrosetta.rosetta.protocols.minimization_packing.MinMoverCreator, : pyrosetta.rosetta.protocols.minimization_packing.MinMoverCreator) pyrosetta.rosetta.protocols.minimization_packing.MinMoverCreator ¶
C++: protocols::minimization_packing::MinMoverCreator::operator=(const class protocols::minimization_packing::MinMoverCreator &) –> class protocols::minimization_packing::MinMoverCreator &
- create_mover(self: pyrosetta.rosetta.protocols.minimization_packing.MinMoverCreator) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::minimization_packing::MinMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>
- keyname(self: pyrosetta.rosetta.protocols.minimization_packing.MinMoverCreator) str ¶
C++: protocols::minimization_packing::MinMoverCreator::keyname() const –> std::string
- static mover_name() str ¶
C++: protocols::minimization_packing::MinMoverCreator::mover_name() –> std::string
- class pyrosetta.rosetta.protocols.minimization_packing.MinPackMover¶
Bases:
Mover
a mover that packs and minimizes the side-chains. It uses a ScoreFunction for packing and either a PackerTask, or a TaskFactory that generates a PackerTask for instructions on what rotamer sets are allowed at each residue position during packing.
- apply(self: pyrosetta.rosetta.protocols.minimization_packing.MinPackMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::minimization_packing::MinPackMover::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.minimization_packing.MinPackMover, : pyrosetta.rosetta.protocols.minimization_packing.MinPackMover) pyrosetta.rosetta.protocols.minimization_packing.MinPackMover ¶
C++: protocols::minimization_packing::MinPackMover::operator=(const class protocols::minimization_packing::MinPackMover &) –> class protocols::minimization_packing::MinPackMover &
- 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.minimization_packing.MinPackMover) pyrosetta.rosetta.protocols.moves.Mover ¶
required in the context of the parser/scripting scheme
C++: protocols::minimization_packing::MinPackMover::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.minimization_packing.MinPackMover) pyrosetta.rosetta.protocols.moves.Mover ¶
required in the context of the parser/scripting scheme
C++: protocols::minimization_packing::MinPackMover::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.minimization_packing.MinPackMover) str ¶
C++: protocols::minimization_packing::MinPackMover::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 > > &
- init(self: pyrosetta.rosetta.protocols.minimization_packing.MinPackMover) None ¶
C++: protocols::minimization_packing::MinPackMover::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::minimization_packing::MinPackMover::mover_name() –> std::string
- static name() str ¶
C++: protocols::moves::Mover::name() –> std::string
- off_rotamer_pack(*args, **kwargs)¶
Overloaded function.
off_rotamer_pack(self: pyrosetta.rosetta.protocols.minimization_packing.MinPackMover, : bool) -> None
C++: protocols::minimization_packing::MinPackMover::off_rotamer_pack(bool) –> void
off_rotamer_pack(self: pyrosetta.rosetta.protocols.minimization_packing.MinPackMover) -> bool
C++: protocols::minimization_packing::MinPackMover::off_rotamer_pack() const –> bool
- parse_my_tag(self: pyrosetta.rosetta.protocols.minimization_packing.MinPackMover, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None ¶
parse XML (specifically in the context of the parser/scripting scheme)
C++: protocols::minimization_packing::MinPackMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- parse_score_function(self: pyrosetta.rosetta.protocols.minimization_packing.MinPackMover, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None ¶
parse “scorefxn” XML option (can be employed virtually by derived Packing movers)
C++: protocols::minimization_packing::MinPackMover::parse_score_function(class std::shared_ptr<const class utility::tag::Tag>, const class basic::datacache::DataMap &) –> void
- parse_task_operations(self: pyrosetta.rosetta.protocols.minimization_packing.MinPackMover, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None ¶
parse “task_operations” XML option (can be employed virtually by derived Packing movers)
C++: protocols::minimization_packing::MinPackMover::parse_task_operations(class std::shared_ptr<const class utility::tag::Tag>, const 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::minimization_packing::MinPackMover::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
- score_function(*args, **kwargs)¶
Overloaded function.
score_function(self: pyrosetta.rosetta.protocols.minimization_packing.MinPackMover, sf: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None
C++: protocols::minimization_packing::MinPackMover::score_function(class std::shared_ptr<const class core::scoring::ScoreFunction>) –> void
score_function(self: pyrosetta.rosetta.protocols.minimization_packing.MinPackMover) -> pyrosetta.rosetta.core.scoring.ScoreFunction
C++: protocols::minimization_packing::MinPackMover::score_function() const –> class std::shared_ptr<const class core::scoring::ScoreFunction>
- set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) None ¶
C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void
- set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) None ¶
C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void
- set_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
- task(*args, **kwargs)¶
Overloaded function.
task(self: pyrosetta.rosetta.protocols.minimization_packing.MinPackMover, t: pyrosetta.rosetta.core.pack.task.PackerTask) -> None
C++: protocols::minimization_packing::MinPackMover::task(class std::shared_ptr<const class core::pack::task::PackerTask>) –> void
task(self: pyrosetta.rosetta.protocols.minimization_packing.MinPackMover) -> pyrosetta.rosetta.core.pack.task.PackerTask
C++: protocols::minimization_packing::MinPackMover::task() const –> class std::shared_ptr<const class core::pack::task::PackerTask>
- task_factory(*args, **kwargs)¶
Overloaded function.
task_factory(self: pyrosetta.rosetta.protocols.minimization_packing.MinPackMover, tf: pyrosetta.rosetta.core.pack.task.TaskFactory) -> None
C++: protocols::minimization_packing::MinPackMover::task_factory(class std::shared_ptr<const class core::pack::task::TaskFactory>) –> void
task_factory(self: pyrosetta.rosetta.protocols.minimization_packing.MinPackMover) -> pyrosetta.rosetta.core.pack.task.TaskFactory
C++: protocols::minimization_packing::MinPackMover::task_factory() const –> class std::shared_ptr<const class core::pack::task::TaskFactory>
- task_is_valid(self: pyrosetta.rosetta.protocols.minimization_packing.MinPackMover, pose: pyrosetta.rosetta.core.pose.Pose) bool ¶
C++: protocols::minimization_packing::MinPackMover::task_is_valid(const class core::pose::Pose &) const –> bool
- 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.minimization_packing.MinPackMoverCreator¶
Bases:
MoverCreator
- assign(self: pyrosetta.rosetta.protocols.minimization_packing.MinPackMoverCreator, : pyrosetta.rosetta.protocols.minimization_packing.MinPackMoverCreator) pyrosetta.rosetta.protocols.minimization_packing.MinPackMoverCreator ¶
C++: protocols::minimization_packing::MinPackMoverCreator::operator=(const class protocols::minimization_packing::MinPackMoverCreator &) –> class protocols::minimization_packing::MinPackMoverCreator &
- create_mover(self: pyrosetta.rosetta.protocols.minimization_packing.MinPackMoverCreator) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::minimization_packing::MinPackMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>
- keyname(self: pyrosetta.rosetta.protocols.minimization_packing.MinPackMoverCreator) str ¶
C++: protocols::minimization_packing::MinPackMoverCreator::keyname() const –> std::string
- class pyrosetta.rosetta.protocols.minimization_packing.MinimalRotamer¶
Bases:
pybind11_object
- aa(self: pyrosetta.rosetta.protocols.minimization_packing.MinimalRotamer) pyrosetta.rosetta.core.chemical.AA ¶
C++: protocols::minimization_packing::MinimalRotamer::aa() const –> enum core::chemical::AA
- same(self: pyrosetta.rosetta.protocols.minimization_packing.MinimalRotamer, : pyrosetta.rosetta.protocols.minimization_packing.MinimalRotamer) bool ¶
C++: protocols::minimization_packing::MinimalRotamer::same(const class protocols::minimization_packing::MinimalRotamer &) const –> bool
- same_residue_type(self: pyrosetta.rosetta.protocols.minimization_packing.MinimalRotamer, : pyrosetta.rosetta.protocols.minimization_packing.MinimalRotamer) bool ¶
C++: protocols::minimization_packing::MinimalRotamer::same_residue_type(const class protocols::minimization_packing::MinimalRotamer &) const –> bool
- class pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover¶
Bases:
Mover
A protocols::moves::Mover that packs the side-chains using a rotamer library It uses a ScoreFunction for packing and a PackerTask, or a TaskFactory that generates a PackerTask, for instructions on what rotamer sets are allowed at each residue position during packing
- Common Methods:
PackRotamersMover.apply
please derive from PackRotamersMover instead of attempting to add protocol-specific stuff here!
- apply(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
- Performs side-chain packing based on the input PackerTask
using the input ScoreFunction
- example(s):
packmover.apply(pose)
- See Also:
PackerTask ScoreFunction
C++: protocols::minimization_packing::PackRotamersMover::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover, : pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover) pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover ¶
C++: protocols::minimization_packing::PackRotamersMover::operator=(const class protocols::minimization_packing::PackRotamersMover &) –> class protocols::minimization_packing::PackRotamersMover &
- 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.minimization_packing.PackRotamersMover) pyrosetta.rosetta.protocols.moves.Mover ¶
required in the context of the parser/scripting scheme
C++: protocols::minimization_packing::PackRotamersMover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>
- static complex_type_generator_for_pack_rotamers_mover(xsd: utility::tag::XMLSchemaDefinition) utility::tag::XMLSchemaComplexTypeGenerator ¶
C++: protocols::minimization_packing::PackRotamersMover::complex_type_generator_for_pack_rotamers_mover(class utility::tag::XMLSchemaDefinition &) –> class std::shared_ptr<class utility::tag::XMLSchemaComplexTypeGenerator>
- create(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>
- fresh_instance(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover) pyrosetta.rosetta.protocols.moves.Mover ¶
required in the context of the parser/scripting scheme
C++: protocols::minimization_packing::PackRotamersMover::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.minimization_packing.PackRotamersMover) str ¶
C++: protocols::minimization_packing::PackRotamersMover::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_task_factory_with_operations(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover, : pyrosetta.rosetta.std.list_std_shared_ptr_core_pack_task_operation_TaskOperation_t) None ¶
C++: protocols::minimization_packing::PackRotamersMover::initialize_task_factory_with_operations(const class std::list<class std::shared_ptr<class core::pack::task::operation::TaskOperation>, class std::allocator<class std::shared_ptr<class core::pack::task::operation::TaskOperation> > > &) –> void
- last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) float ¶
C++: protocols::moves::Mover::last_proposal_density_ratio() –> double
- static list_options_read(opts: pyrosetta.rosetta.std.list_utility_keys_VariantKey_utility_options_OptionKey_t) None ¶
C++: protocols::minimization_packing::PackRotamersMover::list_options_read(class std::list<class utility::keys::VariantKey<class utility::options::OptionKey>, class std::allocator<class utility::keys::VariantKey<class utility::options::OptionKey> > > &) –> void
- static mover_name() str ¶
C++: protocols::minimization_packing::PackRotamersMover::mover_name() –> std::string
- static name() str ¶
C++: protocols::moves::Mover::name() –> std::string
- nloop(*args, **kwargs)¶
Overloaded function.
nloop(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover, nloop_in: int) -> None
C++: protocols::minimization_packing::PackRotamersMover::nloop(unsigned long) –> void
nloop(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover) -> int
C++: protocols::minimization_packing::PackRotamersMover::nloop() const –> unsigned long
- parse_my_tag(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None ¶
parse XML (specifically in the context of the parser/scripting scheme)
C++: protocols::minimization_packing::PackRotamersMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- parse_score_function(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None ¶
parse “scorefxn” XML option (can be employed virtually by derived Packing movers)
C++: protocols::minimization_packing::PackRotamersMover::parse_score_function(class std::shared_ptr<const class utility::tag::Tag>, const class basic::datacache::DataMap &) –> void
- parse_task_operations(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None ¶
parse “task_operations” XML option (can be employed virtually by derived Packing movers)
C++: protocols::minimization_packing::PackRotamersMover::parse_task_operations(class std::shared_ptr<const class utility::tag::Tag>, const 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::minimization_packing::PackRotamersMover::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
- rotamer_sets(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover) pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets ¶
Returns the RotamerSets object being used for packing
This is only valid after a call to setup or apply.
C++: protocols::minimization_packing::PackRotamersMover::rotamer_sets() const –> class std::shared_ptr<const class core::pack::rotamer_set::RotamerSets>
- score_function(*args, **kwargs)¶
Overloaded function.
score_function(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover, sf: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None
Sets the ScoreFunction to <sf>
- example(s):
packmover.score_function(scorefxn)
- See Also:
PackRotamersMover PackRotamersMover.task
C++: protocols::minimization_packing::PackRotamersMover::score_function(class std::shared_ptr<const class core::scoring::ScoreFunction>) –> void
score_function(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover) -> pyrosetta.rosetta.core.scoring.ScoreFunction
Returns the ScoreFunction
- example(s):
packmover.score_function()
- See Also:
PackRotamersMover PackRotamersMover.task
C++: protocols::minimization_packing::PackRotamersMover::score_function() const –> class std::shared_ptr<const class core::scoring::ScoreFunction>
- set_annealer_observer(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover, observer: pyrosetta.rosetta.core.pack.annealer.AnnealerObserver) None ¶
C++: protocols::minimization_packing::PackRotamersMover::set_annealer_observer(class std::shared_ptr<class core::pack::annealer::AnnealerObserver>) –> 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.minimization_packing.PackRotamersMover) -> None
show(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover, output: pyrosetta.rosetta.std.ostream) -> None
C++: protocols::minimization_packing::PackRotamersMover::show(std::ostream &) const –> void
- task(*args, **kwargs)¶
Overloaded function.
task(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover, t: pyrosetta.rosetta.core.pack.task.PackerTask) -> None
Sets the PackerTask to <t>
- example(s):
packmover.task(task_pack)
- See Also:
PackRotamersMover PackRotamersMover.task_factory
C++: protocols::minimization_packing::PackRotamersMover::task(class std::shared_ptr<const class core::pack::task::PackerTask>) –> void
task(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover) -> pyrosetta.rosetta.core.pack.task.PackerTask
Returns the PackerTask
- example(s):
packmover.task()
- See Also:
PackRotamersMover PackRotamersMover.task_factory
C++: protocols::minimization_packing::PackRotamersMover::task() const –> class std::shared_ptr<const class core::pack::task::PackerTask>
- task_factory(*args, **kwargs)¶
Overloaded function.
task_factory(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover, tf: pyrosetta.rosetta.core.pack.task.TaskFactory) -> None
Sets the TaskFactory to <tf>
- example(s):
packmover.task_factory(task_design)
- See Also:
PackRotamersMover PackRotamersMover.task
C++: protocols::minimization_packing::PackRotamersMover::task_factory(class std::shared_ptr<const class core::pack::task::TaskFactory>) –> void
task_factory(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover) -> pyrosetta.rosetta.core.pack.task.TaskFactory
Returns the TaskFactory
- example(s):
packmover.task_factory()
- See Also:
PackRotamersMover PackRotamersMover.task
C++: protocols::minimization_packing::PackRotamersMover::task_factory() const –> class std::shared_ptr<const class core::pack::task::TaskFactory>
- task_is_valid(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover, pose: pyrosetta.rosetta.core.pose.Pose) bool ¶
C++: protocols::minimization_packing::PackRotamersMover::task_is_valid(const class core::pose::Pose &) const –> bool
- 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.minimization_packing.PackRotamersMoverCreator¶
Bases:
MoverCreator
- assign(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverCreator, : pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverCreator) pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverCreator ¶
C++: protocols::minimization_packing::PackRotamersMoverCreator::operator=(const class protocols::minimization_packing::PackRotamersMoverCreator &) –> class protocols::minimization_packing::PackRotamersMoverCreator &
- create_mover(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverCreator) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::minimization_packing::PackRotamersMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>
- keyname(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverCreator) str ¶
C++: protocols::minimization_packing::PackRotamersMoverCreator::keyname() const –> std::string
- static mover_name() str ¶
C++: protocols::minimization_packing::PackRotamersMoverCreator::mover_name() –> std::string
- class pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazy¶
Bases:
PackRotamersMover
a mover that packs the side-chains using a rotamer library in a lazy fashion.
- apply(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
- Performs side-chain packing based on the input PackerTask
using the input ScoreFunction
- example(s):
packmover.apply(pose)
- See Also:
PackerTask ScoreFunction
C++: protocols::minimization_packing::PackRotamersMover::apply(class core::pose::Pose &) –> void
- apply_to_rotpack(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazy, pose: pyrosetta.rosetta.core.pose.Pose, rot_to_pack: pyrosetta.rosetta.utility.vector0_int) None ¶
C++: protocols::minimization_packing::PackRotamersMoverLazy::apply_to_rotpack(class core::pose::Pose &, class utility::vector0<int, class std::allocator<int> >) –> void
- assign(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazy, : pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazy) pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazy ¶
C++: protocols::minimization_packing::PackRotamersMoverLazy::operator=(const class protocols::minimization_packing::PackRotamersMoverLazy &) –> class protocols::minimization_packing::PackRotamersMoverLazy &
- call_setup(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazy, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::minimization_packing::PackRotamersMoverLazy::call_setup(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.minimization_packing.PackRotamersMover) pyrosetta.rosetta.protocols.moves.Mover ¶
required in the context of the parser/scripting scheme
C++: protocols::minimization_packing::PackRotamersMover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>
- static complex_type_generator_for_pack_rotamers_mover(xsd: utility::tag::XMLSchemaDefinition) utility::tag::XMLSchemaComplexTypeGenerator ¶
C++: protocols::minimization_packing::PackRotamersMover::complex_type_generator_for_pack_rotamers_mover(class utility::tag::XMLSchemaDefinition &) –> class std::shared_ptr<class utility::tag::XMLSchemaComplexTypeGenerator>
- create(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>
- fresh_instance(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover) pyrosetta.rosetta.protocols.moves.Mover ¶
required in the context of the parser/scripting scheme
C++: protocols::minimization_packing::PackRotamersMover::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.minimization_packing.PackRotamersMover) str ¶
C++: protocols::minimization_packing::PackRotamersMover::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_task_factory_with_operations(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover, : pyrosetta.rosetta.std.list_std_shared_ptr_core_pack_task_operation_TaskOperation_t) None ¶
C++: protocols::minimization_packing::PackRotamersMover::initialize_task_factory_with_operations(const class std::list<class std::shared_ptr<class core::pack::task::operation::TaskOperation>, class std::allocator<class std::shared_ptr<class core::pack::task::operation::TaskOperation> > > &) –> void
- last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) float ¶
C++: protocols::moves::Mover::last_proposal_density_ratio() –> double
- static list_options_read(opts: pyrosetta.rosetta.std.list_utility_keys_VariantKey_utility_options_OptionKey_t) None ¶
C++: protocols::minimization_packing::PackRotamersMover::list_options_read(class std::list<class utility::keys::VariantKey<class utility::options::OptionKey>, class std::allocator<class utility::keys::VariantKey<class utility::options::OptionKey> > > &) –> void
- static mover_name() str ¶
C++: protocols::minimization_packing::PackRotamersMover::mover_name() –> std::string
- static name() str ¶
C++: protocols::moves::Mover::name() –> std::string
- nloop(*args, **kwargs)¶
Overloaded function.
nloop(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover, nloop_in: int) -> None
C++: protocols::minimization_packing::PackRotamersMover::nloop(unsigned long) –> void
nloop(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover) -> int
C++: protocols::minimization_packing::PackRotamersMover::nloop() const –> unsigned long
- parse_my_tag(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazy, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None ¶
C++: protocols::minimization_packing::PackRotamersMoverLazy::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- parse_score_function(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None ¶
parse “scorefxn” XML option (can be employed virtually by derived Packing movers)
C++: protocols::minimization_packing::PackRotamersMover::parse_score_function(class std::shared_ptr<const class utility::tag::Tag>, const class basic::datacache::DataMap &) –> void
- parse_task_operations(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None ¶
parse “task_operations” XML option (can be employed virtually by derived Packing movers)
C++: protocols::minimization_packing::PackRotamersMover::parse_task_operations(class std::shared_ptr<const class utility::tag::Tag>, const 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::minimization_packing::PackRotamersMover::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
- rotamer_sets(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover) pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets ¶
Returns the RotamerSets object being used for packing
This is only valid after a call to setup or apply.
C++: protocols::minimization_packing::PackRotamersMover::rotamer_sets() const –> class std::shared_ptr<const class core::pack::rotamer_set::RotamerSets>
- score_function(*args, **kwargs)¶
Overloaded function.
score_function(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover, sf: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None
Sets the ScoreFunction to <sf>
- example(s):
packmover.score_function(scorefxn)
- See Also:
PackRotamersMover PackRotamersMover.task
C++: protocols::minimization_packing::PackRotamersMover::score_function(class std::shared_ptr<const class core::scoring::ScoreFunction>) –> void
score_function(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover) -> pyrosetta.rosetta.core.scoring.ScoreFunction
Returns the ScoreFunction
- example(s):
packmover.score_function()
- See Also:
PackRotamersMover PackRotamersMover.task
C++: protocols::minimization_packing::PackRotamersMover::score_function() const –> class std::shared_ptr<const class core::scoring::ScoreFunction>
- set_annealer_observer(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover, observer: pyrosetta.rosetta.core.pack.annealer.AnnealerObserver) None ¶
C++: protocols::minimization_packing::PackRotamersMover::set_annealer_observer(class std::shared_ptr<class core::pack::annealer::AnnealerObserver>) –> 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.minimization_packing.PackRotamersMover) -> None
show(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover, output: pyrosetta.rosetta.std.ostream) -> None
C++: protocols::minimization_packing::PackRotamersMover::show(std::ostream &) const –> void
- task(*args, **kwargs)¶
Overloaded function.
task(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover, t: pyrosetta.rosetta.core.pack.task.PackerTask) -> None
Sets the PackerTask to <t>
- example(s):
packmover.task(task_pack)
- See Also:
PackRotamersMover PackRotamersMover.task_factory
C++: protocols::minimization_packing::PackRotamersMover::task(class std::shared_ptr<const class core::pack::task::PackerTask>) –> void
task(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover) -> pyrosetta.rosetta.core.pack.task.PackerTask
Returns the PackerTask
- example(s):
packmover.task()
- See Also:
PackRotamersMover PackRotamersMover.task_factory
C++: protocols::minimization_packing::PackRotamersMover::task() const –> class std::shared_ptr<const class core::pack::task::PackerTask>
- task_factory(*args, **kwargs)¶
Overloaded function.
task_factory(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover, tf: pyrosetta.rosetta.core.pack.task.TaskFactory) -> None
Sets the TaskFactory to <tf>
- example(s):
packmover.task_factory(task_design)
- See Also:
PackRotamersMover PackRotamersMover.task
C++: protocols::minimization_packing::PackRotamersMover::task_factory(class std::shared_ptr<const class core::pack::task::TaskFactory>) –> void
task_factory(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover) -> pyrosetta.rosetta.core.pack.task.TaskFactory
Returns the TaskFactory
- example(s):
packmover.task_factory()
- See Also:
PackRotamersMover PackRotamersMover.task
C++: protocols::minimization_packing::PackRotamersMover::task_factory() const –> class std::shared_ptr<const class core::pack::task::TaskFactory>
- task_is_valid(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover, pose: pyrosetta.rosetta.core.pose.Pose) bool ¶
C++: protocols::minimization_packing::PackRotamersMover::task_is_valid(const class core::pose::Pose &) const –> bool
- 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.minimization_packing.PackRotamersMoverLazyCreator¶
Bases:
PackRotamersMoverCreator
- assign(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazyCreator, : pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazyCreator) pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazyCreator ¶
C++: protocols::minimization_packing::PackRotamersMoverLazyCreator::operator=(const class protocols::minimization_packing::PackRotamersMoverLazyCreator &) –> class protocols::minimization_packing::PackRotamersMoverLazyCreator &
- create_mover(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverCreator) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::minimization_packing::PackRotamersMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>
- keyname(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverCreator) str ¶
C++: protocols::minimization_packing::PackRotamersMoverCreator::keyname() const –> std::string
- static mover_name() str ¶
C++: protocols::minimization_packing::PackRotamersMoverLazyCreator::mover_name() –> std::string
- class pyrosetta.rosetta.protocols.minimization_packing.PertMinMover¶
Bases:
Mover
Random perturbation, followed by minimization
- apply(self: pyrosetta.rosetta.protocols.minimization_packing.PertMinMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::minimization_packing::PertMinMover::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.minimization_packing.PertMinMover, : pyrosetta.rosetta.protocols.minimization_packing.PertMinMover) pyrosetta.rosetta.protocols.minimization_packing.PertMinMover ¶
C++: protocols::minimization_packing::PertMinMover::operator=(const class protocols::minimization_packing::PertMinMover &) –> class protocols::minimization_packing::PertMinMover &
- 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.minimization_packing.PertMinMover) pyrosetta.rosetta.protocols.moves.Mover ¶
required in the context of the parser/scripting scheme
C++: protocols::minimization_packing::PertMinMover::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.minimization_packing.PertMinMover) pyrosetta.rosetta.protocols.moves.Mover ¶
required in the context of the parser/scripting scheme
C++: protocols::minimization_packing::PertMinMover::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.minimization_packing.PertMinMover) str ¶
C++: protocols::minimization_packing::PertMinMover::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
- min(self: pyrosetta.rosetta.protocols.minimization_packing.PertMinMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::minimization_packing::PertMinMover::min(class core::pose::Pose &) const –> void
- movemap(self: pyrosetta.rosetta.protocols.minimization_packing.PertMinMover) pyrosetta.rosetta.core.select.movemap.MoveMapFactory ¶
C++: protocols::minimization_packing::PertMinMover::movemap() const –> class std::shared_ptr<const class core::select::movemap::MoveMapFactory>
- movemap_factory(self: pyrosetta.rosetta.protocols.minimization_packing.PertMinMover, setting: pyrosetta.rosetta.core.select.movemap.MoveMapFactory) None ¶
C++: protocols::minimization_packing::PertMinMover::movemap_factory(class std::shared_ptr<const class core::select::movemap::MoveMapFactory>) –> void
- static mover_name() str ¶
C++: protocols::minimization_packing::PertMinMover::mover_name() –> std::string
- static name() str ¶
C++: protocols::moves::Mover::name() –> std::string
- parse_my_tag(self: pyrosetta.rosetta.protocols.minimization_packing.PertMinMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None ¶
parse XML tag (to use this Mover in Rosetta Scripts)
C++: protocols::minimization_packing::PertMinMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- pert(self: pyrosetta.rosetta.protocols.minimization_packing.PertMinMover, pose: pyrosetta.rosetta.core.pose.Pose, resi: pyrosetta.rosetta.utility.vector1_bool) None ¶
C++: protocols::minimization_packing::PertMinMover::pert(class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &) const –> void
- pert_size(*args, **kwargs)¶
Overloaded function.
pert_size(self: pyrosetta.rosetta.protocols.minimization_packing.PertMinMover) -> float
C++: protocols::minimization_packing::PertMinMover::pert_size() const –> double
pert_size(self: pyrosetta.rosetta.protocols.minimization_packing.PertMinMover, setting: float) -> None
C++: protocols::minimization_packing::PertMinMover::pert_size(double) –> 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::minimization_packing::PertMinMover::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
- residues(*args, **kwargs)¶
Overloaded function.
residues(self: pyrosetta.rosetta.protocols.minimization_packing.PertMinMover) -> pyrosetta.rosetta.core.select.residue_selector.ResidueSelector
C++: protocols::minimization_packing::PertMinMover::residues() const –> class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>
residues(self: pyrosetta.rosetta.protocols.minimization_packing.PertMinMover, setting: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) -> None
C++: protocols::minimization_packing::PertMinMover::residues(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void
- sc_only(*args, **kwargs)¶
Overloaded function.
sc_only(self: pyrosetta.rosetta.protocols.minimization_packing.PertMinMover) -> bool
C++: protocols::minimization_packing::PertMinMover::sc_only() const –> bool
sc_only(self: pyrosetta.rosetta.protocols.minimization_packing.PertMinMover, setting: bool) -> None
C++: protocols::minimization_packing::PertMinMover::sc_only(bool) –> void
- scorefxn(*args, **kwargs)¶
Overloaded function.
scorefxn(self: pyrosetta.rosetta.protocols.minimization_packing.PertMinMover) -> pyrosetta.rosetta.core.scoring.ScoreFunction
C++: protocols::minimization_packing::PertMinMover::scorefxn() const –> class std::shared_ptr<const class core::scoring::ScoreFunction>
scorefxn(self: pyrosetta.rosetta.protocols.minimization_packing.PertMinMover, setting: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None
C++: protocols::minimization_packing::PertMinMover::scorefxn(class std::shared_ptr<const class core::scoring::ScoreFunction>) –> 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.minimization_packing.PertMinMover) -> None
show(self: pyrosetta.rosetta.protocols.minimization_packing.PertMinMover, output: pyrosetta.rosetta.std.ostream) -> None
C++: protocols::minimization_packing::PertMinMover::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 &
- uniform(*args, **kwargs)¶
Overloaded function.
uniform(self: pyrosetta.rosetta.protocols.minimization_packing.PertMinMover) -> bool
C++: protocols::minimization_packing::PertMinMover::uniform() const –> bool
uniform(self: pyrosetta.rosetta.protocols.minimization_packing.PertMinMover, setting: bool) -> None
C++: protocols::minimization_packing::PertMinMover::uniform(bool) –> void
- class pyrosetta.rosetta.protocols.minimization_packing.PertMinMoverCreator¶
Bases:
MoverCreator
- assign(self: pyrosetta.rosetta.protocols.minimization_packing.PertMinMoverCreator, : pyrosetta.rosetta.protocols.minimization_packing.PertMinMoverCreator) pyrosetta.rosetta.protocols.minimization_packing.PertMinMoverCreator ¶
C++: protocols::minimization_packing::PertMinMoverCreator::operator=(const class protocols::minimization_packing::PertMinMoverCreator &) –> class protocols::minimization_packing::PertMinMoverCreator &
- create_mover(self: pyrosetta.rosetta.protocols.minimization_packing.PertMinMoverCreator) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::minimization_packing::PertMinMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>
- keyname(self: pyrosetta.rosetta.protocols.minimization_packing.PertMinMoverCreator) str ¶
C++: protocols::minimization_packing::PertMinMoverCreator::keyname() const –> std::string
- class pyrosetta.rosetta.protocols.minimization_packing.RepackSidechainsMover¶
Bases:
Mover
A protocols::moves::Mover that packs the side-chains (very similar to pack_missing_sidechains()
- apply(self: pyrosetta.rosetta.protocols.minimization_packing.RepackSidechainsMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::minimization_packing::RepackSidechainsMover::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.minimization_packing.RepackSidechainsMover, : pyrosetta.rosetta.protocols.minimization_packing.RepackSidechainsMover) pyrosetta.rosetta.protocols.minimization_packing.RepackSidechainsMover ¶
C++: protocols::minimization_packing::RepackSidechainsMover::operator=(const class protocols::minimization_packing::RepackSidechainsMover &) –> class protocols::minimization_packing::RepackSidechainsMover &
- 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.minimization_packing.RepackSidechainsMover) pyrosetta.rosetta.protocols.moves.Mover ¶
required in the context of the parser/scripting scheme
C++: protocols::minimization_packing::RepackSidechainsMover::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.minimization_packing.RepackSidechainsMover) pyrosetta.rosetta.protocols.moves.Mover ¶
required in the context of the parser/scripting scheme
C++: protocols::minimization_packing::RepackSidechainsMover::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.minimization_packing.RepackSidechainsMover) str ¶
C++: protocols::minimization_packing::RepackSidechainsMover::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.minimization_packing.RepackSidechainsMover, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None ¶
parse XML (specifically in the context of the parser/scripting scheme)
C++: protocols::minimization_packing::RepackSidechainsMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- parse_score_function(self: pyrosetta.rosetta.protocols.minimization_packing.RepackSidechainsMover, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None ¶
parse “scorefxn” XML option (can be employed virtually by derived Packing movers)
C++: protocols::minimization_packing::RepackSidechainsMover::parse_score_function(class std::shared_ptr<const class utility::tag::Tag>, const 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
- scorefxn(self: pyrosetta.rosetta.protocols.minimization_packing.RepackSidechainsMover) pyrosetta.rosetta.core.scoring.ScoreFunction ¶
C++: protocols::minimization_packing::RepackSidechainsMover::scorefxn() const –> class std::shared_ptr<const class core::scoring::ScoreFunction>
- set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) None ¶
C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void
- set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) None ¶
C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void
- set_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_scorefxn(self: pyrosetta.rosetta.protocols.minimization_packing.RepackSidechainsMover, sf: pyrosetta.rosetta.core.scoring.ScoreFunction) None ¶
C++: protocols::minimization_packing::RepackSidechainsMover::set_scorefxn(class std::shared_ptr<const class core::scoring::ScoreFunction>) –> void
- set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) None ¶
Set the ‘type’ string
C++: protocols::moves::Mover::set_type(const std::string &) –> void
- show(*args, **kwargs)¶
Overloaded function.
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.minimization_packing.RepackSidechainsMoverCreator¶
Bases:
MoverCreator
- assign(self: pyrosetta.rosetta.protocols.minimization_packing.RepackSidechainsMoverCreator, : pyrosetta.rosetta.protocols.minimization_packing.RepackSidechainsMoverCreator) pyrosetta.rosetta.protocols.minimization_packing.RepackSidechainsMoverCreator ¶
C++: protocols::minimization_packing::RepackSidechainsMoverCreator::operator=(const class protocols::minimization_packing::RepackSidechainsMoverCreator &) –> class protocols::minimization_packing::RepackSidechainsMoverCreator &
- create_mover(self: pyrosetta.rosetta.protocols.minimization_packing.RepackSidechainsMoverCreator) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::minimization_packing::RepackSidechainsMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>
- keyname(self: pyrosetta.rosetta.protocols.minimization_packing.RepackSidechainsMoverCreator) str ¶
C++: protocols::minimization_packing::RepackSidechainsMoverCreator::keyname() const –> std::string
- static mover_name() str ¶
C++: protocols::minimization_packing::RepackSidechainsMoverCreator::mover_name() –> std::string
- provide_xml_schema(self: pyrosetta.rosetta.protocols.moves.MoverCreator, xsd: utility::tag::XMLSchemaDefinition) None ¶
Describe the schema for the Mover that this Creator is responsible for
C++: protocols::moves::MoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void
- class pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMinMover¶
Bases:
Mover
- apply(self: pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMinMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
- Apply Rotamer-Trials with minimization to pose, using the score function
and tasks provided by the constructor
C++: protocols::minimization_packing::RotamerTrialsMinMover::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMinMover, : pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMinMover) pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMinMover ¶
C++: protocols::minimization_packing::RotamerTrialsMinMover::operator=(const class protocols::minimization_packing::RotamerTrialsMinMover &) –> class protocols::minimization_packing::RotamerTrialsMinMover &
- 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.minimization_packing.RotamerTrialsMinMover) pyrosetta.rosetta.protocols.moves.Mover ¶
Return a copy of this mover instance (for RosettaScripts)
C++: protocols::minimization_packing::RotamerTrialsMinMover::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.minimization_packing.RotamerTrialsMinMover) pyrosetta.rosetta.protocols.moves.Mover ¶
Return a new mover instance (for RosettaScripts)
C++: protocols::minimization_packing::RotamerTrialsMinMover::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.minimization_packing.RotamerTrialsMinMover) str ¶
C++: protocols::minimization_packing::RotamerTrialsMinMover::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 > > &
- init(self: pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMinMover) None ¶
C++: protocols::minimization_packing::RotamerTrialsMinMover::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::minimization_packing::RotamerTrialsMinMover::mover_name() –> std::string
- static name() str ¶
C++: protocols::moves::Mover::name() –> std::string
- parse_my_tag(self: pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMinMover, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None ¶
Parse XML for RosettaScripts
C++: protocols::minimization_packing::RotamerTrialsMinMover::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::minimization_packing::RotamerTrialsMinMover::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
- score_function(self: pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMinMover, sf: pyrosetta.rosetta.core.scoring.ScoreFunction) None ¶
C++: protocols::minimization_packing::RotamerTrialsMinMover::score_function(class std::shared_ptr<const class core::scoring::ScoreFunction>) –> 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.minimization_packing.RotamerTrialsMinMover) -> None
show(self: pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMinMover, output: pyrosetta.rosetta.std.ostream) -> None
C++: protocols::minimization_packing::RotamerTrialsMinMover::show(std::ostream &) const –> void
- task_factory(self: pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMinMover, tf: pyrosetta.rosetta.core.pack.task.TaskFactory) None ¶
C++: protocols::minimization_packing::RotamerTrialsMinMover::task_factory(class std::shared_ptr<const class core::pack::task::TaskFactory>) –> 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.minimization_packing.RotamerTrialsMinMoverCreator¶
Bases:
MoverCreator
- assign(self: pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMinMoverCreator, : pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMinMoverCreator) pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMinMoverCreator ¶
C++: protocols::minimization_packing::RotamerTrialsMinMoverCreator::operator=(const class protocols::minimization_packing::RotamerTrialsMinMoverCreator &) –> class protocols::minimization_packing::RotamerTrialsMinMoverCreator &
- create_mover(self: pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMinMoverCreator) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::minimization_packing::RotamerTrialsMinMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>
- keyname(self: pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMinMoverCreator) str ¶
C++: protocols::minimization_packing::RotamerTrialsMinMoverCreator::keyname() const –> std::string
- class pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMover¶
Bases:
Mover
- apply(self: pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::minimization_packing::RotamerTrialsMover::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMover, : pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMover) pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMover ¶
C++: protocols::minimization_packing::RotamerTrialsMover::operator=(const class protocols::minimization_packing::RotamerTrialsMover &) –> class protocols::minimization_packing::RotamerTrialsMover &
- 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.minimization_packing.RotamerTrialsMover) pyrosetta.rosetta.protocols.moves.Mover ¶
clone this object
C++: protocols::minimization_packing::RotamerTrialsMover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>
- static complex_type_generator_for_rotamer_trials_mover(xsd: utility::tag::XMLSchemaDefinition) utility::tag::XMLSchemaComplexTypeGenerator ¶
C++: protocols::minimization_packing::RotamerTrialsMover::complex_type_generator_for_rotamer_trials_mover(class utility::tag::XMLSchemaDefinition &) –> class std::shared_ptr<class utility::tag::XMLSchemaComplexTypeGenerator>
- create(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>
- fresh_instance(self: pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMover) pyrosetta.rosetta.protocols.moves.Mover ¶
create this type of object
C++: protocols::minimization_packing::RotamerTrialsMover::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.minimization_packing.RotamerTrialsMover) str ¶
C++: protocols::minimization_packing::RotamerTrialsMover::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::minimization_packing::RotamerTrialsMover::mover_name() –> std::string
- static name() str ¶
C++: protocols::moves::Mover::name() –> std::string
- parse_my_tag(self: pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None ¶
C++: protocols::minimization_packing::RotamerTrialsMover::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::minimization_packing::RotamerTrialsMover::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
- score_function(self: pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMover, sf: pyrosetta.rosetta.core.scoring.ScoreFunction) None ¶
C++: protocols::minimization_packing::RotamerTrialsMover::score_function(class std::shared_ptr<const class core::scoring::ScoreFunction>) –> 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.minimization_packing.RotamerTrialsMover) -> None
show(self: pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMover, output: pyrosetta.rosetta.std.ostream) -> None
C++: protocols::minimization_packing::RotamerTrialsMover::show(std::ostream &) const –> void
- task_factory(self: pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMover, tf: pyrosetta.rosetta.core.pack.task.TaskFactory) None ¶
C++: protocols::minimization_packing::RotamerTrialsMover::task_factory(class std::shared_ptr<const class core::pack::task::TaskFactory>) –> 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.minimization_packing.RotamerTrialsMoverCreator¶
Bases:
MoverCreator
- assign(self: pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMoverCreator, : pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMoverCreator) pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMoverCreator ¶
C++: protocols::minimization_packing::RotamerTrialsMoverCreator::operator=(const class protocols::minimization_packing::RotamerTrialsMoverCreator &) –> class protocols::minimization_packing::RotamerTrialsMoverCreator &
- create_mover(self: pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMoverCreator) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::minimization_packing::RotamerTrialsMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>
- keyname(self: pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMoverCreator) str ¶
C++: protocols::minimization_packing::RotamerTrialsMoverCreator::keyname() const –> std::string
- class pyrosetta.rosetta.protocols.minimization_packing.RotamerizeMover¶
Bases:
Mover
a mover that replaces the repackable parts - sidechains, bases, etc. - based purely on geometric similarity to the starting structure. The purpose is to generate the best case output of a repacking calculation as a positive control for benchmarking and parameter fitting. Thus, the soft rep potential was originally derived as the score function that gave the best fit between repacked and rotamerized structures for a large test set.
- apply(self: pyrosetta.rosetta.protocols.minimization_packing.RotamerizeMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::minimization_packing::RotamerizeMover::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.minimization_packing.RotamerizeMover, : pyrosetta.rosetta.protocols.minimization_packing.RotamerizeMover) pyrosetta.rosetta.protocols.minimization_packing.RotamerizeMover ¶
C++: protocols::minimization_packing::RotamerizeMover::operator=(const class protocols::minimization_packing::RotamerizeMover &) –> class protocols::minimization_packing::RotamerizeMover &
- 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.minimization_packing.RotamerizeMover) str ¶
C++: protocols::minimization_packing::RotamerizeMover::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
- rotamer_sets(self: pyrosetta.rosetta.protocols.minimization_packing.RotamerizeMover) pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets ¶
C++: protocols::minimization_packing::RotamerizeMover::rotamer_sets() const –> class std::shared_ptr<const class core::pack::rotamer_set::RotamerSets>
- 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
- task(*args, **kwargs)¶
Overloaded function.
task(self: pyrosetta.rosetta.protocols.minimization_packing.RotamerizeMover, t: pyrosetta.rosetta.core.pack.task.PackerTask) -> None
C++: protocols::minimization_packing::RotamerizeMover::task(class std::shared_ptr<class core::pack::task::PackerTask>) –> void
task(self: pyrosetta.rosetta.protocols.minimization_packing.RotamerizeMover) -> pyrosetta.rosetta.core.pack.task.PackerTask
C++: protocols::minimization_packing::RotamerizeMover::task() const –> class std::shared_ptr<class core::pack::task::PackerTask>
- task_factory(*args, **kwargs)¶
Overloaded function.
task_factory(self: pyrosetta.rosetta.protocols.minimization_packing.RotamerizeMover, tf: pyrosetta.rosetta.core.pack.task.TaskFactory) -> None
C++: protocols::minimization_packing::RotamerizeMover::task_factory(class std::shared_ptr<const class core::pack::task::TaskFactory>) –> void
task_factory(self: pyrosetta.rosetta.protocols.minimization_packing.RotamerizeMover) -> pyrosetta.rosetta.core.pack.task.TaskFactory
C++: protocols::minimization_packing::RotamerizeMover::task_factory() const –> class std::shared_ptr<const class core::pack::task::TaskFactory>
- task_is_valid(self: pyrosetta.rosetta.protocols.minimization_packing.RotamerizeMover, pose: pyrosetta.rosetta.core.pose.Pose) bool ¶
C++: protocols::minimization_packing::RotamerizeMover::task_is_valid(const class core::pose::Pose &) const –> bool
- 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.minimization_packing.SaneMinMover¶
Bases:
Mover
performing energy minimization of a ScoreFunction over the allowable degrees of freedom, defined by a MoveMap. Unlike the classic MinMover, the only method for setting Minimization options is via the MinimizerOptions class.
- apply(self: pyrosetta.rosetta.protocols.minimization_packing.SaneMinMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
Minimizes the DOFs of pose specified in the MoveMap
C++: protocols::minimization_packing::SaneMinMover::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.minimization_packing.SaneMinMover, : pyrosetta.rosetta.protocols.minimization_packing.SaneMinMover) pyrosetta.rosetta.protocols.minimization_packing.SaneMinMover ¶
C++: protocols::minimization_packing::SaneMinMover::operator=(const class protocols::minimization_packing::SaneMinMover &) –> class protocols::minimization_packing::SaneMinMover &
- cartesian(self: pyrosetta.rosetta.protocols.minimization_packing.SaneMinMover) bool ¶
C++: protocols::minimization_packing::SaneMinMover::cartesian() const –> bool
- clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) None ¶
Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.
clear_info is called by jd2 before calling apply
C++: protocols::moves::Mover::clear_info() –> void
- clone(self: pyrosetta.rosetta.protocols.minimization_packing.SaneMinMover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::minimization_packing::SaneMinMover::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.minimization_packing.SaneMinMover) str ¶
C++: protocols::minimization_packing::SaneMinMover::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
- min_options(self: pyrosetta.rosetta.protocols.minimization_packing.SaneMinMover) pyrosetta.rosetta.core.optimization.MinimizerOptions ¶
C++: protocols::minimization_packing::SaneMinMover::min_options() const –> class std::shared_ptr<class core::optimization::MinimizerOptions>
- move_map(self: pyrosetta.rosetta.protocols.minimization_packing.SaneMinMover) pyrosetta.rosetta.core.kinematics.MoveMap ¶
C++: protocols::minimization_packing::SaneMinMover::move_map() const –> class std::shared_ptr<class core::kinematics::MoveMap>
- static mover_name() str ¶
C++: protocols::minimization_packing::SaneMinMover::mover_name() –> std::string
- static name() str ¶
C++: protocols::moves::Mover::name() –> std::string
- parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None ¶
Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.
C++: protocols::moves::Mover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None ¶
- Provide citations to the passed CitationCollectionList
Subclasses should add the info for themselves and any other classes they use.
The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.
C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void
- static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None ¶
C++: protocols::minimization_packing::SaneMinMover::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
- score_function(self: pyrosetta.rosetta.protocols.minimization_packing.SaneMinMover) pyrosetta.rosetta.core.scoring.ScoreFunction ¶
C++: protocols::minimization_packing::SaneMinMover::score_function() const –> class std::shared_ptr<class core::scoring::ScoreFunction>
- set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) None ¶
C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void
- set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) None ¶
C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void
- set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
setter for poses contained for rms
C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void
- set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe
C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void
- set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) None ¶
Set the ‘type’ string
C++: protocols::moves::Mover::set_type(const std::string &) –> void
- show(*args, **kwargs)¶
Overloaded function.
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.minimization_packing.SaneMinMoverCreator¶
Bases:
MoverCreator
- assign(self: pyrosetta.rosetta.protocols.minimization_packing.SaneMinMoverCreator, : pyrosetta.rosetta.protocols.minimization_packing.SaneMinMoverCreator) pyrosetta.rosetta.protocols.minimization_packing.SaneMinMoverCreator ¶
C++: protocols::minimization_packing::SaneMinMoverCreator::operator=(const class protocols::minimization_packing::SaneMinMoverCreator &) –> class protocols::minimization_packing::SaneMinMoverCreator &
- create_mover(self: pyrosetta.rosetta.protocols.minimization_packing.SaneMinMoverCreator) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::minimization_packing::SaneMinMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>
- keyname(self: pyrosetta.rosetta.protocols.minimization_packing.SaneMinMoverCreator) str ¶
C++: protocols::minimization_packing::SaneMinMoverCreator::keyname() const –> std::string
- class pyrosetta.rosetta.protocols.minimization_packing.SetReturningPackRotamersMover¶
Bases:
PackRotamersMover
- apply(self: pyrosetta.rosetta.protocols.minimization_packing.SetReturningPackRotamersMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::minimization_packing::SetReturningPackRotamersMover::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.minimization_packing.SetReturningPackRotamersMover, : pyrosetta.rosetta.protocols.minimization_packing.SetReturningPackRotamersMover) pyrosetta.rosetta.protocols.minimization_packing.SetReturningPackRotamersMover ¶
C++: protocols::minimization_packing::SetReturningPackRotamersMover::operator=(const class protocols::minimization_packing::SetReturningPackRotamersMover &) –> class protocols::minimization_packing::SetReturningPackRotamersMover &
- 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.minimization_packing.PackRotamersMover) pyrosetta.rosetta.protocols.moves.Mover ¶
required in the context of the parser/scripting scheme
C++: protocols::minimization_packing::PackRotamersMover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>
- static complex_type_generator_for_pack_rotamers_mover(xsd: utility::tag::XMLSchemaDefinition) utility::tag::XMLSchemaComplexTypeGenerator ¶
C++: protocols::minimization_packing::PackRotamersMover::complex_type_generator_for_pack_rotamers_mover(class utility::tag::XMLSchemaDefinition &) –> class std::shared_ptr<class utility::tag::XMLSchemaComplexTypeGenerator>
- create(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>
- fresh_instance(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover) pyrosetta.rosetta.protocols.moves.Mover ¶
required in the context of the parser/scripting scheme
C++: protocols::minimization_packing::PackRotamersMover::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.minimization_packing.SetReturningPackRotamersMover) str ¶
C++: protocols::minimization_packing::SetReturningPackRotamersMover::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_repacked_poses(self: pyrosetta.rosetta.protocols.minimization_packing.SetReturningPackRotamersMover, v: pyrosetta.rosetta.utility.vector1_core_pose_Pose) None ¶
C++: protocols::minimization_packing::SetReturningPackRotamersMover::get_repacked_poses(class utility::vector1<class core::pose::Pose, class std::allocator<class core::pose::Pose> > &) –> void
- 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_task_factory_with_operations(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover, : pyrosetta.rosetta.std.list_std_shared_ptr_core_pack_task_operation_TaskOperation_t) None ¶
C++: protocols::minimization_packing::PackRotamersMover::initialize_task_factory_with_operations(const class std::list<class std::shared_ptr<class core::pack::task::operation::TaskOperation>, class std::allocator<class std::shared_ptr<class core::pack::task::operation::TaskOperation> > > &) –> void
- last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) float ¶
C++: protocols::moves::Mover::last_proposal_density_ratio() –> double
- static list_options_read(opts: pyrosetta.rosetta.std.list_utility_keys_VariantKey_utility_options_OptionKey_t) None ¶
C++: protocols::minimization_packing::PackRotamersMover::list_options_read(class std::list<class utility::keys::VariantKey<class utility::options::OptionKey>, class std::allocator<class utility::keys::VariantKey<class utility::options::OptionKey> > > &) –> void
- static mover_name() str ¶
C++: protocols::minimization_packing::PackRotamersMover::mover_name() –> std::string
- static name() str ¶
C++: protocols::moves::Mover::name() –> std::string
- nloop(*args, **kwargs)¶
Overloaded function.
nloop(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover, nloop_in: int) -> None
C++: protocols::minimization_packing::PackRotamersMover::nloop(unsigned long) –> void
nloop(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover) -> int
C++: protocols::minimization_packing::PackRotamersMover::nloop() const –> unsigned long
- output_repacked_poses(self: pyrosetta.rosetta.protocols.minimization_packing.SetReturningPackRotamersMover, filename_prefix: str) None ¶
C++: protocols::minimization_packing::SetReturningPackRotamersMover::output_repacked_poses(std::string) –> void
- parse_my_tag(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None ¶
parse XML (specifically in the context of the parser/scripting scheme)
C++: protocols::minimization_packing::PackRotamersMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- parse_score_function(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None ¶
parse “scorefxn” XML option (can be employed virtually by derived Packing movers)
C++: protocols::minimization_packing::PackRotamersMover::parse_score_function(class std::shared_ptr<const class utility::tag::Tag>, const class basic::datacache::DataMap &) –> void
- parse_task_operations(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None ¶
parse “task_operations” XML option (can be employed virtually by derived Packing movers)
C++: protocols::minimization_packing::PackRotamersMover::parse_task_operations(class std::shared_ptr<const class utility::tag::Tag>, const 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::minimization_packing::PackRotamersMover::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
- rotamer_sets(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover) pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets ¶
Returns the RotamerSets object being used for packing
This is only valid after a call to setup or apply.
C++: protocols::minimization_packing::PackRotamersMover::rotamer_sets() const –> class std::shared_ptr<const class core::pack::rotamer_set::RotamerSets>
- score_function(*args, **kwargs)¶
Overloaded function.
score_function(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover, sf: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None
Sets the ScoreFunction to <sf>
- example(s):
packmover.score_function(scorefxn)
- See Also:
PackRotamersMover PackRotamersMover.task
C++: protocols::minimization_packing::PackRotamersMover::score_function(class std::shared_ptr<const class core::scoring::ScoreFunction>) –> void
score_function(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover) -> pyrosetta.rosetta.core.scoring.ScoreFunction
Returns the ScoreFunction
- example(s):
packmover.score_function()
- See Also:
PackRotamersMover PackRotamersMover.task
C++: protocols::minimization_packing::PackRotamersMover::score_function() const –> class std::shared_ptr<const class core::scoring::ScoreFunction>
- set_annealer_observer(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover, observer: pyrosetta.rosetta.core.pack.annealer.AnnealerObserver) None ¶
C++: protocols::minimization_packing::PackRotamersMover::set_annealer_observer(class std::shared_ptr<class core::pack::annealer::AnnealerObserver>) –> 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.minimization_packing.PackRotamersMover) -> None
show(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover, output: pyrosetta.rosetta.std.ostream) -> None
C++: protocols::minimization_packing::PackRotamersMover::show(std::ostream &) const –> void
- task(*args, **kwargs)¶
Overloaded function.
task(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover, t: pyrosetta.rosetta.core.pack.task.PackerTask) -> None
Sets the PackerTask to <t>
- example(s):
packmover.task(task_pack)
- See Also:
PackRotamersMover PackRotamersMover.task_factory
C++: protocols::minimization_packing::PackRotamersMover::task(class std::shared_ptr<const class core::pack::task::PackerTask>) –> void
task(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover) -> pyrosetta.rosetta.core.pack.task.PackerTask
Returns the PackerTask
- example(s):
packmover.task()
- See Also:
PackRotamersMover PackRotamersMover.task_factory
C++: protocols::minimization_packing::PackRotamersMover::task() const –> class std::shared_ptr<const class core::pack::task::PackerTask>
- task_factory(*args, **kwargs)¶
Overloaded function.
task_factory(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover, tf: pyrosetta.rosetta.core.pack.task.TaskFactory) -> None
Sets the TaskFactory to <tf>
- example(s):
packmover.task_factory(task_design)
- See Also:
PackRotamersMover PackRotamersMover.task
C++: protocols::minimization_packing::PackRotamersMover::task_factory(class std::shared_ptr<const class core::pack::task::TaskFactory>) –> void
task_factory(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover) -> pyrosetta.rosetta.core.pack.task.TaskFactory
Returns the TaskFactory
- example(s):
packmover.task_factory()
- See Also:
PackRotamersMover PackRotamersMover.task
C++: protocols::minimization_packing::PackRotamersMover::task_factory() const –> class std::shared_ptr<const class core::pack::task::TaskFactory>
- task_is_valid(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover, pose: pyrosetta.rosetta.core.pose.Pose) bool ¶
C++: protocols::minimization_packing::PackRotamersMover::task_is_valid(const class core::pose::Pose &) const –> bool
- 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.minimization_packing.TaskAwareMinMover¶
Bases:
Mover
this class wraps MinMover, but ensures that its MoveMap always contains up-to-date information about sidechain mobility. It takes its base movemap, allows sidechain freedom at any position mobile in a Factory-generated PackerTask, and passes the new movemap to MinMover. The MinMover’s MoveMap does not accumulate state over many calls to apply().
- apply(self: pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::minimization_packing::TaskAwareMinMover::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover, : pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover) pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover ¶
C++: protocols::minimization_packing::TaskAwareMinMover::operator=(const class protocols::minimization_packing::TaskAwareMinMover &) –> class protocols::minimization_packing::TaskAwareMinMover &
- bb(*args, **kwargs)¶
Overloaded function.
bb(self: pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover, val: bool) -> None
C++: protocols::minimization_packing::TaskAwareMinMover::bb(bool) –> void
bb(self: pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover) -> bool
C++: protocols::minimization_packing::TaskAwareMinMover::bb() const –> bool
- chi(*args, **kwargs)¶
Overloaded function.
chi(self: pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover, val: bool) -> None
C++: protocols::minimization_packing::TaskAwareMinMover::chi(bool) –> void
chi(self: pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover) -> bool
C++: protocols::minimization_packing::TaskAwareMinMover::chi() const –> bool
- clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) None ¶
Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.
clear_info is called by jd2 before calling apply
C++: protocols::moves::Mover::clear_info() –> void
- clone(self: pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::minimization_packing::TaskAwareMinMover::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.minimization_packing.TaskAwareMinMover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::minimization_packing::TaskAwareMinMover::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.minimization_packing.TaskAwareMinMover) str ¶
C++: protocols::minimization_packing::TaskAwareMinMover::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 > > &
- jump(*args, **kwargs)¶
Overloaded function.
jump(self: pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover, j: bool) -> None
C++: protocols::minimization_packing::TaskAwareMinMover::jump(const bool) –> void
jump(self: pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover) -> bool
C++: protocols::minimization_packing::TaskAwareMinMover::jump() const –> bool
- 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::minimization_packing::TaskAwareMinMover::mover_name() –> std::string
- static name() str ¶
C++: protocols::moves::Mover::name() –> std::string
- parse_my_tag(self: pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None ¶
parse XML (specifically in the context of the parser/scripting scheme)
C++: protocols::minimization_packing::TaskAwareMinMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- parse_task_operations(self: pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None ¶
parse “task_operations” XML option
C++: protocols::minimization_packing::TaskAwareMinMover::parse_task_operations(class std::shared_ptr<const class utility::tag::Tag>, const 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::minimization_packing::TaskAwareMinMover::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.minimization_packing.TaskAwareMinMoverCreator¶
Bases:
MoverCreator
- assign(self: pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMoverCreator, : pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMoverCreator) pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMoverCreator ¶
C++: protocols::minimization_packing::TaskAwareMinMoverCreator::operator=(const class protocols::minimization_packing::TaskAwareMinMoverCreator &) –> class protocols::minimization_packing::TaskAwareMinMoverCreator &
- create_mover(self: pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMoverCreator) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::minimization_packing::TaskAwareMinMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>
- keyname(self: pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMoverCreator) str ¶
C++: protocols::minimization_packing::TaskAwareMinMoverCreator::keyname() const –> std::string
- class pyrosetta.rosetta.protocols.minimization_packing.UserDefinedGroupDiscriminator¶
Bases:
GroupDiscriminator
- assign(self: pyrosetta.rosetta.protocols.minimization_packing.UserDefinedGroupDiscriminator, : pyrosetta.rosetta.protocols.minimization_packing.UserDefinedGroupDiscriminator) pyrosetta.rosetta.protocols.minimization_packing.UserDefinedGroupDiscriminator ¶
C++: protocols::minimization_packing::UserDefinedGroupDiscriminator::operator=(const class protocols::minimization_packing::UserDefinedGroupDiscriminator &) –> class protocols::minimization_packing::UserDefinedGroupDiscriminator &
- clone(self: pyrosetta.rosetta.protocols.minimization_packing.UserDefinedGroupDiscriminator) pyrosetta.rosetta.protocols.minimization_packing.GroupDiscriminator ¶
C++: protocols::minimization_packing::UserDefinedGroupDiscriminator::clone() const –> class std::shared_ptr<class protocols::minimization_packing::GroupDiscriminator>
- group_id(self: pyrosetta.rosetta.protocols.minimization_packing.UserDefinedGroupDiscriminator, pose: pyrosetta.rosetta.core.pose.Pose, seqpos: int) int ¶
C++: protocols::minimization_packing::UserDefinedGroupDiscriminator::group_id(const class core::pose::Pose &, unsigned long) const –> unsigned long
- set_group_ids(self: pyrosetta.rosetta.protocols.minimization_packing.UserDefinedGroupDiscriminator, group_ids_input: pyrosetta.rosetta.utility.vector1_unsigned_long) None ¶
C++: protocols::minimization_packing::UserDefinedGroupDiscriminator::set_group_ids(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void