simple_moves¶
Bindings for protocols::simple_moves namespace
- class pyrosetta.rosetta.protocols.simple_moves.AddCavitiesMover¶
Bases:
Mover
- add_suckers(self: pyrosetta.rosetta.protocols.simple_moves.AddCavitiesMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::simple_moves::AddCavitiesMover::add_suckers(class core::pose::Pose &) –> void
- apply(self: pyrosetta.rosetta.protocols.simple_moves.AddCavitiesMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::simple_moves::AddCavitiesMover::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.simple_moves.AddCavitiesMover, : pyrosetta.rosetta.protocols.simple_moves.AddCavitiesMover) pyrosetta.rosetta.protocols.simple_moves.AddCavitiesMover ¶
C++: protocols::simple_moves::AddCavitiesMover::operator=(const class protocols::simple_moves::AddCavitiesMover &) –> class protocols::simple_moves::AddCavitiesMover &
- clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) None ¶
Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.
clear_info is called by jd2 before calling apply
C++: protocols::moves::Mover::clear_info() –> void
- clear_suckers(self: pyrosetta.rosetta.protocols.simple_moves.AddCavitiesMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::simple_moves::AddCavitiesMover::clear_suckers(class core::pose::Pose &) –> 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_cavities(self: pyrosetta.rosetta.protocols.simple_moves.AddCavitiesMover, pose: pyrosetta.rosetta.core.pose.Pose, nbdis: float, nbcount: int, minsep: float) pyrosetta.rosetta.utility.vector1_core_scoring_packstat_CavityBall ¶
C++: protocols::simple_moves::AddCavitiesMover::get_cavities(const class core::pose::Pose &, double, int, double) –> class utility::vector1<class core::scoring::packstat::CavityBall, class std::allocator<class core::scoring::packstat::CavityBall> >
- 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.simple_moves.AddCavitiesMover) str ¶
C++: protocols::simple_moves::AddCavitiesMover::get_name() const –> std::string
- get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose ¶
C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>
- get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>
- get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t ¶
C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>
- get_type(self: pyrosetta.rosetta.protocols.moves.Mover) str ¶
C++: protocols::moves::Mover::get_type() const –> std::string
- info(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.list_std_string_t ¶
non-const accessor
C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &
- last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) float ¶
C++: protocols::moves::Mover::last_proposal_density_ratio() –> double
- static name() str ¶
C++: protocols::moves::Mover::name() –> std::string
- parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None ¶
Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.
C++: protocols::moves::Mover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None ¶
- Provide citations to the passed CitationCollectionList
Subclasses should add the info for themselves and any other classes they use.
The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.
C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void
- static register_options() None ¶
Overload this static method if you access options within the mover.
These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.
C++: protocols::moves::Mover::register_options() –> void
- reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) bool ¶
- Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on
each use.
C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool
- reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) bool ¶
- Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input
pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).
C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool
- reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) None ¶
resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.
C++: protocols::moves::Mover::reset_status() –> void
- set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) None ¶
C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void
- set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) None ¶
C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void
- set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
setter for poses contained for rms
C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void
- set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe
C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void
- set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) None ¶
Set the ‘type’ string
C++: protocols::moves::Mover::set_type(const std::string &) –> void
- show(*args, **kwargs)¶
Overloaded function.
show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None
Outputs details about the Mover, including current settings.
C++: protocols::moves::Mover::show(std::ostream &) const –> void
- test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
- : Unit test support function. Apply one move to a given pose.
Allows extra test specific functions to be called before applying
C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void
- type(*args, **kwargs)¶
Overloaded function.
type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None
Set the ‘type’ string
C++: protocols::moves::Mover::type(const std::string &) –> void
type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str
Get the set ‘type’ string
C++: protocols::moves::Mover::type() const –> const std::string &
- class pyrosetta.rosetta.protocols.simple_moves.AddChainMover¶
Bases:
Mover
- add_new_chain(self: pyrosetta.rosetta.protocols.simple_moves.AddChainMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::simple_moves::AddChainMover::add_new_chain(class core::pose::Pose &) const –> void
- apply(self: pyrosetta.rosetta.protocols.simple_moves.AddChainMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::simple_moves::AddChainMover::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.simple_moves.AddChainMover, : pyrosetta.rosetta.protocols.simple_moves.AddChainMover) pyrosetta.rosetta.protocols.simple_moves.AddChainMover ¶
C++: protocols::simple_moves::AddChainMover::operator=(const class protocols::simple_moves::AddChainMover &) –> class protocols::simple_moves::AddChainMover &
- 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.simple_moves.AddChainMover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::simple_moves::AddChainMover::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>
- fname(*args, **kwargs)¶
Overloaded function.
fname(self: pyrosetta.rosetta.protocols.simple_moves.AddChainMover, f: str) -> None
C++: protocols::simple_moves::AddChainMover::fname(const std::string &) –> void
fname(self: pyrosetta.rosetta.protocols.simple_moves.AddChainMover) -> str
C++: protocols::simple_moves::AddChainMover::fname() const –> std::string
- fresh_instance(self: pyrosetta.rosetta.protocols.simple_moves.AddChainMover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::simple_moves::AddChainMover::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.simple_moves.AddChainMover) str ¶
C++: protocols::simple_moves::AddChainMover::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::simple_moves::AddChainMover::mover_name() –> std::string
- static name() str ¶
C++: protocols::moves::Mover::name() –> std::string
- new_chain(*args, **kwargs)¶
Overloaded function.
new_chain(self: pyrosetta.rosetta.protocols.simple_moves.AddChainMover, n: bool) -> None
C++: protocols::simple_moves::AddChainMover::new_chain(const bool) –> void
new_chain(self: pyrosetta.rosetta.protocols.simple_moves.AddChainMover) -> bool
C++: protocols::simple_moves::AddChainMover::new_chain() const –> bool
- parse_my_tag(self: pyrosetta.rosetta.protocols.simple_moves.AddChainMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None ¶
C++: protocols::simple_moves::AddChainMover::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: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) None ¶
C++: protocols::simple_moves::AddChainMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void
- random_access(*args, **kwargs)¶
Overloaded function.
random_access(self: pyrosetta.rosetta.protocols.simple_moves.AddChainMover) -> bool
C++: protocols::simple_moves::AddChainMover::random_access() const –> bool
random_access(self: pyrosetta.rosetta.protocols.simple_moves.AddChainMover, b: bool) -> None
C++: protocols::simple_moves::AddChainMover::random_access(const bool) –> 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(*args, **kwargs)¶
Overloaded function.
scorefxn(self: pyrosetta.rosetta.protocols.simple_moves.AddChainMover, s: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None
C++: protocols::simple_moves::AddChainMover::scorefxn(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void
scorefxn(self: pyrosetta.rosetta.protocols.simple_moves.AddChainMover) -> pyrosetta.rosetta.core.scoring.ScoreFunction
C++: protocols::simple_moves::AddChainMover::scorefxn() 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
- spm_reference_name(self: pyrosetta.rosetta.protocols.simple_moves.AddChainMover) str ¶
C++: protocols::simple_moves::AddChainMover::spm_reference_name() const –> std::string
- swap_chain(self: pyrosetta.rosetta.protocols.simple_moves.AddChainMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::simple_moves::AddChainMover::swap_chain(class core::pose::Pose &) const –> void
- swap_chain_number(*args, **kwargs)¶
Overloaded function.
swap_chain_number(self: pyrosetta.rosetta.protocols.simple_moves.AddChainMover, wc: int) -> None
C++: protocols::simple_moves::AddChainMover::swap_chain_number(const unsigned long) –> void
swap_chain_number(self: pyrosetta.rosetta.protocols.simple_moves.AddChainMover) -> int
C++: protocols::simple_moves::AddChainMover::swap_chain_number() const –> unsigned long
- 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 &
- update_PDBInfo(*args, **kwargs)¶
Overloaded function.
update_PDBInfo(self: pyrosetta.rosetta.protocols.simple_moves.AddChainMover, n: bool) -> None
C++: protocols::simple_moves::AddChainMover::update_PDBInfo(const bool) –> void
update_PDBInfo(self: pyrosetta.rosetta.protocols.simple_moves.AddChainMover) -> bool
C++: protocols::simple_moves::AddChainMover::update_PDBInfo() const –> bool
- class pyrosetta.rosetta.protocols.simple_moves.AddChainMoverCreator¶
Bases:
MoverCreator
- assign(self: pyrosetta.rosetta.protocols.simple_moves.AddChainMoverCreator, : pyrosetta.rosetta.protocols.simple_moves.AddChainMoverCreator) pyrosetta.rosetta.protocols.simple_moves.AddChainMoverCreator ¶
C++: protocols::simple_moves::AddChainMoverCreator::operator=(const class protocols::simple_moves::AddChainMoverCreator &) –> class protocols::simple_moves::AddChainMoverCreator &
- create_mover(self: pyrosetta.rosetta.protocols.simple_moves.AddChainMoverCreator) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::simple_moves::AddChainMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>
- keyname(self: pyrosetta.rosetta.protocols.simple_moves.AddChainMoverCreator) str ¶
C++: protocols::simple_moves::AddChainMoverCreator::keyname() const –> std::string
- provide_xml_schema(self: pyrosetta.rosetta.protocols.simple_moves.AddChainMoverCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) None ¶
C++: protocols::simple_moves::AddChainMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void
- class pyrosetta.rosetta.protocols.simple_moves.AddJobPairData¶
Bases:
Mover
Add an arbitrary piece of data to the current Job, which will be output in the silent file, database, etc. This is useful for adding metadata to keep track of data generated using multiple experimental conditions. Currently ONLY RosettaScript interface supported.
The data appended to the Job consists of a key and a value. The key is a string, and the value can be either a real or string.
- apply(self: pyrosetta.rosetta.protocols.simple_moves.AddJobPairData, : pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::simple_moves::AddJobPairData::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.simple_moves.AddJobPairData, : pyrosetta.rosetta.protocols.simple_moves.AddJobPairData) pyrosetta.rosetta.protocols.simple_moves.AddJobPairData ¶
C++: protocols::simple_moves::AddJobPairData::operator=(const class protocols::simple_moves::AddJobPairData &) –> class protocols::simple_moves::AddJobPairData &
- 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.simple_moves.AddJobPairData) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::simple_moves::AddJobPairData::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.simple_moves.AddJobPairData) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::simple_moves::AddJobPairData::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.simple_moves.AddJobPairData) str ¶
C++: protocols::simple_moves::AddJobPairData::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::simple_moves::AddJobPairData::mover_name() –> std::string
- static name() str ¶
C++: protocols::moves::Mover::name() –> std::string
- parse_my_tag(self: pyrosetta.rosetta.protocols.simple_moves.AddJobPairData, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None ¶
C++: protocols::simple_moves::AddJobPairData::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: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) None ¶
C++: protocols::simple_moves::AddJobPairData::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.simple_moves.AddJobPairDataCreator¶
Bases:
MoverCreator
- assign(self: pyrosetta.rosetta.protocols.simple_moves.AddJobPairDataCreator, : pyrosetta.rosetta.protocols.simple_moves.AddJobPairDataCreator) pyrosetta.rosetta.protocols.simple_moves.AddJobPairDataCreator ¶
C++: protocols::simple_moves::AddJobPairDataCreator::operator=(const class protocols::simple_moves::AddJobPairDataCreator &) –> class protocols::simple_moves::AddJobPairDataCreator &
- create_mover(self: pyrosetta.rosetta.protocols.simple_moves.AddJobPairDataCreator) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::simple_moves::AddJobPairDataCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>
- keyname(self: pyrosetta.rosetta.protocols.simple_moves.AddJobPairDataCreator) str ¶
C++: protocols::simple_moves::AddJobPairDataCreator::keyname() const –> std::string
- provide_xml_schema(self: pyrosetta.rosetta.protocols.simple_moves.AddJobPairDataCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) None ¶
C++: protocols::simple_moves::AddJobPairDataCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void
- class pyrosetta.rosetta.protocols.simple_moves.AddPDBInfoMover¶
Bases:
Mover
- apply(self: pyrosetta.rosetta.protocols.simple_moves.AddPDBInfoMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::simple_moves::AddPDBInfoMover::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.simple_moves.AddPDBInfoMover, : pyrosetta.rosetta.protocols.simple_moves.AddPDBInfoMover) pyrosetta.rosetta.protocols.simple_moves.AddPDBInfoMover ¶
C++: protocols::simple_moves::AddPDBInfoMover::operator=(const class protocols::simple_moves::AddPDBInfoMover &) –> class protocols::simple_moves::AddPDBInfoMover &
- 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.simple_moves.AddPDBInfoMover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::simple_moves::AddPDBInfoMover::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.simple_moves.AddPDBInfoMover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::simple_moves::AddPDBInfoMover::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.simple_moves.AddPDBInfoMover) str ¶
C++: protocols::simple_moves::AddPDBInfoMover::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::simple_moves::AddPDBInfoMover::mover_name() –> std::string
- static name() str ¶
C++: protocols::moves::Mover::name() –> std::string
- parse_my_tag(self: pyrosetta.rosetta.protocols.simple_moves.AddPDBInfoMover, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None ¶
C++: protocols::simple_moves::AddPDBInfoMover::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: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) None ¶
C++: protocols::simple_moves::AddPDBInfoMover::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.simple_moves.AddPDBInfoMoverCreator¶
Bases:
MoverCreator
- assign(self: pyrosetta.rosetta.protocols.simple_moves.AddPDBInfoMoverCreator, : pyrosetta.rosetta.protocols.simple_moves.AddPDBInfoMoverCreator) pyrosetta.rosetta.protocols.simple_moves.AddPDBInfoMoverCreator ¶
C++: protocols::simple_moves::AddPDBInfoMoverCreator::operator=(const class protocols::simple_moves::AddPDBInfoMoverCreator &) –> class protocols::simple_moves::AddPDBInfoMoverCreator &
- create_mover(self: pyrosetta.rosetta.protocols.simple_moves.AddPDBInfoMoverCreator) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::simple_moves::AddPDBInfoMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>
- keyname(self: pyrosetta.rosetta.protocols.simple_moves.AddPDBInfoMoverCreator) str ¶
C++: protocols::simple_moves::AddPDBInfoMoverCreator::keyname() const –> std::string
- provide_xml_schema(self: pyrosetta.rosetta.protocols.simple_moves.AddPDBInfoMoverCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) None ¶
C++: protocols::simple_moves::AddPDBInfoMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void
- class pyrosetta.rosetta.protocols.simple_moves.AddResidueCouplingConstraint¶
Bases:
Mover
The mover is designed to improve the design process by using information from co-evolutionary correlation matrices. These matrices can be created by different methods, e.g. GREMLIN or plmDCA. The matrices get input as tensor of the shape [N, A, N, A] where N is the length of the protein and A is the length of the alphabet (typically 21 amino acids + 1 for gaps).
GRELIN alphabet order: ARNDCQEGHILKMFPSTWYV- plmDCA alphabet order: ACDEFGHIKLMNPQRSTVWY-
The order of the alphabet used can be defined by the user. To access the measure of co-evolution between, e.g., residue 1 (ALA) and residue 2 (ARG) the tensor lookup would be [1, 0, 2, 1] (using the GREMLIN alphabet order). The co-evolution strength is multiplied by a user defined strength factor (default=1) and then added as new term to the scoring function.
- apply(self: pyrosetta.rosetta.protocols.simple_moves.AddResidueCouplingConstraint, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::simple_moves::AddResidueCouplingConstraint::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.simple_moves.AddResidueCouplingConstraint, : pyrosetta.rosetta.protocols.simple_moves.AddResidueCouplingConstraint) pyrosetta.rosetta.protocols.simple_moves.AddResidueCouplingConstraint ¶
C++: protocols::simple_moves::AddResidueCouplingConstraint::operator=(const class protocols::simple_moves::AddResidueCouplingConstraint &) –> class protocols::simple_moves::AddResidueCouplingConstraint &
- 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.simple_moves.AddResidueCouplingConstraint) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::simple_moves::AddResidueCouplingConstraint::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.simple_moves.AddResidueCouplingConstraint) str ¶
C++: protocols::simple_moves::AddResidueCouplingConstraint::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::simple_moves::AddResidueCouplingConstraint::mover_name() –> std::string
- static name() str ¶
C++: protocols::moves::Mover::name() –> std::string
- parse_my_tag(self: pyrosetta.rosetta.protocols.simple_moves.AddResidueCouplingConstraint, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None ¶
C++: protocols::simple_moves::AddResidueCouplingConstraint::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: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) None ¶
C++: protocols::simple_moves::AddResidueCouplingConstraint::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.simple_moves.AddResidueCouplingConstraintCreator¶
Bases:
MoverCreator
- assign(self: pyrosetta.rosetta.protocols.simple_moves.AddResidueCouplingConstraintCreator, : pyrosetta.rosetta.protocols.simple_moves.AddResidueCouplingConstraintCreator) pyrosetta.rosetta.protocols.simple_moves.AddResidueCouplingConstraintCreator ¶
C++: protocols::simple_moves::AddResidueCouplingConstraintCreator::operator=(const class protocols::simple_moves::AddResidueCouplingConstraintCreator &) –> class protocols::simple_moves::AddResidueCouplingConstraintCreator &
- create_mover(self: pyrosetta.rosetta.protocols.simple_moves.AddResidueCouplingConstraintCreator) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::simple_moves::AddResidueCouplingConstraintCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>
- keyname(self: pyrosetta.rosetta.protocols.simple_moves.AddResidueCouplingConstraintCreator) str ¶
C++: protocols::simple_moves::AddResidueCouplingConstraintCreator::keyname() const –> std::string
- provide_xml_schema(self: pyrosetta.rosetta.protocols.simple_moves.AddResidueCouplingConstraintCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) None ¶
C++: protocols::simple_moves::AddResidueCouplingConstraintCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void
- class pyrosetta.rosetta.protocols.simple_moves.AddResidueLabelMover¶
Bases:
Mover
- apply(self: pyrosetta.rosetta.protocols.simple_moves.AddResidueLabelMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::simple_moves::AddResidueLabelMover::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.simple_moves.AddResidueLabelMover, : pyrosetta.rosetta.protocols.simple_moves.AddResidueLabelMover) pyrosetta.rosetta.protocols.simple_moves.AddResidueLabelMover ¶
C++: protocols::simple_moves::AddResidueLabelMover::operator=(const class protocols::simple_moves::AddResidueLabelMover &) –> class protocols::simple_moves::AddResidueLabelMover &
- 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.simple_moves.AddResidueLabelMover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::simple_moves::AddResidueLabelMover::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.simple_moves.AddResidueLabelMover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::simple_moves::AddResidueLabelMover::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.simple_moves.AddResidueLabelMover) str ¶
C++: protocols::simple_moves::AddResidueLabelMover::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.simple_moves.AddResidueLabelMover, tag: pyrosetta.rosetta.utility.tag.Tag, data_map: pyrosetta.rosetta.basic.datacache.DataMap) None ¶
C++: protocols::simple_moves::AddResidueLabelMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None ¶
- Provide citations to the passed CitationCollectionList
Subclasses should add the info for themselves and any other classes they use.
The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.
C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void
- static register_options() None ¶
Overload this static method if you access options within the mover.
These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.
C++: protocols::moves::Mover::register_options() –> void
- reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) bool ¶
- Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on
each use.
C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool
- reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) bool ¶
- Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input
pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).
C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool
- reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) None ¶
resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.
C++: protocols::moves::Mover::reset_status() –> void
- set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) None ¶
C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void
- set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) None ¶
C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void
- set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
setter for poses contained for rms
C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void
- set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe
C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void
- set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) None ¶
Set the ‘type’ string
C++: protocols::moves::Mover::set_type(const std::string &) –> void
- show(*args, **kwargs)¶
Overloaded function.
show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None
Outputs details about the Mover, including current settings.
C++: protocols::moves::Mover::show(std::ostream &) const –> void
- test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
- : Unit test support function. Apply one move to a given pose.
Allows extra test specific functions to be called before applying
C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void
- type(*args, **kwargs)¶
Overloaded function.
type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None
Set the ‘type’ string
C++: protocols::moves::Mover::type(const std::string &) –> void
type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str
Get the set ‘type’ string
C++: protocols::moves::Mover::type() const –> const std::string &
- class pyrosetta.rosetta.protocols.simple_moves.AddResidueLabelMoverCreator¶
Bases:
MoverCreator
- assign(self: pyrosetta.rosetta.protocols.simple_moves.AddResidueLabelMoverCreator, : pyrosetta.rosetta.protocols.simple_moves.AddResidueLabelMoverCreator) pyrosetta.rosetta.protocols.simple_moves.AddResidueLabelMoverCreator ¶
C++: protocols::simple_moves::AddResidueLabelMoverCreator::operator=(const class protocols::simple_moves::AddResidueLabelMoverCreator &) –> class protocols::simple_moves::AddResidueLabelMoverCreator &
- create_mover(self: pyrosetta.rosetta.protocols.simple_moves.AddResidueLabelMoverCreator) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::simple_moves::AddResidueLabelMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>
- keyname(self: pyrosetta.rosetta.protocols.simple_moves.AddResidueLabelMoverCreator) str ¶
C++: protocols::simple_moves::AddResidueLabelMoverCreator::keyname() const –> std::string
- static mover_name() str ¶
C++: protocols::simple_moves::AddResidueLabelMoverCreator::mover_name() –> std::string
- provide_xml_schema(self: pyrosetta.rosetta.protocols.simple_moves.AddResidueLabelMoverCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) None ¶
C++: protocols::simple_moves::AddResidueLabelMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void
- class pyrosetta.rosetta.protocols.simple_moves.AddSapConstraintMover¶
Bases:
Mover
Adds variant types to selected residues
- apply(self: pyrosetta.rosetta.protocols.simple_moves.AddSapConstraintMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::simple_moves::AddSapConstraintMover::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.simple_moves.AddSapConstraintMover, ot: pyrosetta.rosetta.protocols.simple_moves.AddSapConstraintMover) pyrosetta.rosetta.protocols.simple_moves.AddSapConstraintMover ¶
C++: protocols::simple_moves::AddSapConstraintMover::operator=(const class protocols::simple_moves::AddSapConstraintMover &) –> class protocols::simple_moves::AddSapConstraintMover &
- 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.simple_moves.AddSapConstraintMover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::simple_moves::AddSapConstraintMover::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.simple_moves.AddSapConstraintMover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::simple_moves::AddSapConstraintMover::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.simple_moves.AddSapConstraintMover) str ¶
C++: protocols::simple_moves::AddSapConstraintMover::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::simple_moves::AddSapConstraintMover::mover_name() –> std::string
- static name() str ¶
C++: protocols::moves::Mover::name() –> std::string
- parse_my_tag(self: pyrosetta.rosetta.protocols.simple_moves.AddSapConstraintMover, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None ¶
C++: protocols::simple_moves::AddSapConstraintMover::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: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) None ¶
C++: protocols::simple_moves::AddSapConstraintMover::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_full_accuracy_when_scoring(self: pyrosetta.rosetta.protocols.simple_moves.AddSapConstraintMover, full_accuracy: bool) None ¶
C++: protocols::simple_moves::AddSapConstraintMover::set_full_accuracy_when_scoring(bool) –> void
- set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
setter for poses contained for rms
C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void
- set_name(self: pyrosetta.rosetta.protocols.simple_moves.AddSapConstraintMover, name: str) None ¶
C++: protocols::simple_moves::AddSapConstraintMover::set_name(const std::string &) –> 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_packing_correction(self: pyrosetta.rosetta.protocols.simple_moves.AddSapConstraintMover, correction: float) None ¶
C++: protocols::simple_moves::AddSapConstraintMover::set_packing_correction(double) –> void
- set_penalty_per_sap(self: pyrosetta.rosetta.protocols.simple_moves.AddSapConstraintMover, penalty: float) None ¶
C++: protocols::simple_moves::AddSapConstraintMover::set_penalty_per_sap(double) –> void
- set_sap_calculate_selector(self: pyrosetta.rosetta.protocols.simple_moves.AddSapConstraintMover, selector_in: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) None ¶
C++: protocols::simple_moves::AddSapConstraintMover::set_sap_calculate_selector(const class std::shared_ptr<const class core::select::residue_selector::ResidueSelector> &) –> void
- set_sap_goal(self: pyrosetta.rosetta.protocols.simple_moves.AddSapConstraintMover, goal: float) None ¶
C++: protocols::simple_moves::AddSapConstraintMover::set_sap_goal(double) –> void
- set_sap_lb_goal(self: pyrosetta.rosetta.protocols.simple_moves.AddSapConstraintMover, goal: float) None ¶
C++: protocols::simple_moves::AddSapConstraintMover::set_sap_lb_goal(double) –> void
- set_sasa_selector(self: pyrosetta.rosetta.protocols.simple_moves.AddSapConstraintMover, selector_in: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) None ¶
C++: protocols::simple_moves::AddSapConstraintMover::set_sasa_selector(const class std::shared_ptr<const class core::select::residue_selector::ResidueSelector> &) –> void
- set_score_selector(self: pyrosetta.rosetta.protocols.simple_moves.AddSapConstraintMover, selector_in: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) None ¶
Set the ResidueSelector used by this mover.
C++: protocols::simple_moves::AddSapConstraintMover::set_score_selector(const class std::shared_ptr<const class core::select::residue_selector::ResidueSelector> &) –> void
- set_speed(self: pyrosetta.rosetta.protocols.simple_moves.AddSapConstraintMover, speed: str) None ¶
C++: protocols::simple_moves::AddSapConstraintMover::set_speed(const std::string &) –> 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.simple_moves.AddSapConstraintMoverCreator¶
Bases:
MoverCreator
- assign(self: pyrosetta.rosetta.protocols.simple_moves.AddSapConstraintMoverCreator, : pyrosetta.rosetta.protocols.simple_moves.AddSapConstraintMoverCreator) pyrosetta.rosetta.protocols.simple_moves.AddSapConstraintMoverCreator ¶
C++: protocols::simple_moves::AddSapConstraintMoverCreator::operator=(const class protocols::simple_moves::AddSapConstraintMoverCreator &) –> class protocols::simple_moves::AddSapConstraintMoverCreator &
- create_mover(self: pyrosetta.rosetta.protocols.simple_moves.AddSapConstraintMoverCreator) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::simple_moves::AddSapConstraintMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>
- keyname(self: pyrosetta.rosetta.protocols.simple_moves.AddSapConstraintMoverCreator) str ¶
C++: protocols::simple_moves::AddSapConstraintMoverCreator::keyname() const –> std::string
- provide_xml_schema(self: pyrosetta.rosetta.protocols.simple_moves.AddSapConstraintMoverCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) None ¶
C++: protocols::simple_moves::AddSapConstraintMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void
- class pyrosetta.rosetta.protocols.simple_moves.AddSapMathConstraintMover¶
Bases:
Mover
Adds variant types to selected residues
- add_constraint(self: pyrosetta.rosetta.protocols.simple_moves.AddSapMathConstraintMover, weight: float, name: str) None ¶
C++: protocols::simple_moves::AddSapMathConstraintMover::add_constraint(double, const std::string &) –> void
- apply(self: pyrosetta.rosetta.protocols.simple_moves.AddSapMathConstraintMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::simple_moves::AddSapMathConstraintMover::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.simple_moves.AddSapMathConstraintMover, ot: pyrosetta.rosetta.protocols.simple_moves.AddSapMathConstraintMover) pyrosetta.rosetta.protocols.simple_moves.AddSapMathConstraintMover ¶
C++: protocols::simple_moves::AddSapMathConstraintMover::operator=(const class protocols::simple_moves::AddSapMathConstraintMover &) –> class protocols::simple_moves::AddSapMathConstraintMover &
- 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.simple_moves.AddSapMathConstraintMover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::simple_moves::AddSapMathConstraintMover::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.simple_moves.AddSapMathConstraintMover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::simple_moves::AddSapMathConstraintMover::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.simple_moves.AddSapMathConstraintMover) str ¶
C++: protocols::simple_moves::AddSapMathConstraintMover::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::simple_moves::AddSapMathConstraintMover::mover_name() –> std::string
- static name() str ¶
C++: protocols::moves::Mover::name() –> std::string
- parse_my_tag(self: pyrosetta.rosetta.protocols.simple_moves.AddSapMathConstraintMover, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None ¶
C++: protocols::simple_moves::AddSapMathConstraintMover::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: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) None ¶
C++: protocols::simple_moves::AddSapMathConstraintMover::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_lower_bound(self: pyrosetta.rosetta.protocols.simple_moves.AddSapMathConstraintMover, lower: float) None ¶
C++: protocols::simple_moves::AddSapMathConstraintMover::set_lower_bound(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_penalty_per_unit(self: pyrosetta.rosetta.protocols.simple_moves.AddSapMathConstraintMover, penalty: float) None ¶
C++: protocols::simple_moves::AddSapMathConstraintMover::set_penalty_per_unit(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
- set_upper_bound(self: pyrosetta.rosetta.protocols.simple_moves.AddSapMathConstraintMover, upper: float) None ¶
C++: protocols::simple_moves::AddSapMathConstraintMover::set_upper_bound(double) –> 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.simple_moves.AddSapMathConstraintMoverCreator¶
Bases:
MoverCreator
- assign(self: pyrosetta.rosetta.protocols.simple_moves.AddSapMathConstraintMoverCreator, : pyrosetta.rosetta.protocols.simple_moves.AddSapMathConstraintMoverCreator) pyrosetta.rosetta.protocols.simple_moves.AddSapMathConstraintMoverCreator ¶
C++: protocols::simple_moves::AddSapMathConstraintMoverCreator::operator=(const class protocols::simple_moves::AddSapMathConstraintMoverCreator &) –> class protocols::simple_moves::AddSapMathConstraintMoverCreator &
- create_mover(self: pyrosetta.rosetta.protocols.simple_moves.AddSapMathConstraintMoverCreator) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::simple_moves::AddSapMathConstraintMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>
- keyname(self: pyrosetta.rosetta.protocols.simple_moves.AddSapMathConstraintMoverCreator) str ¶
C++: protocols::simple_moves::AddSapMathConstraintMoverCreator::keyname() const –> std::string
- provide_xml_schema(self: pyrosetta.rosetta.protocols.simple_moves.AddSapMathConstraintMoverCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) None ¶
C++: protocols::simple_moves::AddSapMathConstraintMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void
- class pyrosetta.rosetta.protocols.simple_moves.AlignChainMover¶
Bases:
Mover
Align a chain in the working pose to a chain. CA superposition
source_chain: the chain number in the working pose. 0 means the entire pose. target_chain: the chain number in the target pose. 0 means the entire pose. **target and source chains must have the same length of residues.
- apply(self: pyrosetta.rosetta.protocols.simple_moves.AlignChainMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::simple_moves::AlignChainMover::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.simple_moves.AlignChainMover, : pyrosetta.rosetta.protocols.simple_moves.AlignChainMover) pyrosetta.rosetta.protocols.simple_moves.AlignChainMover ¶
C++: protocols::simple_moves::AlignChainMover::operator=(const class protocols::simple_moves::AlignChainMover &) –> class protocols::simple_moves::AlignChainMover &
- 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.simple_moves.AlignChainMover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::simple_moves::AlignChainMover::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.simple_moves.AlignChainMover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::simple_moves::AlignChainMover::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.simple_moves.AlignChainMover) str ¶
C++: protocols::simple_moves::AlignChainMover::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::simple_moves::AlignChainMover::mover_name() –> std::string
- static name() str ¶
C++: protocols::moves::Mover::name() –> std::string
- parse_my_tag(self: pyrosetta.rosetta.protocols.simple_moves.AlignChainMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None ¶
C++: protocols::simple_moves::AlignChainMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- pose(*args, **kwargs)¶
Overloaded function.
pose(self: pyrosetta.rosetta.protocols.simple_moves.AlignChainMover) -> pyrosetta.rosetta.core.pose.Pose
C++: protocols::simple_moves::AlignChainMover::pose() const –> class std::shared_ptr<class core::pose::Pose>
pose(self: pyrosetta.rosetta.protocols.simple_moves.AlignChainMover, pose: pyrosetta.rosetta.core.pose.Pose) -> None
C++: protocols::simple_moves::AlignChainMover::pose(class std::shared_ptr<class core::pose::Pose>) –> 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: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) None ¶
C++: protocols::simple_moves::AlignChainMover::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
- source_chain(*args, **kwargs)¶
Overloaded function.
source_chain(self: pyrosetta.rosetta.protocols.simple_moves.AlignChainMover) -> int
C++: protocols::simple_moves::AlignChainMover::source_chain() const –> unsigned long
source_chain(self: pyrosetta.rosetta.protocols.simple_moves.AlignChainMover, s: int) -> None
C++: protocols::simple_moves::AlignChainMover::source_chain(const unsigned long) –> void
- target_chain(*args, **kwargs)¶
Overloaded function.
target_chain(self: pyrosetta.rosetta.protocols.simple_moves.AlignChainMover) -> int
C++: protocols::simple_moves::AlignChainMover::target_chain() const –> unsigned long
target_chain(self: pyrosetta.rosetta.protocols.simple_moves.AlignChainMover, s: int) -> None
C++: protocols::simple_moves::AlignChainMover::target_chain(const unsigned long) –> 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.simple_moves.AlignChainMoverCreator¶
Bases:
MoverCreator
- assign(self: pyrosetta.rosetta.protocols.simple_moves.AlignChainMoverCreator, : pyrosetta.rosetta.protocols.simple_moves.AlignChainMoverCreator) pyrosetta.rosetta.protocols.simple_moves.AlignChainMoverCreator ¶
C++: protocols::simple_moves::AlignChainMoverCreator::operator=(const class protocols::simple_moves::AlignChainMoverCreator &) –> class protocols::simple_moves::AlignChainMoverCreator &
- create_mover(self: pyrosetta.rosetta.protocols.simple_moves.AlignChainMoverCreator) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::simple_moves::AlignChainMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>
- keyname(self: pyrosetta.rosetta.protocols.simple_moves.AlignChainMoverCreator) str ¶
C++: protocols::simple_moves::AlignChainMoverCreator::keyname() const –> std::string
- provide_xml_schema(self: pyrosetta.rosetta.protocols.simple_moves.AlignChainMoverCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) None ¶
C++: protocols::simple_moves::AlignChainMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void
- class pyrosetta.rosetta.protocols.simple_moves.AtomHash¶
Bases:
pybind11_object
- add_point(self: pyrosetta.rosetta.protocols.simple_moves.AtomHash, residx: int, xyz: pyrosetta.rosetta.numeric.xyzVector_double_t) None ¶
C++: protocols::simple_moves::AtomHash::add_point(unsigned long, class numeric::xyzVector<double>) –> void
- assign(self: pyrosetta.rosetta.protocols.simple_moves.AtomHash, : pyrosetta.rosetta.protocols.simple_moves.AtomHash) pyrosetta.rosetta.protocols.simple_moves.AtomHash ¶
C++: protocols::simple_moves::AtomHash::operator=(const class protocols::simple_moves::AtomHash &) –> class protocols::simple_moves::AtomHash &
- get_neighborcount(self: pyrosetta.rosetta.protocols.simple_moves.AtomHash, xyz: pyrosetta.rosetta.numeric.xyzVector_double_t, dlim: float) int ¶
C++: protocols::simple_moves::AtomHash::get_neighborcount(class numeric::xyzVector<double>, double) –> unsigned long
- npoints(self: pyrosetta.rosetta.protocols.simple_moves.AtomHash) int ¶
C++: protocols::simple_moves::AtomHash::npoints() –> int
- reset_and_get_clusters(self: pyrosetta.rosetta.protocols.simple_moves.AtomHash, clusters: pyrosetta.rosetta.utility.vector1_utility_vector1_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t, dredundant: float, dcluster: float) None ¶
C++: protocols::simple_moves::AtomHash::reset_and_get_clusters(class utility::vector1<class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > >, class std::allocator<class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > > > > &, double, double) –> void
- trim_to_heterogeneous_clusters(self: pyrosetta.rosetta.protocols.simple_moves.AtomHash, dlim: float) None ¶
C++: protocols::simple_moves::AtomHash::trim_to_heterogeneous_clusters(double) –> void
- class pyrosetta.rosetta.protocols.simple_moves.AtomHashNode¶
Bases:
pybind11_object
- property idx¶
- property residx¶
- property xyz¶
- class pyrosetta.rosetta.protocols.simple_moves.BBConRotMover¶
Bases:
BBGaussianMover
- apply(self: pyrosetta.rosetta.protocols.simple_moves.BBConRotMover, : pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::simple_moves::BBConRotMover::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.simple_moves.BBConRotMover, : pyrosetta.rosetta.protocols.simple_moves.BBConRotMover) pyrosetta.rosetta.protocols.simple_moves.BBConRotMover ¶
C++: protocols::simple_moves::BBConRotMover::operator=(const class protocols::simple_moves::BBConRotMover &) –> class protocols::simple_moves::BBConRotMover &
- 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.simple_moves.BBGaussianMover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::simple_moves::BBGaussianMover::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>
- factorA(self: pyrosetta.rosetta.protocols.simple_moves.BBConRotMover, fA: float) None ¶
C++: protocols::simple_moves::BBConRotMover::factorA(const double) –> void
- factorB(self: pyrosetta.rosetta.protocols.simple_moves.BBConRotMover, fB: float) None ¶
C++: protocols::simple_moves::BBConRotMover::factorB(const double) –> void
- factorC(self: pyrosetta.rosetta.protocols.simple_moves.BBConRotMover, fC: float) None ¶
C++: protocols::simple_moves::BBConRotMover::factorC(const double) –> void
- finalize_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, pose: pyrosetta.rosetta.core.pose.Pose, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover) None ¶
Callback executed after all Monte Carlo trials are completed.
C++: protocols::canonical_sampling::ThermodynamicMover::finalize_simulation(class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover &) –> void
- 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_A(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover) None ¶
C++: protocols::simple_moves::BBGaussianMover::get_A() –> void
- get_G(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover) None ¶
C++: protocols::simple_moves::BBGaussianMover::get_G() –> void
- get_L_move(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, : pyrosetta.rosetta.core.pose.Pose) float ¶
calculate L matrix and update pose
C++: protocols::simple_moves::BBGaussianMover::get_L_move(class core::pose::Pose &) –> double
- get_L_prime(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover) float ¶
calculate L’, update last_proposal_density
C++: protocols::simple_moves::BBGaussianMover::get_L_prime() –> double
- get_VdRdPhi(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, : pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::simple_moves::BBGaussianMover::get_VdRdPhi(const class core::pose::Pose &) –> void
- 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.simple_moves.BBConRotMover) str ¶
C++: protocols::simple_moves::BBConRotMover::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.simple_moves.BBGaussianMover) None ¶
C++: protocols::simple_moves::BBGaussianMover::init() –> void
- init_kic_loop(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, looplength: int, mm: pyrosetta.rosetta.core.kinematics.MoveMap) None ¶
C++: protocols::simple_moves::BBGaussianMover::init_kic_loop(unsigned long, class std::shared_ptr<const class core::kinematics::MoveMap>) –> void
- initialize_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, pose: pyrosetta.rosetta.core.pose.Pose, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover, cycle: int) None ¶
Callback executed before any Monte Carlo trials are attempted.
C++: protocols::canonical_sampling::ThermodynamicMover::initialize_simulation(class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover &, unsigned long) –> void
- is_multi_trial(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) bool ¶
Return true if the move performs multiple trials on each apply.
last_inner_score_delta_over_temperature()
metropolis_hastings_mover()
set_metropolis_hastings_mover()
C++: protocols::canonical_sampling::ThermodynamicMover::is_multi_trial() –> bool
- last_inner_score_delta_over_temperature(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) float ¶
- If this is a multi-trial move, return the change in internal
score/temperature caused by the last call to apply().
is_multi_trial()
C++: protocols::canonical_sampling::ThermodynamicMover::last_inner_score_delta_over_temperature() –> double
- last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover) float ¶
get the ratio of proposal densities for the last move
C++: protocols::simple_moves::BBGaussianMover::last_proposal_density_ratio() –> double
- metropolis_hastings_mover(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) pyrosetta.rosetta.std.weak_ptr_protocols_canonical_sampling_MetropolisHastingsMover_t ¶
- If this is a multi-trial move, return the MetropolisHastingsMover
being used internally.
is_multi_trial()
C++: protocols::canonical_sampling::ThermodynamicMover::metropolis_hastings_mover() –> class std::weak_ptr<class protocols::canonical_sampling::MetropolisHastingsMover>
- movemap(*args, **kwargs)¶
Overloaded function.
movemap(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, : pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.core.kinematics.MoveMap
Generates the movemap used by this mover for the given pose
C++: protocols::simple_moves::BBGaussianMover::movemap(const class core::pose::Pose &) const –> class std::shared_ptr<const class core::kinematics::MoveMap>
movemap(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, new_movemap: pyrosetta.rosetta.core.kinematics.MoveMap) -> None
C++: protocols::simple_moves::BBGaussianMover::movemap(class std::shared_ptr<const class core::kinematics::MoveMap>) –> void
- movemap_factory(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, new_movemap_factory: pyrosetta.rosetta.core.select.movemap.MoveMapFactory) None ¶
The movemap_factory will be used to generate a movemap, if an explcit one hasn’t already been set.
C++: protocols::simple_moves::BBGaussianMover::movemap_factory(class std::shared_ptr<const class core::select::movemap::MoveMapFactory>) –> void
- static mover_name() str ¶
C++: protocols::simple_moves::BBGaussianMover::mover_name() –> std::string
- static name() str ¶
C++: protocols::moves::Mover::name() –> std::string
- observe_after_metropolis(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover) None ¶
Callback executed after the Metropolis criterion is evaluated.
C++: protocols::canonical_sampling::ThermodynamicMover::observe_after_metropolis(const class protocols::canonical_sampling::MetropolisHastingsMover &) –> void
- 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
- preserve_detailed_balance(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover) bool ¶
get whether detailed balance is preserved (i.e. no Ramachandran biasing)
C++: protocols::simple_moves::BBGaussianMover::preserve_detailed_balance() const –> bool
- 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: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) None ¶
C++: protocols::simple_moves::BBGaussianMover::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
- resize(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, : int, : int, : int) None ¶
C++: protocols::simple_moves::BBGaussianMover::resize(unsigned long, unsigned long, unsigned long) –> 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_metropolis_hastings_mover(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, metropolis_hastings_mover: pyrosetta.rosetta.std.weak_ptr_protocols_canonical_sampling_MetropolisHastingsMover_t) None ¶
- If this is a multi-trial move, set the MetropolisHastingsMover to
be used internally.
is_multi_trial()
C++: protocols::canonical_sampling::ThermodynamicMover::set_metropolis_hastings_mover(class std::weak_ptr<class protocols::canonical_sampling::MetropolisHastingsMover>) –> 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_preserve_detailed_balance(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, preserve_detailed_balance: bool) None ¶
set whether detailed balance is preserved (i.e. no Ramachandran biasing)
C++: protocols::simple_moves::BBGaussianMover::set_preserve_detailed_balance(bool) –> 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
- torsion_id_ranges(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, : pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.utility.vector1_core_id_TorsionID_Range ¶
dummy
C++: protocols::simple_moves::BBGaussianMover::torsion_id_ranges(class core::pose::Pose &) –> class utility::vector1<class core::id::TorsionID_Range, class std::allocator<class core::id::TorsionID_Range> >
- 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.simple_moves.BBDihedralSamplerMover¶
Bases:
Mover
Mover interface to BBDihedralSampler ( 1D ). Samples using BBDihedralSamplers randomly using residues set in the movemap. If multiple samplers are given, will randomly sample on them.
- add_sampler(self: pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover, sampler: protocols::simple_moves::bb_sampler::BBDihedralSampler) None ¶
Add a sampler to this mover.
C++: protocols::simple_moves::BBDihedralSamplerMover::add_sampler(class std::shared_ptr<class protocols::simple_moves::bb_sampler::BBDihedralSampler>) –> void
- apply(self: pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::simple_moves::BBDihedralSamplerMover::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover, : pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover) pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover ¶
C++: protocols::simple_moves::BBDihedralSamplerMover::operator=(const class protocols::simple_moves::BBDihedralSamplerMover &) –> class protocols::simple_moves::BBDihedralSamplerMover &
- 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.simple_moves.BBDihedralSamplerMover) pyrosetta.rosetta.protocols.moves.Mover ¶
required in the context of the parser/scripting scheme
C++: protocols::simple_moves::BBDihedralSamplerMover::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.simple_moves.BBDihedralSamplerMover) pyrosetta.rosetta.protocols.moves.Mover ¶
required in the context of the parser/scripting scheme
C++: protocols::simple_moves::BBDihedralSamplerMover::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.simple_moves.BBDihedralSamplerMover) str ¶
C++: protocols::simple_moves::BBDihedralSamplerMover::get_name() const –> std::string
- get_name_of_last_sampler_used(self: pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover) str ¶
Return the name of the last sampler used during the last apply
C++: protocols::simple_moves::BBDihedralSamplerMover::get_name_of_last_sampler_used() –> 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.simple_moves.BBDihedralSamplerMover, 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::simple_moves::BBDihedralSamplerMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- provide_citation_info(self: pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None ¶
Provide the citation.
C++: protocols::simple_moves::BBDihedralSamplerMover::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_dihedral_mask(self: pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover, mask: pyrosetta.rosetta.std.map_unsigned_long_utility_vector1_unsigned_long_std_allocator_unsigned_long_t_std_allocator_std_pair_const_unsigned_long_utility_vector1_unsigned_long_std_allocator_unsigned_long_t) None ¶
- Limit the torsions that are sampled using a mask.
- Mask is a vector of torsions we are allowed to sample at each residue.
NOT every residue must be present - only the ones we need to mask. This helps for carbohydrates, since not every residue has all possible dihedrals, even if we have samplers to use.
C++: protocols::simple_moves::BBDihedralSamplerMover::set_dihedral_mask(class std::map<unsigned long, class utility::vector1<unsigned long, class std::allocator<unsigned long> >, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, class utility::vector1<unsigned long, class std::allocator<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_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_residue_selector(self: pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) None ¶
Sets residues from a residue selector.
C++: protocols::simple_moves::BBDihedralSamplerMover::set_residue_selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void
- set_sampler(self: pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover, sampler: protocols::simple_moves::bb_sampler::BBDihedralSampler) None ¶
Set a single sampler this mover will use.
C++: protocols::simple_moves::BBDihedralSamplerMover::set_sampler(class std::shared_ptr<class protocols::simple_moves::bb_sampler::BBDihedralSampler>) –> void
- set_single_resnum(self: pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover, resnum: int) None ¶
Set a single resnum instead of a movemap.
C++: protocols::simple_moves::BBDihedralSamplerMover::set_single_resnum(unsigned long) –> void
- set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) None ¶
Set the ‘type’ string
C++: protocols::moves::Mover::set_type(const std::string &) –> void
- show(*args, **kwargs)¶
Overloaded function.
show(self: pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover) -> None
show(self: pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover, output: pyrosetta.rosetta.std.ostream) -> None
C++: protocols::simple_moves::BBDihedralSamplerMover::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.simple_moves.BBDihedralSamplerMoverCreator¶
Bases:
MoverCreator
- assign(self: pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMoverCreator, : pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMoverCreator) pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMoverCreator ¶
C++: protocols::simple_moves::BBDihedralSamplerMoverCreator::operator=(const class protocols::simple_moves::BBDihedralSamplerMoverCreator &) –> class protocols::simple_moves::BBDihedralSamplerMoverCreator &
- create_mover(self: pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMoverCreator) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::simple_moves::BBDihedralSamplerMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>
- keyname(self: pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMoverCreator) str ¶
C++: protocols::simple_moves::BBDihedralSamplerMoverCreator::keyname() const –> std::string
- static mover_name() str ¶
C++: protocols::simple_moves::BBDihedralSamplerMoverCreator::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.simple_moves.BBG8T3AMover¶
Bases:
BBGaussianMover
a particular gaussian mover from the original paper
using 8 torsion angles as DOF, 3 atoms (Ca,C,O) as end
- apply(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::simple_moves::BBGaussianMover::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover, : pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover) pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover ¶
C++: protocols::simple_moves::BBG8T3AMover::operator=(const class protocols::simple_moves::BBG8T3AMover &) –> class protocols::simple_moves::BBG8T3AMover &
- 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.simple_moves.BBG8T3AMover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::simple_moves::BBG8T3AMover::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>
- factorA(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, fA: float) None ¶
C++: protocols::simple_moves::BBGaussianMover::factorA(const double) –> void
- factorB(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, fB: float) None ¶
C++: protocols::simple_moves::BBGaussianMover::factorB(const double) –> void
- finalize_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, pose: pyrosetta.rosetta.core.pose.Pose, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover) None ¶
Callback executed after all Monte Carlo trials are completed.
C++: protocols::canonical_sampling::ThermodynamicMover::finalize_simulation(class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover &) –> void
- 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_A(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover) None ¶
C++: protocols::simple_moves::BBGaussianMover::get_A() –> void
- get_G(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover) None ¶
C++: protocols::simple_moves::BBGaussianMover::get_G() –> void
- get_L_move(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, : pyrosetta.rosetta.core.pose.Pose) float ¶
calculate L matrix and update pose
C++: protocols::simple_moves::BBGaussianMover::get_L_move(class core::pose::Pose &) –> double
- get_L_prime(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover) float ¶
calculate L’, update last_proposal_density
C++: protocols::simple_moves::BBGaussianMover::get_L_prime() –> double
- get_VdRdPhi(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, : pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::simple_moves::BBGaussianMover::get_VdRdPhi(const class core::pose::Pose &) –> void
- 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.simple_moves.BBG8T3AMover) str ¶
C++: protocols::simple_moves::BBG8T3AMover::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.simple_moves.BBGaussianMover) None ¶
C++: protocols::simple_moves::BBGaussianMover::init() –> void
- init_kic_loop(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, looplength: int, mm: pyrosetta.rosetta.core.kinematics.MoveMap) None ¶
C++: protocols::simple_moves::BBGaussianMover::init_kic_loop(unsigned long, class std::shared_ptr<const class core::kinematics::MoveMap>) –> void
- initialize_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, pose: pyrosetta.rosetta.core.pose.Pose, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover, cycle: int) None ¶
Callback executed before any Monte Carlo trials are attempted.
C++: protocols::canonical_sampling::ThermodynamicMover::initialize_simulation(class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover &, unsigned long) –> void
- is_multi_trial(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) bool ¶
Return true if the move performs multiple trials on each apply.
last_inner_score_delta_over_temperature()
metropolis_hastings_mover()
set_metropolis_hastings_mover()
C++: protocols::canonical_sampling::ThermodynamicMover::is_multi_trial() –> bool
- last_inner_score_delta_over_temperature(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) float ¶
- If this is a multi-trial move, return the change in internal
score/temperature caused by the last call to apply().
is_multi_trial()
C++: protocols::canonical_sampling::ThermodynamicMover::last_inner_score_delta_over_temperature() –> double
- last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover) float ¶
get the ratio of proposal densities for the last move
C++: protocols::simple_moves::BBGaussianMover::last_proposal_density_ratio() –> double
- metropolis_hastings_mover(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) pyrosetta.rosetta.std.weak_ptr_protocols_canonical_sampling_MetropolisHastingsMover_t ¶
- If this is a multi-trial move, return the MetropolisHastingsMover
being used internally.
is_multi_trial()
C++: protocols::canonical_sampling::ThermodynamicMover::metropolis_hastings_mover() –> class std::weak_ptr<class protocols::canonical_sampling::MetropolisHastingsMover>
- movemap(*args, **kwargs)¶
Overloaded function.
movemap(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, : pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.core.kinematics.MoveMap
Generates the movemap used by this mover for the given pose
C++: protocols::simple_moves::BBGaussianMover::movemap(const class core::pose::Pose &) const –> class std::shared_ptr<const class core::kinematics::MoveMap>
movemap(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, new_movemap: pyrosetta.rosetta.core.kinematics.MoveMap) -> None
C++: protocols::simple_moves::BBGaussianMover::movemap(class std::shared_ptr<const class core::kinematics::MoveMap>) –> void
- movemap_factory(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, new_movemap_factory: pyrosetta.rosetta.core.select.movemap.MoveMapFactory) None ¶
The movemap_factory will be used to generate a movemap, if an explcit one hasn’t already been set.
C++: protocols::simple_moves::BBGaussianMover::movemap_factory(class std::shared_ptr<const class core::select::movemap::MoveMapFactory>) –> void
- static mover_name() str ¶
C++: protocols::simple_moves::BBGaussianMover::mover_name() –> std::string
- static name() str ¶
C++: protocols::moves::Mover::name() –> std::string
- observe_after_metropolis(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover) None ¶
Callback executed after the Metropolis criterion is evaluated.
C++: protocols::canonical_sampling::ThermodynamicMover::observe_after_metropolis(const class protocols::canonical_sampling::MetropolisHastingsMover &) –> void
- 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
- preserve_detailed_balance(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover) bool ¶
get whether detailed balance is preserved (i.e. no Ramachandran biasing)
C++: protocols::simple_moves::BBGaussianMover::preserve_detailed_balance() const –> bool
- 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: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) None ¶
C++: protocols::simple_moves::BBGaussianMover::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
- resize(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, : int, : int, : int) None ¶
C++: protocols::simple_moves::BBGaussianMover::resize(unsigned long, unsigned long, unsigned long) –> 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_metropolis_hastings_mover(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, metropolis_hastings_mover: pyrosetta.rosetta.std.weak_ptr_protocols_canonical_sampling_MetropolisHastingsMover_t) None ¶
- If this is a multi-trial move, set the MetropolisHastingsMover to
be used internally.
is_multi_trial()
C++: protocols::canonical_sampling::ThermodynamicMover::set_metropolis_hastings_mover(class std::weak_ptr<class protocols::canonical_sampling::MetropolisHastingsMover>) –> 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_preserve_detailed_balance(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, preserve_detailed_balance: bool) None ¶
set whether detailed balance is preserved (i.e. no Ramachandran biasing)
C++: protocols::simple_moves::BBGaussianMover::set_preserve_detailed_balance(bool) –> 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
- torsion_id_ranges(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, : pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.utility.vector1_core_id_TorsionID_Range ¶
dummy
C++: protocols::simple_moves::BBGaussianMover::torsion_id_ranges(class core::pose::Pose &) –> class utility::vector1<class core::id::TorsionID_Range, class std::allocator<class core::id::TorsionID_Range> >
- 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.simple_moves.BBGaussianMover¶
Bases:
ThermodynamicMover
the basic class for implementing Gaussian Perturbation of bb
“Monte Carlo update for chain molecules: Biased Gaussian steps in torsional space” “The Journal of Chemical Physics, Vol. 114, No. 18. (2001), pp. 8154-8158.” Two steps for perturbing the backbone and keeping the geometry constrain Step 1: Gaussian Biased steps in torsional space: the end atoms of the moving segment should be choosen by user and to keep the geometry constrain(6), the DOF of the moving segment > 6 Step 2: “pivot” update the bb conformation, or followed by a chainclosure method (BBConRot)
- apply(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::simple_moves::BBGaussianMover::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, : pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover) pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover ¶
C++: protocols::simple_moves::BBGaussianMover::operator=(const class protocols::simple_moves::BBGaussianMover &) –> class protocols::simple_moves::BBGaussianMover &
- 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.simple_moves.BBGaussianMover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::simple_moves::BBGaussianMover::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>
- factorA(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, fA: float) None ¶
C++: protocols::simple_moves::BBGaussianMover::factorA(const double) –> void
- factorB(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, fB: float) None ¶
C++: protocols::simple_moves::BBGaussianMover::factorB(const double) –> void
- finalize_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, pose: pyrosetta.rosetta.core.pose.Pose, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover) None ¶
Callback executed after all Monte Carlo trials are completed.
C++: protocols::canonical_sampling::ThermodynamicMover::finalize_simulation(class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover &) –> void
- 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_A(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover) None ¶
C++: protocols::simple_moves::BBGaussianMover::get_A() –> void
- get_G(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover) None ¶
C++: protocols::simple_moves::BBGaussianMover::get_G() –> void
- get_L_move(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, : pyrosetta.rosetta.core.pose.Pose) float ¶
calculate L matrix and update pose
C++: protocols::simple_moves::BBGaussianMover::get_L_move(class core::pose::Pose &) –> double
- get_L_prime(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover) float ¶
calculate L’, update last_proposal_density
C++: protocols::simple_moves::BBGaussianMover::get_L_prime() –> double
- get_VdRdPhi(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, : pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::simple_moves::BBGaussianMover::get_VdRdPhi(const class core::pose::Pose &) –> void
- 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.simple_moves.BBGaussianMover) str ¶
C++: protocols::simple_moves::BBGaussianMover::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.simple_moves.BBGaussianMover) None ¶
C++: protocols::simple_moves::BBGaussianMover::init() –> void
- init_kic_loop(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, looplength: int, mm: pyrosetta.rosetta.core.kinematics.MoveMap) None ¶
C++: protocols::simple_moves::BBGaussianMover::init_kic_loop(unsigned long, class std::shared_ptr<const class core::kinematics::MoveMap>) –> void
- initialize_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, pose: pyrosetta.rosetta.core.pose.Pose, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover, cycle: int) None ¶
Callback executed before any Monte Carlo trials are attempted.
C++: protocols::canonical_sampling::ThermodynamicMover::initialize_simulation(class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover &, unsigned long) –> void
- is_multi_trial(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) bool ¶
Return true if the move performs multiple trials on each apply.
last_inner_score_delta_over_temperature()
metropolis_hastings_mover()
set_metropolis_hastings_mover()
C++: protocols::canonical_sampling::ThermodynamicMover::is_multi_trial() –> bool
- last_inner_score_delta_over_temperature(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) float ¶
- If this is a multi-trial move, return the change in internal
score/temperature caused by the last call to apply().
is_multi_trial()
C++: protocols::canonical_sampling::ThermodynamicMover::last_inner_score_delta_over_temperature() –> double
- last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover) float ¶
get the ratio of proposal densities for the last move
C++: protocols::simple_moves::BBGaussianMover::last_proposal_density_ratio() –> double
- metropolis_hastings_mover(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) pyrosetta.rosetta.std.weak_ptr_protocols_canonical_sampling_MetropolisHastingsMover_t ¶
- If this is a multi-trial move, return the MetropolisHastingsMover
being used internally.
is_multi_trial()
C++: protocols::canonical_sampling::ThermodynamicMover::metropolis_hastings_mover() –> class std::weak_ptr<class protocols::canonical_sampling::MetropolisHastingsMover>
- movemap(*args, **kwargs)¶
Overloaded function.
movemap(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, : pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.core.kinematics.MoveMap
Generates the movemap used by this mover for the given pose
C++: protocols::simple_moves::BBGaussianMover::movemap(const class core::pose::Pose &) const –> class std::shared_ptr<const class core::kinematics::MoveMap>
movemap(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, new_movemap: pyrosetta.rosetta.core.kinematics.MoveMap) -> None
C++: protocols::simple_moves::BBGaussianMover::movemap(class std::shared_ptr<const class core::kinematics::MoveMap>) –> void
- movemap_factory(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, new_movemap_factory: pyrosetta.rosetta.core.select.movemap.MoveMapFactory) None ¶
The movemap_factory will be used to generate a movemap, if an explcit one hasn’t already been set.
C++: protocols::simple_moves::BBGaussianMover::movemap_factory(class std::shared_ptr<const class core::select::movemap::MoveMapFactory>) –> void
- static mover_name() str ¶
C++: protocols::simple_moves::BBGaussianMover::mover_name() –> std::string
- static name() str ¶
C++: protocols::moves::Mover::name() –> std::string
- observe_after_metropolis(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover) None ¶
Callback executed after the Metropolis criterion is evaluated.
C++: protocols::canonical_sampling::ThermodynamicMover::observe_after_metropolis(const class protocols::canonical_sampling::MetropolisHastingsMover &) –> void
- 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
- preserve_detailed_balance(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover) bool ¶
get whether detailed balance is preserved (i.e. no Ramachandran biasing)
C++: protocols::simple_moves::BBGaussianMover::preserve_detailed_balance() const –> bool
- 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: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) None ¶
C++: protocols::simple_moves::BBGaussianMover::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
- resize(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, : int, : int, : int) None ¶
C++: protocols::simple_moves::BBGaussianMover::resize(unsigned long, unsigned long, unsigned long) –> 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_metropolis_hastings_mover(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, metropolis_hastings_mover: pyrosetta.rosetta.std.weak_ptr_protocols_canonical_sampling_MetropolisHastingsMover_t) None ¶
- If this is a multi-trial move, set the MetropolisHastingsMover to
be used internally.
is_multi_trial()
C++: protocols::canonical_sampling::ThermodynamicMover::set_metropolis_hastings_mover(class std::weak_ptr<class protocols::canonical_sampling::MetropolisHastingsMover>) –> 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_preserve_detailed_balance(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, preserve_detailed_balance: bool) None ¶
set whether detailed balance is preserved (i.e. no Ramachandran biasing)
C++: protocols::simple_moves::BBGaussianMover::set_preserve_detailed_balance(bool) –> 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
- torsion_id_ranges(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, : pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.utility.vector1_core_id_TorsionID_Range ¶
dummy
C++: protocols::simple_moves::BBGaussianMover::torsion_id_ranges(class core::pose::Pose &) –> class utility::vector1<class core::id::TorsionID_Range, class std::allocator<class core::id::TorsionID_Range> >
- 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.simple_moves.BBGaussianMoverCreator¶
Bases:
MoverCreator
- assign(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMoverCreator, : pyrosetta.rosetta.protocols.simple_moves.BBGaussianMoverCreator) pyrosetta.rosetta.protocols.simple_moves.BBGaussianMoverCreator ¶
C++: protocols::simple_moves::BBGaussianMoverCreator::operator=(const class protocols::simple_moves::BBGaussianMoverCreator &) –> class protocols::simple_moves::BBGaussianMoverCreator &
- create_mover(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMoverCreator) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::simple_moves::BBGaussianMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>
- keyname(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMoverCreator) str ¶
C++: protocols::simple_moves::BBGaussianMoverCreator::keyname() const –> std::string
- provide_xml_schema(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMoverCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) None ¶
C++: protocols::simple_moves::BBGaussianMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void
- class pyrosetta.rosetta.protocols.simple_moves.BackboneMover¶
Bases:
ThermodynamicMover
BackboneMover class has elements of the MC temperature to do repetitions of bb moves (small, shear, wobble, etc.).
- angle_max(*args, **kwargs)¶
Overloaded function.
angle_max(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, angle: float) -> None
- Set the maximum angle of perturbation, independent of
secondary structure. new_angle = old_angle +/- ( angle_max/2 )
- Example:
bbmover.angle_max(25)
- See also:
ShearMover SmallMover
C++: protocols::simple_moves::BackboneMover::angle_max(const double) –> void
angle_max(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, type: str, angle: float) -> None
- Sets the max angle of perturbation for residues with <type>
secondary structure. (<type> must be ‘H’, ‘E’, or ‘L’.) new_angle = old_angle +/- ( angle_max/2 )
- Example:
bbmover.angle_max(‘H’, 25)
- See also:
ShearMover SmallMover
C++: protocols::simple_moves::BackboneMover::angle_max(const char, const double) –> void
angle_max(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, angle_max_in: pyrosetta.rosetta.std.map_char_double) -> None
- Sets the max angle of perturbation, for secondary structures
‘H’, ‘E’, and ‘L’. new_angle = old_angle +/- ( angle_max/2 )
C++: protocols::simple_moves::BackboneMover::angle_max(class std::map<char, double, struct std::less<char>, class std::allocator<struct std::pair<const char, double> > >) –> void
- apply(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, : pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::simple_moves::BackboneMover::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, : pyrosetta.rosetta.protocols.simple_moves.BackboneMover) pyrosetta.rosetta.protocols.simple_moves.BackboneMover ¶
C++: protocols::simple_moves::BackboneMover::operator=(const class protocols::simple_moves::BackboneMover &) –> class protocols::simple_moves::BackboneMover &
- static backbone_mover_complex_type_namer(tag_name: str) str ¶
C++: protocols::simple_moves::BackboneMover::backbone_mover_complex_type_namer(std::string) –> std::string
- check_rama(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover) bool ¶
C++: protocols::simple_moves::BackboneMover::check_rama() –> bool
- clear(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover) None ¶
C++: protocols::simple_moves::BackboneMover::clear() –> 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.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>
- static complex_type_generator_for_backbone_mover(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) pyrosetta.rosetta.utility.tag.XMLSchemaComplexTypeGenerator ¶
C++: protocols::simple_moves::BackboneMover::complex_type_generator_for_backbone_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>
- finalize_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, pose: pyrosetta.rosetta.core.pose.Pose, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover) None ¶
Callback executed after all Monte Carlo trials are completed.
C++: protocols::canonical_sampling::ThermodynamicMover::finalize_simulation(class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover &) –> void
- 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_angle_max(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, type: str) float ¶
- Gets the max angle of perturbation for residues with <type>
secondary structure. (<type> must be ‘H’, ‘E’, or ‘L’.)
- Example:
bbmover.angle_max(‘H’)
- See also:
ShearMover SmallMover
C++: protocols::simple_moves::BackboneMover::get_angle_max(const char) const –> double
- 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.simple_moves.BackboneMover) str ¶
C++: protocols::simple_moves::BackboneMover::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_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, pose: pyrosetta.rosetta.core.pose.Pose, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover, cycle: int) None ¶
Callback executed before any Monte Carlo trials are attempted.
C++: protocols::canonical_sampling::ThermodynamicMover::initialize_simulation(class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover &, unsigned long) –> void
- is_multi_trial(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) bool ¶
Return true if the move performs multiple trials on each apply.
last_inner_score_delta_over_temperature()
metropolis_hastings_mover()
set_metropolis_hastings_mover()
C++: protocols::canonical_sampling::ThermodynamicMover::is_multi_trial() –> bool
- last_inner_score_delta_over_temperature(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) float ¶
- If this is a multi-trial move, return the change in internal
score/temperature caused by the last call to apply().
is_multi_trial()
C++: protocols::canonical_sampling::ThermodynamicMover::last_inner_score_delta_over_temperature() –> double
- last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) float ¶
Return the proposal density ratio for last apply method.
C++: protocols::canonical_sampling::ThermodynamicMover::last_proposal_density_ratio() –> double
- make_move(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, : pyrosetta.rosetta.core.pose.Pose) bool ¶
C++: protocols::simple_moves::BackboneMover::make_move(class core::pose::Pose &) –> bool
- metropolis_hastings_mover(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) pyrosetta.rosetta.std.weak_ptr_protocols_canonical_sampling_MetropolisHastingsMover_t ¶
- If this is a multi-trial move, return the MetropolisHastingsMover
being used internally.
is_multi_trial()
C++: protocols::canonical_sampling::ThermodynamicMover::metropolis_hastings_mover() –> class std::weak_ptr<class protocols::canonical_sampling::MetropolisHastingsMover>
- move_with_rama(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, pose: pyrosetta.rosetta.core.pose.Pose) bool ¶
C++: protocols::simple_moves::BackboneMover::move_with_rama(class core::pose::Pose &) –> bool
- move_with_scorefxn(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, pose: pyrosetta.rosetta.core.pose.Pose) bool ¶
C++: protocols::simple_moves::BackboneMover::move_with_scorefxn(class core::pose::Pose &) –> bool
- movemap(*args, **kwargs)¶
Overloaded function.
movemap(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, new_movemap: pyrosetta.rosetta.core.kinematics.MoveMap) -> None
C++: protocols::simple_moves::BackboneMover::movemap(class std::shared_ptr<class core::kinematics::MoveMap>) –> void
movemap(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, pose: pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.core.kinematics.MoveMap
Get the movemap for this pose.
C++: protocols::simple_moves::BackboneMover::movemap(const class core::pose::Pose &) –> class std::shared_ptr<const class core::kinematics::MoveMap>
- movemap_factory(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, new_movemap_factory: pyrosetta.rosetta.core.select.movemap.MoveMapFactory) None ¶
C++: protocols::simple_moves::BackboneMover::movemap_factory(class std::shared_ptr<const class core::select::movemap::MoveMapFactory>) –> void
- static name() str ¶
C++: protocols::moves::Mover::name() –> std::string
- nmoves(*args, **kwargs)¶
Overloaded function.
nmoves(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, nmoves_in: int) -> None
C++: protocols::simple_moves::BackboneMover::nmoves(const unsigned long) –> void
nmoves(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover) -> int
C++: protocols::simple_moves::BackboneMover::nmoves() const –> unsigned long
- observe_after_metropolis(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover) None ¶
Callback executed after the Metropolis criterion is evaluated.
C++: protocols::canonical_sampling::ThermodynamicMover::observe_after_metropolis(const class protocols::canonical_sampling::MetropolisHastingsMover &) –> void
- parse_my_tag(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None ¶
C++: protocols::simple_moves::BackboneMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- preserve_detailed_balance(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover) bool ¶
get whether detailed balance is preserved (i.e. no Ramachandran biasing)
C++: protocols::simple_moves::BackboneMover::preserve_detailed_balance() const –> bool
- 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(*args, **kwargs)¶
Overloaded function.
scorefxn(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover) -> pyrosetta.rosetta.core.scoring.ScoreFunction
If set, this scorefunction will be used instead of the original rama method (default = not set).
C++: protocols::simple_moves::BackboneMover::scorefxn() const –> class std::shared_ptr<class core::scoring::ScoreFunction>
scorefxn(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None
C++: protocols::simple_moves::BackboneMover::scorefxn(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void
- selector(*args, **kwargs)¶
Overloaded function.
selector(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover) -> pyrosetta.rosetta.core.select.residue_selector.ResidueSelector
- Return the residue selector that can be used to dynamically select residues to perturb
at runtime.
C++: protocols::simple_moves::BackboneMover::selector() const –> class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>
selector(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) -> None
C++: protocols::simple_moves::BackboneMover::selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void
- set_angles(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, : float) None ¶
C++: protocols::simple_moves::BackboneMover::set_angles(double) –> void
- set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) None ¶
C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void
- set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) None ¶
C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void
- set_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_metropolis_hastings_mover(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, metropolis_hastings_mover: pyrosetta.rosetta.std.weak_ptr_protocols_canonical_sampling_MetropolisHastingsMover_t) None ¶
- If this is a multi-trial move, set the MetropolisHastingsMover to
be used internally.
is_multi_trial()
C++: protocols::canonical_sampling::ThermodynamicMover::set_metropolis_hastings_mover(class std::weak_ptr<class protocols::canonical_sampling::MetropolisHastingsMover>) –> 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_preserve_detailed_balance(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, preserve_detailed_balance: bool) None ¶
set whether detailed balance is preserved (i.e. no Ramachandran biasing)
C++: protocols::simple_moves::BackboneMover::set_preserve_detailed_balance(bool) –> void
- set_residue_selector(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) None ¶
Set the ResidueSelector that this mover will use.
Clones the input.
C++: protocols::simple_moves::BackboneMover::set_residue_selector(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
- set_warn_empty_list(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, warn_empty: bool) None ¶
Set to warn of an empty setup list. Default true.
C++: protocols::simple_moves::BackboneMover::set_warn_empty_list(bool) –> void
- setup_list(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, : pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::simple_moves::BackboneMover::setup_list(class core::pose::Pose &) –> void
- show(*args, **kwargs)¶
Overloaded function.
show(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover) -> None
show(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, output: pyrosetta.rosetta.std.ostream) -> None
C++: protocols::simple_moves::BackboneMover::show(std::ostream &) const –> void
- temperature(*args, **kwargs)¶
Overloaded function.
temperature(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, temperature_in: float) -> None
C++: protocols::simple_moves::BackboneMover::temperature(const double) –> void
temperature(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover) -> float
C++: protocols::simple_moves::BackboneMover::temperature() const –> double
- test_move(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, : pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::simple_moves::BackboneMover::test_move(class core::pose::Pose &) –> void
- torsion_id_ranges(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, pose: pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.utility.vector1_core_id_TorsionID_Range ¶
- Return a list specifying which torsions may be perturbed by
apply(), and the in what range each perturbation may be.
This method should probably not be pure virtual, and in fact should probably not even exist. I searched most of the codebase, and could only find it being used in one pilot app. It is also a somewhat difficult method to write, which means that most of the implementations are either untested or no-ops. It might be better to remove the method altogether and implement it on a class-by-class basis as necessary.
C++: protocols::canonical_sampling::ThermodynamicMover::torsion_id_ranges(class core::pose::Pose &) –> class utility::vector1<class core::id::TorsionID_Range, class std::allocator<class core::id::TorsionID_Range> >
- 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.simple_moves.ChainSplitMover¶
Bases:
Mover
ChainSplitMover splits a pose into two chains given a cutpoint. This may be necessary for evaluating a domain interface using classes such as the InterfaceAnalyzerMover
- apply(self: pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::simple_moves::ChainSplitMover::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover, : pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover) pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover ¶
C++: protocols::simple_moves::ChainSplitMover::operator=(const class protocols::simple_moves::ChainSplitMover &) –> class protocols::simple_moves::ChainSplitMover &
- 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.simple_moves.ChainSplitMover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::simple_moves::ChainSplitMover::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.simple_moves.ChainSplitMover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::simple_moves::ChainSplitMover::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.simple_moves.ChainSplitMover) str ¶
C++: protocols::simple_moves::ChainSplitMover::get_name() const –> std::string
- get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose ¶
C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>
- get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>
- get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t ¶
C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>
- get_type(self: pyrosetta.rosetta.protocols.moves.Mover) str ¶
C++: protocols::moves::Mover::get_type() const –> std::string
- info(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.list_std_string_t ¶
non-const accessor
C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &
- last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) float ¶
C++: protocols::moves::Mover::last_proposal_density_ratio() –> double
- static name() str ¶
C++: protocols::moves::Mover::name() –> std::string
- parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None ¶
Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.
C++: protocols::moves::Mover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None ¶
- Provide citations to the passed CitationCollectionList
Subclasses should add the info for themselves and any other classes they use.
The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.
C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void
- static register_options() None ¶
Overload this static method if you access options within the mover.
These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.
C++: protocols::moves::Mover::register_options() –> void
- reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) bool ¶
- Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on
each use.
C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool
- reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) bool ¶
- Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input
pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).
C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool
- reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) None ¶
resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.
C++: protocols::moves::Mover::reset_status() –> void
- set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) None ¶
C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void
- set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) None ¶
C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void
- set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
setter for poses contained for rms
C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void
- set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe
C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void
- set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) None ¶
Set the ‘type’ string
C++: protocols::moves::Mover::set_type(const std::string &) –> void
- show(*args, **kwargs)¶
Overloaded function.
show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None
Outputs details about the Mover, including current settings.
C++: protocols::moves::Mover::show(std::ostream &) const –> void
- test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
- : Unit test support function. Apply one move to a given pose.
Allows extra test specific functions to be called before applying
C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void
- type(*args, **kwargs)¶
Overloaded function.
type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None
Set the ‘type’ string
C++: protocols::moves::Mover::type(const std::string &) –> void
type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str
Get the set ‘type’ string
C++: protocols::moves::Mover::type() const –> const std::string &
- class pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover¶
Bases:
MoverApplyingMover
Basic mover used primarily for setting up atomic protocols, especially in generator functions.
As the Topology Broker system includes more claims and is more widely adopted, This should not be used in favor of the Broker system.
Holds the Pose’s original FoldTree
Applies its ChangeFoldTreeMover
Applies its Main mover
Returns the Pose’s original FoldTree
- apply(self: pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
Holds the Pose’s original FoldTree
Applies the ChangeFoldTreeMover
Applies the Main mover
Returns the Pose’s original FoldTree
C++: protocols::simple_moves::ChangeAndResetFoldTreeMover::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover, : pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover) pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover ¶
C++: protocols::simple_moves::ChangeAndResetFoldTreeMover::operator=(const class protocols::simple_moves::ChangeAndResetFoldTreeMover &) –> class protocols::simple_moves::ChangeAndResetFoldTreeMover &
- 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.simple_moves.ChangeAndResetFoldTreeMover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::simple_moves::ChangeAndResetFoldTreeMover::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.simple_moves.ChangeAndResetFoldTreeMover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::simple_moves::ChangeAndResetFoldTreeMover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>
- ft_mover(self: pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover) pyrosetta.rosetta.protocols.moves.ChangeFoldTreeMover ¶
Get the ChangeFoldTreeMover
C++: protocols::simple_moves::ChangeAndResetFoldTreeMover::ft_mover() const –> class std::shared_ptr<class protocols::moves::ChangeFoldTreeMover>
- 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.simple_moves.ChangeAndResetFoldTreeMover) str ¶
C++: protocols::simple_moves::ChangeAndResetFoldTreeMover::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 ¶