docking¶
Bindings for protocols::docking namespace
- class pyrosetta.rosetta.protocols.docking.ConformerSwitchMover¶
Bases:
Mover
this mover does the conformer swap in RosettaDock’s ensemble docking. It takes in a multi-model PDB file as an ensemble, and does swaps conformers by superpositioning over interface residues, and selects a conformer based on a partition function using a ScoreFunction.
- apply(self: pyrosetta.rosetta.protocols.docking.ConformerSwitchMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::docking::ConformerSwitchMover::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.docking.ConformerSwitchMover, : pyrosetta.rosetta.protocols.docking.ConformerSwitchMover) pyrosetta.rosetta.protocols.docking.ConformerSwitchMover ¶
C++: protocols::docking::ConformerSwitchMover::operator=(const class protocols::docking::ConformerSwitchMover &) –> class protocols::docking::ConformerSwitchMover &
- clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) None ¶
Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.
clear_info is called by jd2 before calling apply
C++: protocols::moves::Mover::clear_info() –> void
- clone(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
Return a clone of the Mover object.
C++: protocols::moves::Mover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>
- create(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>
- fresh_instance(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
Generates a new Mover object freshly created with the default ctor.
C++: protocols::moves::Mover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>
- get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose ¶
fpd
Mechanism by which a mover may return multiple output poses from a single input pose.
Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.
C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>
- get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) protocols::jobdist::BasicJob ¶
C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>
- get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) str ¶
- A tag is a unique identifier used to identify structures produced
by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.
C++: protocols::moves::Mover::get_current_tag() const –> std::string
- get_ensemble(self: pyrosetta.rosetta.protocols.docking.ConformerSwitchMover) protocols::docking::DockingEnsemble ¶
C++: protocols::docking::ConformerSwitchMover::get_ensemble() –> class std::shared_ptr<class protocols::docking::DockingEnsemble>
- 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.docking.ConformerSwitchMover) str ¶
C++: protocols::docking::ConformerSwitchMover::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_temperature(self: pyrosetta.rosetta.protocols.docking.ConformerSwitchMover) float ¶
C++: protocols::docking::ConformerSwitchMover::get_temperature() const –> double
- get_type(self: pyrosetta.rosetta.protocols.moves.Mover) str ¶
C++: protocols::moves::Mover::get_type() const –> std::string
- info(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.list_std_string_t ¶
non-const accessor
C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &
- last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) float ¶
C++: protocols::moves::Mover::last_proposal_density_ratio() –> double
- static mover_name() str ¶
C++: protocols::docking::ConformerSwitchMover::mover_name() –> std::string
- static name() str ¶
C++: protocols::moves::Mover::name() –> std::string
- parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None ¶
Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.
C++: protocols::moves::Mover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None ¶
- Provide citations to the passed CitationCollectionList
Subclasses should add the info for themselves and any other classes they use.
The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.
C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void
- static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None ¶
C++: protocols::docking::ConformerSwitchMover::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_random_confomer(self: pyrosetta.rosetta.protocols.docking.ConformerSwitchMover, rand: bool) None ¶
C++: protocols::docking::ConformerSwitchMover::set_random_confomer(bool) –> void
- set_specific_conformer(self: pyrosetta.rosetta.protocols.docking.ConformerSwitchMover, conformer_num_in: int) None ¶
C++: protocols::docking::ConformerSwitchMover::set_specific_conformer(unsigned long) –> void
- set_temperature(self: pyrosetta.rosetta.protocols.docking.ConformerSwitchMover, temp_in: float) None ¶
C++: protocols::docking::ConformerSwitchMover::set_temperature(double) –> void
- set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) None ¶
Set the ‘type’ string
C++: protocols::moves::Mover::set_type(const std::string &) –> void
- show(*args, **kwargs)¶
Overloaded function.
show(self: pyrosetta.rosetta.protocols.docking.ConformerSwitchMover) -> None
show(self: pyrosetta.rosetta.protocols.docking.ConformerSwitchMover, output: pyrosetta.rosetta.std.ostream) -> None
C++: protocols::docking::ConformerSwitchMover::show(std::ostream &) const –> void
- switch_conformer(self: pyrosetta.rosetta.protocols.docking.ConformerSwitchMover, pose: pyrosetta.rosetta.core.pose.Pose, conf_num: int) None ¶
C++: protocols::docking::ConformerSwitchMover::switch_conformer(class core::pose::Pose &, 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 &
- use_random_conformer(self: pyrosetta.rosetta.protocols.docking.ConformerSwitchMover) bool ¶
C++: protocols::docking::ConformerSwitchMover::use_random_conformer() const –> bool
- class pyrosetta.rosetta.protocols.docking.ConformerSwitchMoverCreator¶
Bases:
MoverCreator
- assign(self: pyrosetta.rosetta.protocols.docking.ConformerSwitchMoverCreator, : pyrosetta.rosetta.protocols.docking.ConformerSwitchMoverCreator) pyrosetta.rosetta.protocols.docking.ConformerSwitchMoverCreator ¶
C++: protocols::docking::ConformerSwitchMoverCreator::operator=(const class protocols::docking::ConformerSwitchMoverCreator &) –> class protocols::docking::ConformerSwitchMoverCreator &
- create_mover(self: pyrosetta.rosetta.protocols.docking.ConformerSwitchMoverCreator) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::docking::ConformerSwitchMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>
- keyname(self: pyrosetta.rosetta.protocols.docking.ConformerSwitchMoverCreator) str ¶
C++: protocols::docking::ConformerSwitchMoverCreator::keyname() const –> std::string
- class pyrosetta.rosetta.protocols.docking.DHR_Type¶
Bases:
pybind11_object
Members:
DockingHighResLegacy
DockingPrepackProtocol
DockMCMProtocol
DockMinMover
SnugDock
- DockMCMProtocol = <DHR_Type.DockMCMProtocol: 2>¶
- DockMinMover = <DHR_Type.DockMinMover: 3>¶
- DockingHighResLegacy = <DHR_Type.DockingHighResLegacy: 0>¶
- DockingPrepackProtocol = <DHR_Type.DockingPrepackProtocol: 1>¶
- SnugDock = <DHR_Type.SnugDock: 4>¶
- property name¶
- property value¶
- class pyrosetta.rosetta.protocols.docking.DockMCMCycle¶
Bases:
Mover
- apply(self: pyrosetta.rosetta.protocols.docking.DockMCMCycle, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::docking::DockMCMCycle::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.docking.DockMCMCycle, : pyrosetta.rosetta.protocols.docking.DockMCMCycle) pyrosetta.rosetta.protocols.docking.DockMCMCycle ¶
C++: protocols::docking::DockMCMCycle::operator=(const class protocols::docking::DockMCMCycle &) –> class protocols::docking::DockMCMCycle &
- 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.docking.DockMCMCycle) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::docking::DockMCMCycle::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_mc(self: pyrosetta.rosetta.protocols.docking.DockMCMCycle) pyrosetta.rosetta.protocols.moves.MonteCarlo ¶
C++: protocols::docking::DockMCMCycle::get_mc() –> class std::shared_ptr<class protocols::moves::MonteCarlo>
- get_name(self: pyrosetta.rosetta.protocols.docking.DockMCMCycle) str ¶
C++: protocols::docking::DockMCMCycle::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_mc(self: pyrosetta.rosetta.protocols.docking.DockMCMCycle, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::docking::DockMCMCycle::init_mc(class core::pose::Pose &) –> void
- last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) float ¶
C++: protocols::moves::Mover::last_proposal_density_ratio() –> double
- movable_jumps(self: pyrosetta.rosetta.protocols.docking.DockMCMCycle) pyrosetta.rosetta.utility.vector1_int ¶
C++: protocols::docking::DockMCMCycle::movable_jumps() const –> const class utility::vector1<int, class std::allocator<int> > &
- 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_cycle_index(self: pyrosetta.rosetta.protocols.docking.DockMCMCycle) None ¶
C++: protocols::docking::DockMCMCycle::reset_cycle_index() –> void
- 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_default(self: pyrosetta.rosetta.protocols.docking.DockMCMCycle) None ¶
Sets the default values for all members
C++: protocols::docking::DockMCMCycle::set_default() –> 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_min_type(self: pyrosetta.rosetta.protocols.docking.DockMCMCycle, min_type: str) None ¶
C++: protocols::docking::DockMCMCycle::set_min_type(std::string) –> void
- set_move_map(self: pyrosetta.rosetta.protocols.docking.DockMCMCycle, movemap: pyrosetta.rosetta.core.kinematics.MoveMap) None ¶
C++: protocols::docking::DockMCMCycle::set_move_map(class std::shared_ptr<class core::kinematics::MoveMap>) –> void
- set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe
C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void
- set_rot_magnitude(self: pyrosetta.rosetta.protocols.docking.DockMCMCycle, value: float) None ¶
C++: protocols::docking::DockMCMCycle::set_rot_magnitude(double) –> void
- set_rtmin(self: pyrosetta.rosetta.protocols.docking.DockMCMCycle, setting: bool) None ¶
C++: protocols::docking::DockMCMCycle::set_rtmin(bool) –> void
- set_scmin(self: pyrosetta.rosetta.protocols.docking.DockMCMCycle, setting: bool) None ¶
C++: protocols::docking::DockMCMCycle::set_scmin(bool) –> void
- set_task_factory(self: pyrosetta.rosetta.protocols.docking.DockMCMCycle, tf: pyrosetta.rosetta.core.pack.task.TaskFactory) None ¶
C++: protocols::docking::DockMCMCycle::set_task_factory(class std::shared_ptr<const class core::pack::task::TaskFactory>) –> void
- set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) None ¶
Set the ‘type’ string
C++: protocols::moves::Mover::set_type(const std::string &) –> void
- show(*args, **kwargs)¶
Overloaded function.
show(self: pyrosetta.rosetta.protocols.docking.DockMCMCycle) -> None
show(self: pyrosetta.rosetta.protocols.docking.DockMCMCycle, out: pyrosetta.rosetta.std.ostream) -> None
C++: protocols::docking::DockMCMCycle::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.docking.DockMCMProtocol¶
Bases:
DockingHighRes
- add_additional_task_operaration(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, task_operation: pyrosetta.rosetta.core.pack.task.operation.TaskOperation) None ¶
C++: protocols::docking::DockingHighRes::add_additional_task_operaration(class std::shared_ptr<class core::pack::task::operation::TaskOperation>) –> void
- apply(self: pyrosetta.rosetta.protocols.docking.DockMCMProtocol, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::docking::DockMCMProtocol::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.docking.DockMCMProtocol, : pyrosetta.rosetta.protocols.docking.DockMCMProtocol) pyrosetta.rosetta.protocols.docking.DockMCMProtocol ¶
C++: protocols::docking::DockMCMProtocol::operator=(const class protocols::docking::DockMCMProtocol &) –> class protocols::docking::DockMCMProtocol &
- 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.docking.DockMCMProtocol) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::docking::DockMCMProtocol::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_additional_task_operarations(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_task_operation_TaskOperation_t ¶
C++: protocols::docking::DockingHighRes::get_additional_task_operarations() –> class utility::vector1<class std::shared_ptr<class core::pack::task::operation::TaskOperation>, class std::allocator<class std::shared_ptr<class core::pack::task::operation::TaskOperation> > >
- 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.docking.DockMCMProtocol) str ¶
C++: protocols::docking::DockMCMProtocol::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_partners(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) str ¶
C++: protocols::docking::DockingHighRes::get_partners() const –> std::string
- get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>
- get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t ¶
C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>
- get_type(self: pyrosetta.rosetta.protocols.moves.Mover) str ¶
C++: protocols::moves::Mover::get_type() const –> std::string
- ignore_default_task(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) bool ¶
C++: protocols::docking::DockingHighRes::ignore_default_task() –> bool
- info(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.list_std_string_t ¶
non-const accessor
C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &
- init(self: pyrosetta.rosetta.protocols.docking.DockMCMProtocol) None ¶
Performs the setup specific to this subclass of DockingHighRes (sets up filters).
C++: protocols::docking::DockMCMProtocol::init() –> void
- last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) float ¶
C++: protocols::moves::Mover::last_proposal_density_ratio() –> double
- movable_jumps(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) pyrosetta.rosetta.utility.vector1_int ¶
C++: protocols::docking::DockingHighRes::movable_jumps() –> class utility::vector1<int, class std::allocator<int> > &
- static mover_name() str ¶
C++: protocols::docking::DockMCMProtocol::mover_name() –> std::string
- static name() str ¶
C++: protocols::moves::Mover::name() –> std::string
- parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None ¶
Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.
C++: protocols::moves::Mover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- partners(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) str ¶
C++: protocols::docking::DockingHighRes::partners() –> std::string
- provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None ¶
- Provide citations to the passed CitationCollectionList
Subclasses should add the info for themselves and any other classes they use.
The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.
C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void
- static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None ¶
C++: protocols::docking::DockMCMProtocol::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
- rt_min(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) bool ¶
C++: protocols::docking::DockingHighRes::rt_min() –> bool
- sc_min(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) bool ¶
C++: protocols::docking::DockingHighRes::sc_min() –> bool
- scorefxn(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) pyrosetta.rosetta.core.scoring.ScoreFunction ¶
C++: protocols::docking::DockingHighRes::scorefxn() const –> class std::shared_ptr<class core::scoring::ScoreFunction>
- scorefxn_docking(self: pyrosetta.rosetta.protocols.docking.DockMCMProtocol) pyrosetta.rosetta.core.scoring.ScoreFunction ¶
C++: protocols::docking::DockMCMProtocol::scorefxn_docking() const –> class std::shared_ptr<const class core::scoring::ScoreFunction>
- scorefxn_pack(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) pyrosetta.rosetta.core.scoring.ScoreFunction ¶
C++: protocols::docking::DockingHighRes::scorefxn_pack() const –> class std::shared_ptr<class core::scoring::ScoreFunction>
- scorefxn_packing(self: pyrosetta.rosetta.protocols.docking.DockMCMProtocol) pyrosetta.rosetta.core.scoring.ScoreFunction ¶
C++: protocols::docking::DockMCMProtocol::scorefxn_packing() const –> class std::shared_ptr<const class core::scoring::ScoreFunction>
- set_additional_task_operarations(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, additional_task_operations: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_task_operation_TaskOperation_t) None ¶
C++: protocols::docking::DockingHighRes::set_additional_task_operarations(class utility::vector1<class std::shared_ptr<class core::pack::task::operation::TaskOperation>, class std::allocator<class std::shared_ptr<class core::pack::task::operation::TaskOperation> > >) –> 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_filter(self: pyrosetta.rosetta.protocols.docking.DockMCMProtocol, filter: pyrosetta.rosetta.protocols.docking.DockingHighResFilter) None ¶
C++: protocols::docking::DockMCMProtocol::set_filter(class std::shared_ptr<class protocols::docking::DockingHighResFilter>) –> void
- set_first_cycle(self: pyrosetta.rosetta.protocols.docking.DockMCMProtocol, num: int) None ¶
C++: protocols::docking::DockMCMProtocol::set_first_cycle(const unsigned long &) –> void
- set_ignore_default_task(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, ignore_default_task: bool) None ¶
C++: protocols::docking::DockingHighRes::set_ignore_default_task(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_interface_definition_task_operation(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, interface_definition: protocols::simple_task_operations::InterfaceTaskOperation) None ¶
C++: protocols::docking::DockingHighRes::set_interface_definition_task_operation(class std::shared_ptr<class protocols::simple_task_operations::InterfaceTaskOperation>) –> void
- set_movable_jumps(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, movable_jumps: pyrosetta.rosetta.utility.vector1_int) None ¶
C++: protocols::docking::DockingHighRes::set_movable_jumps(class utility::vector1<int, class std::allocator<int> >) –> void
- set_move_map(self: pyrosetta.rosetta.protocols.docking.DockMCMProtocol, movemap: pyrosetta.rosetta.core.kinematics.MoveMap) None ¶
C++: protocols::docking::DockMCMProtocol::set_move_map(class std::shared_ptr<class core::kinematics::MoveMap>) –> void
- set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe
C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void
- set_partners(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, partners: str) None ¶
C++: protocols::docking::DockingHighRes::set_partners(std::string) –> void
- set_rt_min(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, rt_min: bool) None ¶
C++: protocols::docking::DockingHighRes::set_rt_min(bool) –> void
- set_sc_min(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, sc_min: bool) None ¶
C++: protocols::docking::DockingHighRes::set_sc_min(bool) –> void
- set_scorefxn(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) None ¶
C++: protocols::docking::DockingHighRes::set_scorefxn(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void
- set_scorefxn_pack(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, scorefxn_pack: pyrosetta.rosetta.core.scoring.ScoreFunction) None ¶
C++: protocols::docking::DockingHighRes::set_scorefxn_pack(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void
- set_second_cycle(self: pyrosetta.rosetta.protocols.docking.DockMCMProtocol, num: int) None ¶
C++: protocols::docking::DockMCMProtocol::set_second_cycle(const unsigned long &) –> void
- set_task_factory(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, tf: pyrosetta.rosetta.core.pack.task.TaskFactory) None ¶
C++: protocols::docking::DockingHighRes::set_task_factory(class std::shared_ptr<const class core::pack::task::TaskFactory>) –> void
- set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) None ¶
Set the ‘type’ string
C++: protocols::moves::Mover::set_type(const std::string &) –> void
- show(*args, **kwargs)¶
Overloaded function.
show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None
Outputs details about the Mover, including current settings.
C++: protocols::moves::Mover::show(std::ostream &) const –> void
- task_factory(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) pyrosetta.rosetta.core.pack.task.TaskFactory ¶
C++: protocols::docking::DockingHighRes::task_factory() –> class std::shared_ptr<const class core::pack::task::TaskFactory>
- 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.docking.DockMCMProtocolCreator¶
Bases:
MoverCreator
- assign(self: pyrosetta.rosetta.protocols.docking.DockMCMProtocolCreator, : pyrosetta.rosetta.protocols.docking.DockMCMProtocolCreator) pyrosetta.rosetta.protocols.docking.DockMCMProtocolCreator ¶
C++: protocols::docking::DockMCMProtocolCreator::operator=(const class protocols::docking::DockMCMProtocolCreator &) –> class protocols::docking::DockMCMProtocolCreator &
- create_mover(self: pyrosetta.rosetta.protocols.docking.DockMCMProtocolCreator) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::docking::DockMCMProtocolCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>
- keyname(self: pyrosetta.rosetta.protocols.docking.DockMCMProtocolCreator) str ¶
C++: protocols::docking::DockMCMProtocolCreator::keyname() const –> std::string
- class pyrosetta.rosetta.protocols.docking.DockMinMover¶
Bases:
DockingHighRes
- add_additional_task_operaration(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, task_operation: pyrosetta.rosetta.core.pack.task.operation.TaskOperation) None ¶
C++: protocols::docking::DockingHighRes::add_additional_task_operaration(class std::shared_ptr<class core::pack::task::operation::TaskOperation>) –> void
- apply(self: pyrosetta.rosetta.protocols.docking.DockMinMover, : pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::docking::DockMinMover::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.docking.DockMinMover, : pyrosetta.rosetta.protocols.docking.DockMinMover) pyrosetta.rosetta.protocols.docking.DockMinMover ¶
C++: protocols::docking::DockMinMover::operator=(const class protocols::docking::DockMinMover &) –> class protocols::docking::DockMinMover &
- clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) None ¶
Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.
clear_info is called by jd2 before calling apply
C++: protocols::moves::Mover::clear_info() –> void
- clone(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
Return a clone of the Mover object.
C++: protocols::moves::Mover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>
- create(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>
- fresh_instance(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
Generates a new Mover object freshly created with the default ctor.
C++: protocols::moves::Mover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>
- get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose ¶
fpd
Mechanism by which a mover may return multiple output poses from a single input pose.
Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.
C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>
- get_additional_task_operarations(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_task_operation_TaskOperation_t ¶
C++: protocols::docking::DockingHighRes::get_additional_task_operarations() –> class utility::vector1<class std::shared_ptr<class core::pack::task::operation::TaskOperation>, class std::allocator<class std::shared_ptr<class core::pack::task::operation::TaskOperation> > >
- 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.docking.DockMinMover) str ¶
C++: protocols::docking::DockMinMover::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_partners(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) str ¶
C++: protocols::docking::DockingHighRes::get_partners() const –> std::string
- get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>
- get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t ¶
C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>
- get_type(self: pyrosetta.rosetta.protocols.moves.Mover) str ¶
C++: protocols::moves::Mover::get_type() const –> std::string
- ignore_default_task(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) bool ¶
C++: protocols::docking::DockingHighRes::ignore_default_task() –> bool
- info(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.list_std_string_t ¶
non-const accessor
C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &
- last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) float ¶
C++: protocols::moves::Mover::last_proposal_density_ratio() –> double
- movable_jumps(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) pyrosetta.rosetta.utility.vector1_int ¶
C++: protocols::docking::DockingHighRes::movable_jumps() –> class utility::vector1<int, class std::allocator<int> > &
- static mover_name() str ¶
C++: protocols::docking::DockMinMover::mover_name() –> std::string
- static name() str ¶
C++: protocols::moves::Mover::name() –> std::string
- parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None ¶
Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.
C++: protocols::moves::Mover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- partners(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) str ¶
C++: protocols::docking::DockingHighRes::partners() –> std::string
- provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None ¶
- Provide citations to the passed CitationCollectionList
Subclasses should add the info for themselves and any other classes they use.
The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.
C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void
- static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None ¶
C++: protocols::docking::DockMinMover::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
- rt_min(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) bool ¶
C++: protocols::docking::DockingHighRes::rt_min() –> bool
- sc_min(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) bool ¶
C++: protocols::docking::DockingHighRes::sc_min() –> bool
- scorefxn(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) pyrosetta.rosetta.core.scoring.ScoreFunction ¶
C++: protocols::docking::DockingHighRes::scorefxn() const –> class std::shared_ptr<class core::scoring::ScoreFunction>
- scorefxn_pack(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) pyrosetta.rosetta.core.scoring.ScoreFunction ¶
C++: protocols::docking::DockingHighRes::scorefxn_pack() const –> class std::shared_ptr<class core::scoring::ScoreFunction>
- set_additional_task_operarations(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, additional_task_operations: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_task_operation_TaskOperation_t) None ¶
C++: protocols::docking::DockingHighRes::set_additional_task_operarations(class utility::vector1<class std::shared_ptr<class core::pack::task::operation::TaskOperation>, class std::allocator<class std::shared_ptr<class core::pack::task::operation::TaskOperation> > >) –> 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_default(self: pyrosetta.rosetta.protocols.docking.DockMinMover) None ¶
Sets up the default values for the obejct including the movemap and minimization type.
C++: protocols::docking::DockMinMover::set_default() –> void
- set_ignore_default_task(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, ignore_default_task: bool) None ¶
C++: protocols::docking::DockingHighRes::set_ignore_default_task(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_interface_definition_task_operation(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, interface_definition: protocols::simple_task_operations::InterfaceTaskOperation) None ¶
C++: protocols::docking::DockingHighRes::set_interface_definition_task_operation(class std::shared_ptr<class protocols::simple_task_operations::InterfaceTaskOperation>) –> void
- set_min_tolerance(self: pyrosetta.rosetta.protocols.docking.DockMinMover, min_tolerance: float) None ¶
C++: protocols::docking::DockMinMover::set_min_tolerance(double) –> void
- set_min_type(self: pyrosetta.rosetta.protocols.docking.DockMinMover, min_type: str) None ¶
setters for member variables
C++: protocols::docking::DockMinMover::set_min_type(std::string) –> void
- set_movable_jumps(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, movable_jumps: pyrosetta.rosetta.utility.vector1_int) None ¶
C++: protocols::docking::DockingHighRes::set_movable_jumps(class utility::vector1<int, class std::allocator<int> >) –> 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_partners(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, partners: str) None ¶
C++: protocols::docking::DockingHighRes::set_partners(std::string) –> void
- set_rt_min(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, rt_min: bool) None ¶
C++: protocols::docking::DockingHighRes::set_rt_min(bool) –> void
- set_sc_min(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, sc_min: bool) None ¶
C++: protocols::docking::DockingHighRes::set_sc_min(bool) –> void
- set_scorefxn(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) None ¶
C++: protocols::docking::DockingHighRes::set_scorefxn(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void
- set_scorefxn_pack(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, scorefxn_pack: pyrosetta.rosetta.core.scoring.ScoreFunction) None ¶
C++: protocols::docking::DockingHighRes::set_scorefxn_pack(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void
- set_task_factory(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, tf: pyrosetta.rosetta.core.pack.task.TaskFactory) None ¶
C++: protocols::docking::DockingHighRes::set_task_factory(class std::shared_ptr<const class core::pack::task::TaskFactory>) –> void
- set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) None ¶
Set the ‘type’ string
C++: protocols::moves::Mover::set_type(const std::string &) –> void
- show(*args, **kwargs)¶
Overloaded function.
show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None
Outputs details about the Mover, including current settings.
C++: protocols::moves::Mover::show(std::ostream &) const –> void
- task_factory(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) pyrosetta.rosetta.core.pack.task.TaskFactory ¶
C++: protocols::docking::DockingHighRes::task_factory() –> class std::shared_ptr<const class core::pack::task::TaskFactory>
- 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.docking.DockMinMoverCreator¶
Bases:
MoverCreator
- assign(self: pyrosetta.rosetta.protocols.docking.DockMinMoverCreator, : pyrosetta.rosetta.protocols.docking.DockMinMoverCreator) pyrosetta.rosetta.protocols.docking.DockMinMoverCreator ¶
C++: protocols::docking::DockMinMoverCreator::operator=(const class protocols::docking::DockMinMoverCreator &) –> class protocols::docking::DockMinMoverCreator &
- create_mover(self: pyrosetta.rosetta.protocols.docking.DockMinMoverCreator) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::docking::DockMinMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>
- keyname(self: pyrosetta.rosetta.protocols.docking.DockMinMoverCreator) str ¶
C++: protocols::docking::DockMinMoverCreator::keyname() const –> std::string
- class pyrosetta.rosetta.protocols.docking.DockSetupMover¶
Bases:
Mover
allows docking using simulated or parallel tempering
- apply(self: pyrosetta.rosetta.protocols.docking.DockSetupMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::docking::DockSetupMover::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.docking.DockSetupMover, rhs: pyrosetta.rosetta.protocols.docking.DockSetupMover) pyrosetta.rosetta.protocols.docking.DockSetupMover ¶
assignment operator
C++: protocols::docking::DockSetupMover::operator=(const class protocols::docking::DockSetupMover &) –> class protocols::docking::DockSetupMover &
- 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.docking.DockSetupMover) pyrosetta.rosetta.protocols.moves.Mover ¶
clone
C++: protocols::docking::DockSetupMover::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.docking.DockSetupMover) str ¶
C++: protocols::docking::DockSetupMover::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::docking::DockSetupMover::mover_name() –> std::string
- static name() str ¶
C++: protocols::moves::Mover::name() –> std::string
- parse_my_tag(self: pyrosetta.rosetta.protocols.docking.DockSetupMover, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None ¶
C++: protocols::docking::DockSetupMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- partners(self: pyrosetta.rosetta.protocols.docking.DockSetupMover) str ¶
C++: protocols::docking::DockSetupMover::partners() const –> const std::string &
- provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None ¶
- Provide citations to the passed CitationCollectionList
Subclasses should add the info for themselves and any other classes they use.
The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.
C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void
- static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None ¶
C++: protocols::docking::DockSetupMover::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_defaults(self: pyrosetta.rosetta.protocols.docking.DockSetupMover) None ¶
Assigns default values to primitive members
C++: protocols::docking::DockSetupMover::set_defaults() –> 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_partners(self: pyrosetta.rosetta.protocols.docking.DockSetupMover, setting: str) None ¶
C++: protocols::docking::DockSetupMover::set_partners(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.docking.DockSetupMover) -> None
show(self: pyrosetta.rosetta.protocols.docking.DockSetupMover, out: pyrosetta.rosetta.std.ostream) -> None
C++: protocols::docking::DockSetupMover::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.docking.DockSetupMoverCreator¶
Bases:
MoverCreator
- assign(self: pyrosetta.rosetta.protocols.docking.DockSetupMoverCreator, : pyrosetta.rosetta.protocols.docking.DockSetupMoverCreator) pyrosetta.rosetta.protocols.docking.DockSetupMoverCreator ¶
C++: protocols::docking::DockSetupMoverCreator::operator=(const class protocols::docking::DockSetupMoverCreator &) –> class protocols::docking::DockSetupMoverCreator &
- create_mover(self: pyrosetta.rosetta.protocols.docking.DockSetupMoverCreator) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::docking::DockSetupMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>
- keyname(self: pyrosetta.rosetta.protocols.docking.DockSetupMoverCreator) str ¶
C++: protocols::docking::DockSetupMoverCreator::keyname() const –> std::string
- class pyrosetta.rosetta.protocols.docking.DockTaskFactory¶
Bases:
pybind11_object
- add_additional_task_operaration(self: pyrosetta.rosetta.protocols.docking.DockTaskFactory, task_operation: pyrosetta.rosetta.core.pack.task.operation.TaskOperation) None ¶
C++: protocols::docking::DockTaskFactory::add_additional_task_operaration(class std::shared_ptr<class core::pack::task::operation::TaskOperation>) –> void
- assign(self: pyrosetta.rosetta.protocols.docking.DockTaskFactory, : pyrosetta.rosetta.protocols.docking.DockTaskFactory) pyrosetta.rosetta.protocols.docking.DockTaskFactory ¶
C++: protocols::docking::DockTaskFactory::operator=(const class protocols::docking::DockTaskFactory &) –> class protocols::docking::DockTaskFactory &
- create_and_attach_task_factory(self: pyrosetta.rosetta.protocols.docking.DockTaskFactory, docker: pyrosetta.rosetta.protocols.docking.DockingHighRes, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
- Creates an appropriate TaskFactory based on command line options and attach it to a DockingHighResOP
Two arguments: DockingHighResOP and a pose.
C++: protocols::docking::DockTaskFactory::create_and_attach_task_factory(class protocols::docking::DockingHighRes *, const class core::pose::Pose &) const –> void
- get_additional_task_operarations(self: pyrosetta.rosetta.protocols.docking.DockTaskFactory) pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_task_operation_TaskOperation_t ¶
C++: protocols::docking::DockTaskFactory::get_additional_task_operarations() –> class utility::vector1<class std::shared_ptr<class core::pack::task::operation::TaskOperation>, class std::allocator<class std::shared_ptr<class core::pack::task::operation::TaskOperation> > >
- get_norepack1(self: pyrosetta.rosetta.protocols.docking.DockTaskFactory) bool ¶
C++: protocols::docking::DockTaskFactory::get_norepack1() const –> bool
- get_norepack2(self: pyrosetta.rosetta.protocols.docking.DockTaskFactory) bool ¶
C++: protocols::docking::DockTaskFactory::get_norepack2() const –> bool
- init_from_options(self: pyrosetta.rosetta.protocols.docking.DockTaskFactory) None ¶
Assigns user specified values to members using command line options
C++: protocols::docking::DockTaskFactory::init_from_options() –> void
- register_options(self: pyrosetta.rosetta.protocols.docking.DockTaskFactory) None ¶
Associates relevant options with the DockTaskFactory class
C++: protocols::docking::DockTaskFactory::register_options() –> void
- set_additional_task_operarations(self: pyrosetta.rosetta.protocols.docking.DockTaskFactory, additional_task_operations: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_task_operation_TaskOperation_t) None ¶
C++: protocols::docking::DockTaskFactory::set_additional_task_operarations(class utility::vector1<class std::shared_ptr<class core::pack::task::operation::TaskOperation>, class std::allocator<class std::shared_ptr<class core::pack::task::operation::TaskOperation> > >) –> void
- set_default(self: pyrosetta.rosetta.protocols.docking.DockTaskFactory) None ¶
Sets booleans to default values
C++: protocols::docking::DockTaskFactory::set_default() –> void
- set_design_chains(self: pyrosetta.rosetta.protocols.docking.DockTaskFactory, design_chains: pyrosetta.rosetta.utility.vector1_char) None ¶
C++: protocols::docking::DockTaskFactory::set_design_chains(class utility::vector1<char, class std::allocator<char> >) –> void
- set_interface_definition_task_operation(self: pyrosetta.rosetta.protocols.docking.DockTaskFactory, interface_definition: protocols::simple_task_operations::InterfaceTaskOperation) None ¶
C++: protocols::docking::DockTaskFactory::set_interface_definition_task_operation(class std::shared_ptr<class protocols::simple_task_operations::InterfaceTaskOperation>) –> void
- set_norepack1(self: pyrosetta.rosetta.protocols.docking.DockTaskFactory, norepack1: bool) None ¶
C++: protocols::docking::DockTaskFactory::set_norepack1(bool) –> void
- set_norepack2(self: pyrosetta.rosetta.protocols.docking.DockTaskFactory, norepack2: bool) None ¶
C++: protocols::docking::DockTaskFactory::set_norepack2(bool) –> void
- set_prepack_only(self: pyrosetta.rosetta.protocols.docking.DockTaskFactory, prepack_only: bool) None ¶
C++: protocols::docking::DockTaskFactory::set_prepack_only(bool) –> void
- class pyrosetta.rosetta.protocols.docking.DockingEnsemble¶
Bases:
pybind11_object
this mover does the conformer swap in RosettaDock’s ensemble docking. It takes in a multi-model PDB file as an ensemble, and does swaps conformers by superpositioning over interface residues, and selects a conformer based on a partition function using a ScoreFunction.
- assign(self: pyrosetta.rosetta.protocols.docking.DockingEnsemble, : pyrosetta.rosetta.protocols.docking.DockingEnsemble) pyrosetta.rosetta.protocols.docking.DockingEnsemble ¶
C++: protocols::docking::DockingEnsemble::operator=(const class protocols::docking::DockingEnsemble &) –> class protocols::docking::DockingEnsemble &
- calculate_highres_ref_energy(*args, **kwargs)¶
Overloaded function.
calculate_highres_ref_energy(self: pyrosetta.rosetta.protocols.docking.DockingEnsemble, conf_num: int) -> None
C++: protocols::docking::DockingEnsemble::calculate_highres_ref_energy(unsigned long) –> void
calculate_highres_ref_energy(self: pyrosetta.rosetta.protocols.docking.DockingEnsemble, pose: pyrosetta.rosetta.core.pose.Pose, partner_num: str) -> None
C++: protocols::docking::DockingEnsemble::calculate_highres_ref_energy(class core::pose::Pose &, std::string) –> void
- calculate_lowres_ref_energy(self: pyrosetta.rosetta.protocols.docking.DockingEnsemble, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::docking::DockingEnsemble::calculate_lowres_ref_energy(class core::pose::Pose &) –> void
- conf_size(self: pyrosetta.rosetta.protocols.docking.DockingEnsemble) int ¶
C++: protocols::docking::DockingEnsemble::conf_size() –> unsigned long
- end_res(self: pyrosetta.rosetta.protocols.docking.DockingEnsemble) int ¶
C++: protocols::docking::DockingEnsemble::end_res() –> unsigned long
- get_conformer(self: pyrosetta.rosetta.protocols.docking.DockingEnsemble, conf_num: int) pyrosetta.rosetta.core.pose.Pose ¶
C++: protocols::docking::DockingEnsemble::get_conformer(unsigned long) –> class core::pose::Pose &
- get_conformer_cen(self: pyrosetta.rosetta.protocols.docking.DockingEnsemble, conf_num: int) pyrosetta.rosetta.core.pose.Pose ¶
C++: protocols::docking::DockingEnsemble::get_conformer_cen(unsigned long) –> class core::pose::Pose &
- get_current_confnum(self: pyrosetta.rosetta.protocols.docking.DockingEnsemble) int ¶
C++: protocols::docking::DockingEnsemble::get_current_confnum() –> unsigned long
- highres_reference_energy(*args, **kwargs)¶
Overloaded function.
highres_reference_energy(self: pyrosetta.rosetta.protocols.docking.DockingEnsemble, conf_num: int) -> float
C++: protocols::docking::DockingEnsemble::highres_reference_energy(unsigned long) –> double
highres_reference_energy(self: pyrosetta.rosetta.protocols.docking.DockingEnsemble) -> float
C++: protocols::docking::DockingEnsemble::highres_reference_energy() –> double
- jump_id(self: pyrosetta.rosetta.protocols.docking.DockingEnsemble) int ¶
C++: protocols::docking::DockingEnsemble::jump_id() –> unsigned long
- lowres_reference_energy(*args, **kwargs)¶
Overloaded function.
lowres_reference_energy(self: pyrosetta.rosetta.protocols.docking.DockingEnsemble, conf_num: int) -> float
C++: protocols::docking::DockingEnsemble::lowres_reference_energy(unsigned long) –> double
lowres_reference_energy(self: pyrosetta.rosetta.protocols.docking.DockingEnsemble) -> float
C++: protocols::docking::DockingEnsemble::lowres_reference_energy() –> double
- partner(self: pyrosetta.rosetta.protocols.docking.DockingEnsemble) str ¶
C++: protocols::docking::DockingEnsemble::partner() –> std::string
- recover_and_pack_conformer_sidechains(self: pyrosetta.rosetta.protocols.docking.DockingEnsemble, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::docking::DockingEnsemble::recover_and_pack_conformer_sidechains(class core::pose::Pose &) –> void
- scorefxn_low(self: pyrosetta.rosetta.protocols.docking.DockingEnsemble) pyrosetta.rosetta.core.scoring.ScoreFunction ¶
C++: protocols::docking::DockingEnsemble::scorefxn_low() –> class std::shared_ptr<const class core::scoring::ScoreFunction>
- set_current_confnum(self: pyrosetta.rosetta.protocols.docking.DockingEnsemble, conf_num: int) None ¶
C++: protocols::docking::DockingEnsemble::set_current_confnum(unsigned long) –> void
- set_packer(self: pyrosetta.rosetta.protocols.docking.DockingEnsemble, packer: protocols::moves::SequenceMover) None ¶
C++: protocols::docking::DockingEnsemble::set_packer(class std::shared_ptr<class protocols::moves::SequenceMover>) –> void
- size(self: pyrosetta.rosetta.protocols.docking.DockingEnsemble) int ¶
C++: protocols::docking::DockingEnsemble::size() –> unsigned long
- start_res(self: pyrosetta.rosetta.protocols.docking.DockingEnsemble) int ¶
C++: protocols::docking::DockingEnsemble::start_res() –> unsigned long
- update_pdblist_file(self: pyrosetta.rosetta.protocols.docking.DockingEnsemble, partner_num: str) None ¶
C++: protocols::docking::DockingEnsemble::update_pdblist_file(std::string) –> void
- class pyrosetta.rosetta.protocols.docking.DockingEnsemblePrepackProtocol¶
Bases:
DockingHighRes
- add_additional_task_operaration(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, task_operation: pyrosetta.rosetta.core.pack.task.operation.TaskOperation) None ¶
C++: protocols::docking::DockingHighRes::add_additional_task_operaration(class std::shared_ptr<class core::pack::task::operation::TaskOperation>) –> void
- apply(self: pyrosetta.rosetta.protocols.docking.DockingEnsemblePrepackProtocol, : pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::docking::DockingEnsemblePrepackProtocol::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.docking.DockingEnsemblePrepackProtocol, : pyrosetta.rosetta.protocols.docking.DockingEnsemblePrepackProtocol) pyrosetta.rosetta.protocols.docking.DockingEnsemblePrepackProtocol ¶
C++: protocols::docking::DockingEnsemblePrepackProtocol::operator=(const class protocols::docking::DockingEnsemblePrepackProtocol &) –> class protocols::docking::DockingEnsemblePrepackProtocol &
- check_ensemble_member_compatibility(self: pyrosetta.rosetta.protocols.docking.DockingEnsemblePrepackProtocol) None ¶
Ensures all members of either ensemble are compatible with one another
C++: protocols::docking::DockingEnsemblePrepackProtocol::check_ensemble_member_compatibility() –> 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>
- 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_additional_task_operarations(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_task_operation_TaskOperation_t ¶
C++: protocols::docking::DockingHighRes::get_additional_task_operarations() –> class utility::vector1<class std::shared_ptr<class core::pack::task::operation::TaskOperation>, class std::allocator<class std::shared_ptr<class core::pack::task::operation::TaskOperation> > >
- 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.docking.DockingEnsemblePrepackProtocol) str ¶
C++: protocols::docking::DockingEnsemblePrepackProtocol::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_partners(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) str ¶
C++: protocols::docking::DockingHighRes::get_partners() const –> std::string
- get_pose_chains(self: pyrosetta.rosetta.protocols.docking.DockingEnsemblePrepackProtocol, : pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.utility.vector1_char ¶
Returns a vector1 of the pdb chains in a pose, in order
C++: protocols::docking::DockingEnsemblePrepackProtocol::get_pose_chains(class core::pose::Pose &) –> class utility::vector1<char, class std::allocator<char> >
- get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>
- get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t ¶
C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>
- get_type(self: pyrosetta.rosetta.protocols.moves.Mover) str ¶
C++: protocols::moves::Mover::get_type() const –> std::string
- ignore_default_task(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) bool ¶
C++: protocols::docking::DockingHighRes::ignore_default_task() –> bool
- info(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.list_std_string_t ¶
non-const accessor
C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &
- last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) float ¶
C++: protocols::moves::Mover::last_proposal_density_ratio() –> double
- movable_jumps(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) pyrosetta.rosetta.utility.vector1_int ¶
C++: protocols::docking::DockingHighRes::movable_jumps() –> class utility::vector1<int, class std::allocator<int> > &
- move_away(self: pyrosetta.rosetta.protocols.docking.DockingEnsemblePrepackProtocol, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::docking::DockingEnsemblePrepackProtocol::move_away(class core::pose::Pose &) –> void
- move_back(self: pyrosetta.rosetta.protocols.docking.DockingEnsemblePrepackProtocol, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::docking::DockingEnsemblePrepackProtocol::move_back(class core::pose::Pose &) –> void
- 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
- partners(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) str ¶
C++: protocols::docking::DockingHighRes::partners() –> std::string
- 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
- rt_min(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) bool ¶
C++: protocols::docking::DockingHighRes::rt_min() –> bool
- sc_min(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) bool ¶
C++: protocols::docking::DockingHighRes::sc_min() –> bool
- scorefxn(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) pyrosetta.rosetta.core.scoring.ScoreFunction ¶
C++: protocols::docking::DockingHighRes::scorefxn() const –> class std::shared_ptr<class core::scoring::ScoreFunction>
- scorefxn_pack(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) pyrosetta.rosetta.core.scoring.ScoreFunction ¶
C++: protocols::docking::DockingHighRes::scorefxn_pack() const –> class std::shared_ptr<class core::scoring::ScoreFunction>
- set_additional_task_operarations(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, additional_task_operations: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_task_operation_TaskOperation_t) None ¶
C++: protocols::docking::DockingHighRes::set_additional_task_operarations(class utility::vector1<class std::shared_ptr<class core::pack::task::operation::TaskOperation>, class std::allocator<class std::shared_ptr<class core::pack::task::operation::TaskOperation> > >) –> 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_ensemble1(self: pyrosetta.rosetta.protocols.docking.DockingEnsemblePrepackProtocol, ensemble1: str) None ¶
C++: protocols::docking::DockingEnsemblePrepackProtocol::set_ensemble1(const std::string &) –> void
- set_ensemble2(self: pyrosetta.rosetta.protocols.docking.DockingEnsemblePrepackProtocol, ensemble2: str) None ¶
C++: protocols::docking::DockingEnsemblePrepackProtocol::set_ensemble2(const std::string &) –> void
- set_ignore_default_task(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, ignore_default_task: bool) None ¶
C++: protocols::docking::DockingHighRes::set_ignore_default_task(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_interface_definition_task_operation(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, interface_definition: protocols::simple_task_operations::InterfaceTaskOperation) None ¶
C++: protocols::docking::DockingHighRes::set_interface_definition_task_operation(class std::shared_ptr<class protocols::simple_task_operations::InterfaceTaskOperation>) –> void
- set_movable_jumps(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, movable_jumps: pyrosetta.rosetta.utility.vector1_int) None ¶
C++: protocols::docking::DockingHighRes::set_movable_jumps(class utility::vector1<int, class std::allocator<int> >) –> 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_partners(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, partners: str) None ¶
C++: protocols::docking::DockingHighRes::set_partners(std::string) –> void
- set_rt_min(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, rt_min: bool) None ¶
C++: protocols::docking::DockingHighRes::set_rt_min(bool) –> void
- set_sc_min(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, sc_min: bool) None ¶
C++: protocols::docking::DockingHighRes::set_sc_min(bool) –> void
- set_scorefxn(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) None ¶
C++: protocols::docking::DockingHighRes::set_scorefxn(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void
- set_scorefxn_pack(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, scorefxn_pack: pyrosetta.rosetta.core.scoring.ScoreFunction) None ¶
C++: protocols::docking::DockingHighRes::set_scorefxn_pack(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void
- set_spanfile1(self: pyrosetta.rosetta.protocols.docking.DockingEnsemblePrepackProtocol, spanfile1: str) None ¶
C++: protocols::docking::DockingEnsemblePrepackProtocol::set_spanfile1(const std::string &) –> void
- set_spanfile2(self: pyrosetta.rosetta.protocols.docking.DockingEnsemblePrepackProtocol, spanfile2: str) None ¶
C++: protocols::docking::DockingEnsemblePrepackProtocol::set_spanfile2(const std::string &) –> void
- set_task_factory(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, tf: pyrosetta.rosetta.core.pack.task.TaskFactory) None ¶
C++: protocols::docking::DockingHighRes::set_task_factory(class std::shared_ptr<const class core::pack::task::TaskFactory>) –> void
- set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) None ¶
Set the ‘type’ string
C++: protocols::moves::Mover::set_type(const std::string &) –> void
- setup_defaults(self: pyrosetta.rosetta.protocols.docking.DockingEnsemblePrepackProtocol) None ¶
Assigns default values to members
C++: protocols::docking::DockingEnsemblePrepackProtocol::setup_defaults() –> void
- setup_pack_operation_movers(self: pyrosetta.rosetta.protocols.docking.DockingEnsemblePrepackProtocol) None ¶
Instantiates and configures movers used by DockingEnsemblePrepackProtocol
C++: protocols::docking::DockingEnsemblePrepackProtocol::setup_pack_operation_movers() –> void
- show(*args, **kwargs)¶
Overloaded function.
show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None
Outputs details about the Mover, including current settings.
C++: protocols::moves::Mover::show(std::ostream &) const –> void
- task_factory(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) pyrosetta.rosetta.core.pack.task.TaskFactory ¶
C++: protocols::docking::DockingHighRes::task_factory() –> class std::shared_ptr<const class core::pack::task::TaskFactory>
- 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.docking.DockingHighRes¶
Bases:
Mover
- add_additional_task_operaration(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, task_operation: pyrosetta.rosetta.core.pack.task.operation.TaskOperation) None ¶
C++: protocols::docking::DockingHighRes::add_additional_task_operaration(class std::shared_ptr<class core::pack::task::operation::TaskOperation>) –> void
- apply(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::docking::DockingHighRes::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, : pyrosetta.rosetta.protocols.docking.DockingHighRes) pyrosetta.rosetta.protocols.docking.DockingHighRes ¶
C++: protocols::docking::DockingHighRes::operator=(const class protocols::docking::DockingHighRes &) –> class protocols::docking::DockingHighRes &
- clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) None ¶
Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.
clear_info is called by jd2 before calling apply
C++: protocols::moves::Mover::clear_info() –> void
- clone(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
Return a clone of the Mover object.
C++: protocols::moves::Mover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>
- create(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>
- fresh_instance(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
Generates a new Mover object freshly created with the default ctor.
C++: protocols::moves::Mover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>
- get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose ¶
fpd
Mechanism by which a mover may return multiple output poses from a single input pose.
Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.
C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>
- get_additional_task_operarations(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_task_operation_TaskOperation_t ¶
C++: protocols::docking::DockingHighRes::get_additional_task_operarations() –> class utility::vector1<class std::shared_ptr<class core::pack::task::operation::TaskOperation>, class std::allocator<class std::shared_ptr<class core::pack::task::operation::TaskOperation> > >
- 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.docking.DockingHighRes) str ¶
C++: protocols::docking::DockingHighRes::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_partners(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) str ¶
C++: protocols::docking::DockingHighRes::get_partners() const –> std::string
- get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>
- get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t ¶
C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>
- get_type(self: pyrosetta.rosetta.protocols.moves.Mover) str ¶
C++: protocols::moves::Mover::get_type() const –> std::string
- ignore_default_task(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) bool ¶
C++: protocols::docking::DockingHighRes::ignore_default_task() –> bool
- info(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.list_std_string_t ¶
non-const accessor
C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &
- last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) float ¶
C++: protocols::moves::Mover::last_proposal_density_ratio() –> double
- movable_jumps(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) pyrosetta.rosetta.utility.vector1_int ¶
C++: protocols::docking::DockingHighRes::movable_jumps() –> class utility::vector1<int, class std::allocator<int> > &
- 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
- partners(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) str ¶
C++: protocols::docking::DockingHighRes::partners() –> std::string
- 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
- rt_min(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) bool ¶
C++: protocols::docking::DockingHighRes::rt_min() –> bool
- sc_min(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) bool ¶
C++: protocols::docking::DockingHighRes::sc_min() –> bool
- scorefxn(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) pyrosetta.rosetta.core.scoring.ScoreFunction ¶
C++: protocols::docking::DockingHighRes::scorefxn() const –> class std::shared_ptr<class core::scoring::ScoreFunction>
- scorefxn_pack(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) pyrosetta.rosetta.core.scoring.ScoreFunction ¶
C++: protocols::docking::DockingHighRes::scorefxn_pack() const –> class std::shared_ptr<class core::scoring::ScoreFunction>
- set_additional_task_operarations(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, additional_task_operations: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_task_operation_TaskOperation_t) None ¶
C++: protocols::docking::DockingHighRes::set_additional_task_operarations(class utility::vector1<class std::shared_ptr<class core::pack::task::operation::TaskOperation>, class std::allocator<class std::shared_ptr<class core::pack::task::operation::TaskOperation> > >) –> 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_ignore_default_task(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, ignore_default_task: bool) None ¶
C++: protocols::docking::DockingHighRes::set_ignore_default_task(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_interface_definition_task_operation(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, interface_definition: protocols::simple_task_operations::InterfaceTaskOperation) None ¶
C++: protocols::docking::DockingHighRes::set_interface_definition_task_operation(class std::shared_ptr<class protocols::simple_task_operations::InterfaceTaskOperation>) –> void
- set_movable_jumps(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, movable_jumps: pyrosetta.rosetta.utility.vector1_int) None ¶
C++: protocols::docking::DockingHighRes::set_movable_jumps(class utility::vector1<int, class std::allocator<int> >) –> 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_partners(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, partners: str) None ¶
C++: protocols::docking::DockingHighRes::set_partners(std::string) –> void
- set_rt_min(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, rt_min: bool) None ¶
C++: protocols::docking::DockingHighRes::set_rt_min(bool) –> void
- set_sc_min(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, sc_min: bool) None ¶
C++: protocols::docking::DockingHighRes::set_sc_min(bool) –> void
- set_scorefxn(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) None ¶
C++: protocols::docking::DockingHighRes::set_scorefxn(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void
- set_scorefxn_pack(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, scorefxn_pack: pyrosetta.rosetta.core.scoring.ScoreFunction) None ¶
C++: protocols::docking::DockingHighRes::set_scorefxn_pack(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void
- set_task_factory(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, tf: pyrosetta.rosetta.core.pack.task.TaskFactory) None ¶
C++: protocols::docking::DockingHighRes::set_task_factory(class std::shared_ptr<const class core::pack::task::TaskFactory>) –> void
- set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) None ¶
Set the ‘type’ string
C++: protocols::moves::Mover::set_type(const std::string &) –> void
- show(*args, **kwargs)¶
Overloaded function.
show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None
Outputs details about the Mover, including current settings.
C++: protocols::moves::Mover::show(std::ostream &) const –> void
- task_factory(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) pyrosetta.rosetta.core.pack.task.TaskFactory ¶
C++: protocols::docking::DockingHighRes::task_factory() –> class std::shared_ptr<const class core::pack::task::TaskFactory>
- 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.docking.DockingHighResFactory¶
Bases:
SingletonBase_protocols_docking_DockingHighResFactory_t
DockingHighResFactory uses the MoverFactory to create instances of DockingHighRes
- create_docking_high_res_mover(self: pyrosetta.rosetta.protocols.docking.DockingHighResFactory, type_name: pyrosetta.rosetta.protocols.docking.DHR_Type) pyrosetta.rosetta.protocols.docking.DockingHighRes ¶
Create the specified DockingHighRes
C++: protocols::docking::DockingHighResFactory::create_docking_high_res_mover(const enum protocols::docking::DHR_Type &) –> class std::shared_ptr<class protocols::docking::DockingHighRes>
- static get_instance() protocols::docking::DockingHighResFactory ¶
C++: utility::SingletonBase<protocols::docking::DockingHighResFactory>::get_instance() –> class protocols::docking::DockingHighResFactory *
- class pyrosetta.rosetta.protocols.docking.DockingHighResFilter¶
Bases:
Filter
High-resolution (all-atom) filter for docking. Checks (1) total_score beats the cutoff given
interface_score must be negative
/// ++ had: 1-score filter 2-fa_rep filter 3-interfaceE filter 4-chainbreak filter TTD: add these other filters
- apply(self: pyrosetta.rosetta.protocols.docking.DockingHighResFilter, pose: pyrosetta.rosetta.core.pose.Pose) bool ¶
C++: protocols::docking::DockingHighResFilter::apply(const class core::pose::Pose &) const –> bool
- clear(self: pyrosetta.rosetta.protocols.filters.Filter) None ¶
used to clear internal variables if needed. Using fresh_instance is preferred since it’s a pure virtual
C++: protocols::filters::Filter::clear() –> void
- clone(self: pyrosetta.rosetta.protocols.docking.DockingHighResFilter) pyrosetta.rosetta.protocols.filters.Filter ¶
C++: protocols::docking::DockingHighResFilter::clone() const –> class std::shared_ptr<class protocols::filters::Filter>
- fresh_instance(self: pyrosetta.rosetta.protocols.docking.DockingHighResFilter) pyrosetta.rosetta.protocols.filters.Filter ¶
C++: protocols::docking::DockingHighResFilter::fresh_instance() const –> class std::shared_ptr<class protocols::filters::Filter>
- get_type(self: pyrosetta.rosetta.protocols.filters.Filter) str ¶
C++: protocols::filters::Filter::get_type() const –> std::string
- get_user_defined_name(self: pyrosetta.rosetta.protocols.filters.Filter) str ¶
C++: protocols::filters::Filter::get_user_defined_name() const –> std::string
- name(self: pyrosetta.rosetta.protocols.filters.Filter) str ¶
C++: protocols::filters::Filter::name() const –> std::string
- parse_my_tag(self: pyrosetta.rosetta.protocols.filters.Filter, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None ¶
Called by FilterFactory when constructing new Filter. Takes care of the specific mover’s parsing.
C++: protocols::filters::Filter::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- provide_citation_info(self: pyrosetta.rosetta.protocols.filters.Filter, : 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 filters wishing to provide citation information.
C++: protocols::filters::Filter::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void
- report(self: pyrosetta.rosetta.protocols.filters.Filter, : pyrosetta.rosetta.std.ostream, : pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::filters::Filter::report(std::ostream &, const class core::pose::Pose &) const –> void
- report_sm(self: pyrosetta.rosetta.protocols.filters.Filter, : pyrosetta.rosetta.core.pose.Pose) float ¶
C++: protocols::filters::Filter::report_sm(const class core::pose::Pose &) const –> double
- score(self: pyrosetta.rosetta.protocols.filters.Filter, pose: pyrosetta.rosetta.core.pose.Pose) float ¶
C++: protocols::filters::Filter::score(class core::pose::Pose &) –> double
- set_moveable_jumps(self: pyrosetta.rosetta.protocols.docking.DockingHighResFilter, movable_jumps: pyrosetta.rosetta.utility.vector1_int) None ¶
C++: protocols::docking::DockingHighResFilter::set_moveable_jumps(const class utility::vector1<int, class std::allocator<int> > &) –> void
- set_score_cutoff(self: pyrosetta.rosetta.protocols.docking.DockingHighResFilter, new_cutoff: float) None ¶
C++: protocols::docking::DockingHighResFilter::set_score_cutoff(double) –> void
- set_score_margin(self: pyrosetta.rosetta.protocols.docking.DockingHighResFilter, new_score_margin: float) None ¶
C++: protocols::docking::DockingHighResFilter::set_score_margin(double) –> void
- set_scorefunction(self: pyrosetta.rosetta.protocols.docking.DockingHighResFilter, scorefunction: pyrosetta.rosetta.core.scoring.ScoreFunction) None ¶
C++: protocols::docking::DockingHighResFilter::set_scorefunction(const class std::shared_ptr<class core::scoring::ScoreFunction>) –> void
- set_user_defined_name(self: pyrosetta.rosetta.protocols.filters.Filter, name: str) None ¶
C++: protocols::filters::Filter::set_user_defined_name(const std::string &) –> void
- class pyrosetta.rosetta.protocols.docking.DockingHighResLegacy¶
Bases:
DockingHighRes
this mover does the high resolution refinement stage of the RosettaDock algorithm
- add_additional_task_operaration(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, task_operation: pyrosetta.rosetta.core.pack.task.operation.TaskOperation) None ¶
C++: protocols::docking::DockingHighRes::add_additional_task_operaration(class std::shared_ptr<class core::pack::task::operation::TaskOperation>) –> void
- apply(self: pyrosetta.rosetta.protocols.docking.DockingHighResLegacy, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::docking::DockingHighResLegacy::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.docking.DockingHighResLegacy, : pyrosetta.rosetta.protocols.docking.DockingHighResLegacy) pyrosetta.rosetta.protocols.docking.DockingHighResLegacy ¶
C++: protocols::docking::DockingHighResLegacy::operator=(const class protocols::docking::DockingHighResLegacy &) –> class protocols::docking::DockingHighResLegacy &
- 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.docking.DockingHighResLegacy) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::docking::DockingHighResLegacy::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>
- define_loops(self: pyrosetta.rosetta.protocols.docking.DockingHighResLegacy, pose: pyrosetta.rosetta.core.pose.Pose, loop_set: pyrosetta.rosetta.protocols.loops.Loops, interface_dist: float) None ¶
C++: protocols::docking::DockingHighResLegacy::define_loops(const class core::pose::Pose &, class std::shared_ptr<class protocols::loops::Loops>, double &) –> void
- design(*args, **kwargs)¶
Overloaded function.
design(self: pyrosetta.rosetta.protocols.docking.DockingHighResLegacy, des: bool) -> None
C++: protocols::docking::DockingHighResLegacy::design(const bool) –> void
design(self: pyrosetta.rosetta.protocols.docking.DockingHighResLegacy) -> bool
C++: protocols::docking::DockingHighResLegacy::design() const –> bool
- 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_additional_task_operarations(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_task_operation_TaskOperation_t ¶
C++: protocols::docking::DockingHighRes::get_additional_task_operarations() –> class utility::vector1<class std::shared_ptr<class core::pack::task::operation::TaskOperation>, class std::allocator<class std::shared_ptr<class core::pack::task::operation::TaskOperation> > >
- 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_mc(self: pyrosetta.rosetta.protocols.docking.DockingHighResLegacy) pyrosetta.rosetta.protocols.moves.MonteCarlo ¶
C++: protocols::docking::DockingHighResLegacy::get_mc() –> class std::shared_ptr<class protocols::moves::MonteCarlo>
- get_name(self: pyrosetta.rosetta.protocols.docking.DockingHighResLegacy) str ¶
C++: protocols::docking::DockingHighResLegacy::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_partners(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) str ¶
C++: protocols::docking::DockingHighRes::get_partners() const –> std::string
- get_rot_magnitude(self: pyrosetta.rosetta.protocols.docking.DockingHighResLegacy) float ¶
C++: protocols::docking::DockingHighResLegacy::get_rot_magnitude() –> double
- 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_trans_magnitude(self: pyrosetta.rosetta.protocols.docking.DockingHighResLegacy) float ¶
C++: protocols::docking::DockingHighResLegacy::get_trans_magnitude() –> double
- get_type(self: pyrosetta.rosetta.protocols.moves.Mover) str ¶
C++: protocols::moves::Mover::get_type() const –> std::string
- ignore_default_task(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) bool ¶
C++: protocols::docking::DockingHighRes::ignore_default_task() –> bool
- info(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.list_std_string_t ¶
non-const accessor
C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &
- last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) float ¶
C++: protocols::moves::Mover::last_proposal_density_ratio() –> double
- movable_jumps(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) pyrosetta.rosetta.utility.vector1_int ¶
C++: protocols::docking::DockingHighRes::movable_jumps() –> class utility::vector1<int, class std::allocator<int> > &
- static mover_name() str ¶
C++: protocols::docking::DockingHighResLegacy::mover_name() –> std::string
- static name() str ¶
C++: protocols::moves::Mover::name() –> std::string
- parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None ¶
Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.
C++: protocols::moves::Mover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- partners(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) str ¶
C++: protocols::docking::DockingHighRes::partners() –> std::string
- provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None ¶
- Provide citations to the passed CitationCollectionList
Subclasses should add the info for themselves and any other classes they use.
The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.
C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void
- static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None ¶
C++: protocols::docking::DockingHighResLegacy::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
- rt_min(self: pyrosetta.rosetta.protocols.docking.DockingHighResLegacy) bool ¶
C++: protocols::docking::DockingHighResLegacy::rt_min() –> bool
- sc_min(self: pyrosetta.rosetta.protocols.docking.DockingHighResLegacy) bool ¶
C++: protocols::docking::DockingHighResLegacy::sc_min() –> bool
- scorefxn(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) pyrosetta.rosetta.core.scoring.ScoreFunction ¶
C++: protocols::docking::DockingHighRes::scorefxn() const –> class std::shared_ptr<class core::scoring::ScoreFunction>
- scorefxn_pack(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) pyrosetta.rosetta.core.scoring.ScoreFunction ¶
C++: protocols::docking::DockingHighRes::scorefxn_pack() const –> class std::shared_ptr<class core::scoring::ScoreFunction>
- set_additional_task_operarations(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, additional_task_operations: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_task_operation_TaskOperation_t) None ¶
C++: protocols::docking::DockingHighRes::set_additional_task_operarations(class utility::vector1<class std::shared_ptr<class core::pack::task::operation::TaskOperation>, class std::allocator<class std::shared_ptr<class core::pack::task::operation::TaskOperation> > >) –> 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_default(self: pyrosetta.rosetta.protocols.docking.DockingHighResLegacy, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::docking::DockingHighResLegacy::set_default(class core::pose::Pose &) –> void
- set_dock_mcm_protocol(self: pyrosetta.rosetta.protocols.docking.DockingHighResLegacy, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::docking::DockingHighResLegacy::set_dock_mcm_protocol(class core::pose::Pose &) –> void
- set_dock_min_protocol(self: pyrosetta.rosetta.protocols.docking.DockingHighResLegacy) None ¶
C++: protocols::docking::DockingHighResLegacy::set_dock_min_protocol() –> void
- set_dock_ppk_protocol(self: pyrosetta.rosetta.protocols.docking.DockingHighResLegacy, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::docking::DockingHighResLegacy::set_dock_ppk_protocol(class core::pose::Pose &) –> void
- set_ignore_default_task(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, ignore_default_task: bool) None ¶
C++: protocols::docking::DockingHighRes::set_ignore_default_task(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_interface_definition_task_operation(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, interface_definition: protocols::simple_task_operations::InterfaceTaskOperation) None ¶
C++: protocols::docking::DockingHighRes::set_interface_definition_task_operation(class std::shared_ptr<class protocols::simple_task_operations::InterfaceTaskOperation>) –> void
- set_min_type(self: pyrosetta.rosetta.protocols.docking.DockingHighResLegacy, min_type_in: str) None ¶
C++: protocols::docking::DockingHighResLegacy::set_min_type(std::string) –> void
- set_movable_jumps(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, movable_jumps: pyrosetta.rosetta.utility.vector1_int) None ¶
C++: protocols::docking::DockingHighRes::set_movable_jumps(class utility::vector1<int, class std::allocator<int> >) –> void
- set_move_map(self: pyrosetta.rosetta.protocols.docking.DockingHighResLegacy, movemap_in: pyrosetta.rosetta.core.kinematics.MoveMap) None ¶
C++: protocols::docking::DockingHighResLegacy::set_move_map(class std::shared_ptr<class core::kinematics::MoveMap>) –> void
- set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe
C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void
- set_partners(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, partners: str) None ¶
C++: protocols::docking::DockingHighRes::set_partners(std::string) –> void
- set_protocol(self: pyrosetta.rosetta.protocols.docking.DockingHighResLegacy, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::docking::DockingHighResLegacy::set_protocol(class core::pose::Pose &) –> void
- set_repack(self: pyrosetta.rosetta.protocols.docking.DockingHighResLegacy, repack_switch: bool) None ¶
C++: protocols::docking::DockingHighResLegacy::set_repack(bool) –> void
- set_rot_magnitude(self: pyrosetta.rosetta.protocols.docking.DockingHighResLegacy, rot_magnitude: float) None ¶
C++: protocols::docking::DockingHighResLegacy::set_rot_magnitude(double) –> void
- set_rt_min(self: pyrosetta.rosetta.protocols.docking.DockingHighResLegacy, rt_min: bool) None ¶
C++: protocols::docking::DockingHighResLegacy::set_rt_min(bool) –> void
- set_sc_min(self: pyrosetta.rosetta.protocols.docking.DockingHighResLegacy, sc_min: bool) None ¶
C++: protocols::docking::DockingHighResLegacy::set_sc_min(bool) –> void
- set_scorefxn(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) None ¶
C++: protocols::docking::DockingHighRes::set_scorefxn(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void
- set_scorefxn_pack(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, scorefxn_pack: pyrosetta.rosetta.core.scoring.ScoreFunction) None ¶
C++: protocols::docking::DockingHighRes::set_scorefxn_pack(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void
- set_task_factory(self: pyrosetta.rosetta.protocols.docking.DockingHighResLegacy, task: pyrosetta.rosetta.core.pack.task.TaskFactory) None ¶
C++: protocols::docking::DockingHighResLegacy::set_task_factory(class std::shared_ptr<class core::pack::task::TaskFactory>) –> void
- set_trans_magnitude(self: pyrosetta.rosetta.protocols.docking.DockingHighResLegacy, trans_magnitude: float) None ¶
C++: protocols::docking::DockingHighResLegacy::set_trans_magnitude(double) –> void
- set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) None ¶
Set the ‘type’ string
C++: protocols::moves::Mover::set_type(const std::string &) –> void
- show(*args, **kwargs)¶
Overloaded function.
show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None
Outputs details about the Mover, including current settings.
C++: protocols::moves::Mover::show(std::ostream &) const –> void
- task_factory(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) pyrosetta.rosetta.core.pack.task.TaskFactory ¶
C++: protocols::docking::DockingHighRes::task_factory() –> class std::shared_ptr<const class core::pack::task::TaskFactory>
- 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.docking.DockingHighResLegacyCreator¶
Bases:
MoverCreator
- assign(self: pyrosetta.rosetta.protocols.docking.DockingHighResLegacyCreator, : pyrosetta.rosetta.protocols.docking.DockingHighResLegacyCreator) pyrosetta.rosetta.protocols.docking.DockingHighResLegacyCreator ¶
C++: protocols::docking::DockingHighResLegacyCreator::operator=(const class protocols::docking::DockingHighResLegacyCreator &) –> class protocols::docking::DockingHighResLegacyCreator &
- create_mover(self: pyrosetta.rosetta.protocols.docking.DockingHighResLegacyCreator) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::docking::DockingHighResLegacyCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>
- keyname(self: pyrosetta.rosetta.protocols.docking.DockingHighResLegacyCreator) str ¶
C++: protocols::docking::DockingHighResLegacyCreator::keyname() const –> std::string
- class pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation¶
Bases:
Mover
this mover carries out the initial perturbation phase of the RosettaDock algorithm based on user-inputted command line options
- apply(self: pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::docking::DockingInitialPerturbation::apply(class core::pose::Pose &) –> void
- apply_body(self: pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation, pose: pyrosetta.rosetta.core.pose.Pose, jump_number: int) None ¶
C++: protocols::docking::DockingInitialPerturbation::apply_body(class core::pose::Pose &, unsigned long) –> void
- assign(self: pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation, : pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation) pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation ¶
C++: protocols::docking::DockingInitialPerturbation::operator=(const class protocols::docking::DockingInitialPerturbation &) –> class protocols::docking::DockingInitialPerturbation &
- 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.docking.DockingInitialPerturbation) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::docking::DockingInitialPerturbation::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.docking.DockingInitialPerturbation) str ¶
C++: protocols::docking::DockingInitialPerturbation::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.docking.DockingInitialPerturbation) None ¶
Calls set_dault, register_from_options and init_from_options
C++: protocols::docking::DockingInitialPerturbation::init() –> void
- init_from_options(self: pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation) None ¶
Assigns user specified values to primitive members using command line options
C++: protocols::docking::DockingInitialPerturbation::init_from_options() –> void
- last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) float ¶
C++: protocols::moves::Mover::last_proposal_density_ratio() –> double
- static mover_name() str ¶
C++: protocols::docking::DockingInitialPerturbation::mover_name() –> std::string
- static name() str ¶
C++: protocols::moves::Mover::name() –> std::string
- or_randomize2(self: pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation, randomize2: bool) None ¶
C++: protocols::docking::DockingInitialPerturbation::or_randomize2(bool) –> void
- parse_my_tag(self: pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None ¶
zhe for rosetta_scripts
C++: protocols::docking::DockingInitialPerturbation::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None ¶
- Provide citations to the passed CitationCollectionList
Subclasses should add the info for themselves and any other classes they use.
The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.
C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void
- static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None ¶
C++: protocols::docking::DockingInitialPerturbation::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void
- static register_options() None ¶
Associates relevant options with the DockingInitialPerturbation class
C++: protocols::docking::DockingInitialPerturbation::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_center(self: pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation, center: bool) None ¶
C++: protocols::docking::DockingInitialPerturbation::set_center(bool) –> void
- set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) None ¶
C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void
- set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) None ¶
C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void
- set_default(self: pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation) None ¶
Sets members to default values
C++: protocols::docking::DockingInitialPerturbation::set_default() –> void
- set_dock_pert(self: pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation, dock_pert: pyrosetta.rosetta.utility.vector1_double) None ¶
C++: protocols::docking::DockingInitialPerturbation::set_dock_pert(const class utility::vector1<double, class std::allocator<double> > &) –> void
- set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
setter for poses contained for rms
C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void
- set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe
C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void
- set_randomize1(self: pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation, randomize1: bool) None ¶
set functions
C++: protocols::docking::DockingInitialPerturbation::set_randomize1(bool) –> void
- set_randomize2(self: pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation, randomize2: bool) None ¶
C++: protocols::docking::DockingInitialPerturbation::set_randomize2(bool) –> void
- set_spin(self: pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation, spin: bool) None ¶
C++: protocols::docking::DockingInitialPerturbation::set_spin(bool) –> void
- set_tilt(self: pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation, tilt: pyrosetta.rosetta.utility.vector1_double) None ¶
C++: protocols::docking::DockingInitialPerturbation::set_tilt(const class utility::vector1<double, class std::allocator<double> > &) –> void
- set_tilt1_center(self: pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation, tilt_center: str) None ¶
C++: protocols::docking::DockingInitialPerturbation::set_tilt1_center(const std::string &) –> void
- set_tilt2_center(self: pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation, tilt_center: str) None ¶
C++: protocols::docking::DockingInitialPerturbation::set_tilt2_center(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
- set_uniform_trans(self: pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation, uniform_trans: float) None ¶
C++: protocols::docking::DockingInitialPerturbation::set_uniform_trans(double) –> void
- set_use_ellipsoidal_randomization(self: pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation, use_ellipsoidal_randomization: bool) None ¶
C++: protocols::docking::DockingInitialPerturbation::set_use_ellipsoidal_randomization(bool) –> void
- show(*args, **kwargs)¶
Overloaded function.
show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None
Outputs details about the Mover, including current settings.
C++: protocols::moves::Mover::show(std::ostream &) const –> void
- test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
- : Unit test support function. Apply one move to a given pose.
Allows extra test specific functions to be called before applying
C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void
- 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.docking.DockingInitialPerturbationCreator¶
Bases:
MoverCreator
- assign(self: pyrosetta.rosetta.protocols.docking.DockingInitialPerturbationCreator, : pyrosetta.rosetta.protocols.docking.DockingInitialPerturbationCreator) pyrosetta.rosetta.protocols.docking.DockingInitialPerturbationCreator ¶
C++: protocols::docking::DockingInitialPerturbationCreator::operator=(const class protocols::docking::DockingInitialPerturbationCreator &) –> class protocols::docking::DockingInitialPerturbationCreator &
- create_mover(self: pyrosetta.rosetta.protocols.docking.DockingInitialPerturbationCreator) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::docking::DockingInitialPerturbationCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>
- keyname(self: pyrosetta.rosetta.protocols.docking.DockingInitialPerturbationCreator) str ¶
C++: protocols::docking::DockingInitialPerturbationCreator::keyname() const –> std::string
- class pyrosetta.rosetta.protocols.docking.DockingLowRes¶
Bases:
Mover
- apply(self: pyrosetta.rosetta.protocols.docking.DockingLowRes, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::docking::DockingLowRes::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.docking.DockingLowRes, : pyrosetta.rosetta.protocols.docking.DockingLowRes) pyrosetta.rosetta.protocols.docking.DockingLowRes ¶
C++: protocols::docking::DockingLowRes::operator=(const class protocols::docking::DockingLowRes &) –> class protocols::docking::DockingLowRes &
- calc_accept_rate(self: pyrosetta.rosetta.protocols.docking.DockingLowRes) None ¶
C++: protocols::docking::DockingLowRes::calc_accept_rate() –> 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.docking.DockingLowRes) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::docking::DockingLowRes::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>
- property first_apply_with_current_setup_¶
- property flags_and_objects_are_in_sync_¶
- 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_accept_rate(self: pyrosetta.rosetta.protocols.docking.DockingLowRes) float ¶
C++: protocols::docking::DockingLowRes::get_accept_rate() –> double
- 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_conformer_ensemble1(self: pyrosetta.rosetta.protocols.docking.DockingLowRes) int ¶
C++: protocols::docking::DockingLowRes::get_current_conformer_ensemble1() –> unsigned long
- get_current_conformer_ensemble2(self: pyrosetta.rosetta.protocols.docking.DockingLowRes) int ¶
C++: protocols::docking::DockingLowRes::get_current_conformer_ensemble2() –> unsigned long
- 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_inner_cycles(self: pyrosetta.rosetta.protocols.docking.DockingLowRes) int ¶
C++: protocols::docking::DockingLowRes::get_inner_cycles() –> unsigned long
- 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_mc(self: pyrosetta.rosetta.protocols.docking.DockingLowRes) pyrosetta.rosetta.protocols.moves.MonteCarlo ¶
C++: protocols::docking::DockingLowRes::get_mc() –> class std::shared_ptr<class protocols::moves::MonteCarlo>
- get_movable_jumps(self: pyrosetta.rosetta.protocols.docking.DockingLowRes) pyrosetta.rosetta.utility.vector1_int ¶
C++: protocols::docking::DockingLowRes::get_movable_jumps() –> class utility::vector1<int, class std::allocator<int> >
- get_name(self: pyrosetta.rosetta.protocols.docking.DockingLowRes) str ¶
C++: protocols::docking::DockingLowRes::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_outer_cycles(self: pyrosetta.rosetta.protocols.docking.DockingLowRes) int ¶
C++: protocols::docking::DockingLowRes::get_outer_cycles() –> unsigned long
- get_pymol_mover(self: pyrosetta.rosetta.protocols.docking.DockingLowRes) protocols::moves::PyMOLMover ¶
C++: protocols::docking::DockingLowRes::get_pymol_mover() –> class std::shared_ptr<class protocols::moves::PyMOLMover>
- get_rb_mover(self: pyrosetta.rosetta.protocols.docking.DockingLowRes) pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover ¶
C++: protocols::docking::DockingLowRes::get_rb_mover() –> class std::shared_ptr<class protocols::rigid::RigidBodyPerturbNoCenterMover>
- get_rb_seq(self: pyrosetta.rosetta.protocols.docking.DockingLowRes) pyrosetta.rosetta.protocols.moves.SequenceMover ¶
C++: protocols::docking::DockingLowRes::get_rb_seq() –> class std::shared_ptr<class protocols::moves::SequenceMover>
- get_rb_trial(self: pyrosetta.rosetta.protocols.docking.DockingLowRes) protocols::moves::TrialMover ¶
C++: protocols::docking::DockingLowRes::get_rb_trial() –> class std::shared_ptr<class protocols::moves::TrialMover>
- get_rot_magnitude(self: pyrosetta.rosetta.protocols.docking.DockingLowRes) float ¶
C++: protocols::docking::DockingLowRes::get_rot_magnitude() –> double
- get_scorefxn(self: pyrosetta.rosetta.protocols.docking.DockingLowRes) pyrosetta.rosetta.core.scoring.ScoreFunction ¶
C++: protocols::docking::DockingLowRes::get_scorefxn() –> class std::shared_ptr<const class core::scoring::ScoreFunction>
- get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>
- get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t ¶
C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>
- get_temperature(self: pyrosetta.rosetta.protocols.docking.DockingLowRes) float ¶
C++: protocols::docking::DockingLowRes::get_temperature() –> double
- get_trans_magnitude(self: pyrosetta.rosetta.protocols.docking.DockingLowRes) float ¶
Option getters - added by SSRB
C++: protocols::docking::DockingLowRes::get_trans_magnitude() –> double
- get_type(self: pyrosetta.rosetta.protocols.moves.Mover) str ¶
C++: protocols::moves::Mover::get_type() const –> std::string
- get_view_in_pymol(self: pyrosetta.rosetta.protocols.docking.DockingLowRes) bool ¶
C++: protocols::docking::DockingLowRes::get_view_in_pymol() –> bool
- info(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.list_std_string_t ¶
non-const accessor
C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &
- last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) float ¶
C++: protocols::moves::Mover::last_proposal_density_ratio() –> double
- lowres_inner_cycle(self: pyrosetta.rosetta.protocols.docking.DockingLowRes, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::docking::DockingLowRes::lowres_inner_cycle(class core::pose::Pose &) –> void
- 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
- pymol_color_change(self: pyrosetta.rosetta.protocols.docking.DockingLowRes, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::docking::DockingLowRes::pymol_color_change(class core::pose::Pose &) –> 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_rb_trial_counters(self: pyrosetta.rosetta.protocols.docking.DockingLowRes) None ¶
C++: protocols::docking::DockingLowRes::reset_rb_trial_counters() –> void
- 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
- rigid_body_trial(self: pyrosetta.rosetta.protocols.docking.DockingLowRes, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
Perform a cycle of rigid-body Monte Carlo moves
C++: protocols::docking::DockingLowRes::rigid_body_trial(class core::pose::Pose &) –> 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_default(self: pyrosetta.rosetta.protocols.docking.DockingLowRes) None ¶
Assigns default values to primitive members
C++: protocols::docking::DockingLowRes::set_default() –> void
- set_inner_cycles(self: pyrosetta.rosetta.protocols.docking.DockingLowRes, inner_cycles: int) None ¶
C++: protocols::docking::DockingLowRes::set_inner_cycles(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_outer_cycles(self: pyrosetta.rosetta.protocols.docking.DockingLowRes, outer_cycles: int) None ¶
C++: protocols::docking::DockingLowRes::set_outer_cycles(unsigned long) –> void
- set_rb_trial(self: pyrosetta.rosetta.protocols.docking.DockingLowRes, rb_trial_in: protocols::moves::TrialMover) None ¶
C++: protocols::docking::DockingLowRes::set_rb_trial(class std::shared_ptr<class protocols::moves::TrialMover>) –> void
- set_rot_magnitude(self: pyrosetta.rosetta.protocols.docking.DockingLowRes, rot_magnitude: float) None ¶
C++: protocols::docking::DockingLowRes::set_rot_magnitude(double) –> void
- set_scorefxn(self: pyrosetta.rosetta.protocols.docking.DockingLowRes, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) None ¶
C++: protocols::docking::DockingLowRes::set_scorefxn(class std::shared_ptr<const class core::scoring::ScoreFunction>) –> void
- set_trans_magnitude(self: pyrosetta.rosetta.protocols.docking.DockingLowRes, trans_magnitude: float) None ¶
C++: protocols::docking::DockingLowRes::set_trans_magnitude(double) –> void
- set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) None ¶
Set the ‘type’ string
C++: protocols::moves::Mover::set_type(const std::string &) –> void
- show(*args, **kwargs)¶
Overloaded function.
show(self: pyrosetta.rosetta.protocols.docking.DockingLowRes) -> None
show(self: pyrosetta.rosetta.protocols.docking.DockingLowRes, out: pyrosetta.rosetta.std.ostream) -> None
C++: protocols::docking::DockingLowRes::show(std::ostream &) const –> void
- sync_magnitudes_with_flags(self: pyrosetta.rosetta.protocols.docking.DockingLowRes) None ¶
C++: protocols::docking::DockingLowRes::sync_magnitudes_with_flags() –> void
- sync_objects_with_flags(self: pyrosetta.rosetta.protocols.docking.DockingLowRes) None ¶
Instantiates non-primitive members based on the value of the primitive members
C++: protocols::docking::DockingLowRes::sync_objects_with_flags() –> 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.docking.DockingLowResEnsemble¶
Bases:
DockingLowRes
- adaptive_inner_cycle(self: pyrosetta.rosetta.protocols.docking.DockingLowResEnsemble, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::docking::DockingLowResEnsemble::adaptive_inner_cycle(class core::pose::Pose &) –> void
- apply(self: pyrosetta.rosetta.protocols.docking.DockingLowRes, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::docking::DockingLowRes::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.docking.DockingLowResEnsemble, : pyrosetta.rosetta.protocols.docking.DockingLowResEnsemble) pyrosetta.rosetta.protocols.docking.DockingLowResEnsemble ¶
C++: protocols::docking::DockingLowResEnsemble::operator=(const class protocols::docking::DockingLowResEnsemble &) –> class protocols::docking::DockingLowResEnsemble &
- calc_accept_rate(self: pyrosetta.rosetta.protocols.docking.DockingLowRes) None ¶
C++: protocols::docking::DockingLowRes::calc_accept_rate() –> void
- calc_ensemble_accept_rate_(self: pyrosetta.rosetta.protocols.docking.DockingLowResEnsemble) None ¶
C++: protocols::docking::DockingLowResEnsemble::calc_ensemble_accept_rate_() –> 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.docking.DockingLowResEnsemble) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::docking::DockingLowResEnsemble::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>
- ensemble_defaults(self: pyrosetta.rosetta.protocols.docking.DockingLowResEnsemble) None ¶
C++: protocols::docking::DockingLowResEnsemble::ensemble_defaults() –> void
- property first_apply_with_current_setup_¶
- property flags_and_objects_are_in_sync_¶
- 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_accept_rate(self: pyrosetta.rosetta.protocols.docking.DockingLowRes) float ¶
C++: protocols::docking::DockingLowRes::get_accept_rate() –> double
- 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_conformer_ensemble1(self: pyrosetta.rosetta.protocols.docking.DockingLowResEnsemble) int ¶
C++: protocols::docking::DockingLowResEnsemble::get_current_conformer_ensemble1() –> unsigned long
- get_current_conformer_ensemble2(self: pyrosetta.rosetta.protocols.docking.DockingLowResEnsemble) int ¶
C++: protocols::docking::DockingLowResEnsemble::get_current_conformer_ensemble2() –> unsigned long
- 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_inner_cycles(self: pyrosetta.rosetta.protocols.docking.DockingLowRes) int ¶
C++: protocols::docking::DockingLowRes::get_inner_cycles() –> unsigned long
- 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_mc(self: pyrosetta.rosetta.protocols.docking.DockingLowRes) pyrosetta.rosetta.protocols.moves.MonteCarlo ¶
C++: protocols::docking::DockingLowRes::get_mc() –> class std::shared_ptr<class protocols::moves::MonteCarlo>
- get_movable_jumps(self: pyrosetta.rosetta.protocols.docking.DockingLowRes) pyrosetta.rosetta.utility.vector1_int ¶
C++: protocols::docking::DockingLowRes::get_movable_jumps() –> class utility::vector1<int, class std::allocator<int> >
- get_name(self: pyrosetta.rosetta.protocols.docking.DockingLowRes) str ¶
C++: protocols::docking::DockingLowRes::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_outer_cycles(self: pyrosetta.rosetta.protocols.docking.DockingLowRes) int ¶
C++: protocols::docking::DockingLowRes::get_outer_cycles() –> unsigned long
- get_pymol_mover(self: pyrosetta.rosetta.protocols.docking.DockingLowRes) protocols::moves::PyMOLMover ¶
C++: protocols::docking::DockingLowRes::get_pymol_mover() –> class std::shared_ptr<class protocols::moves::PyMOLMover>
- get_rb_mover(self: pyrosetta.rosetta.protocols.docking.DockingLowRes) pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover ¶
C++: protocols::docking::DockingLowRes::get_rb_mover() –> class std::shared_ptr<class protocols::rigid::RigidBodyPerturbNoCenterMover>
- get_rb_seq(self: pyrosetta.rosetta.protocols.docking.DockingLowRes) pyrosetta.rosetta.protocols.moves.SequenceMover ¶
C++: protocols::docking::DockingLowRes::get_rb_seq() –> class std::shared_ptr<class protocols::moves::SequenceMover>
- get_rb_trial(self: pyrosetta.rosetta.protocols.docking.DockingLowRes) protocols::moves::TrialMover ¶
C++: protocols::docking::DockingLowRes::get_rb_trial() –> class std::shared_ptr<class protocols::moves::TrialMover>
- get_rot_magnitude(self: pyrosetta.rosetta.protocols.docking.DockingLowRes) float ¶
C++: protocols::docking::DockingLowRes::get_rot_magnitude() –> double
- get_scorefxn(self: pyrosetta.rosetta.protocols.docking.DockingLowRes) pyrosetta.rosetta.core.scoring.ScoreFunction ¶
C++: protocols::docking::DockingLowRes::get_scorefxn() –> class std::shared_ptr<const class core::scoring::ScoreFunction>
- get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>
- get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t ¶
C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>
- get_temperature(self: pyrosetta.rosetta.protocols.docking.DockingLowRes) float ¶
C++: protocols::docking::DockingLowRes::get_temperature() –> double
- get_trans_magnitude(self: pyrosetta.rosetta.protocols.docking.DockingLowRes) float ¶
Option getters - added by SSRB
C++: protocols::docking::DockingLowRes::get_trans_magnitude() –> double
- get_type(self: pyrosetta.rosetta.protocols.moves.Mover) str ¶
C++: protocols::moves::Mover::get_type() const –> std::string
- get_view_in_pymol(self: pyrosetta.rosetta.protocols.docking.DockingLowRes) bool ¶
C++: protocols::docking::DockingLowRes::get_view_in_pymol() –> bool
- info(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.list_std_string_t ¶
non-const accessor
C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &
- initialize_movers(self: pyrosetta.rosetta.protocols.docking.DockingLowResEnsemble) None ¶
C++: protocols::docking::DockingLowResEnsemble::initialize_movers() –> void
- last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) float ¶
C++: protocols::moves::Mover::last_proposal_density_ratio() –> double
- lowres_inner_cycle(self: pyrosetta.rosetta.protocols.docking.DockingLowResEnsemble, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::docking::DockingLowResEnsemble::lowres_inner_cycle(class core::pose::Pose &) –> void
- 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
- pymol_color_change(self: pyrosetta.rosetta.protocols.docking.DockingLowRes, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::docking::DockingLowRes::pymol_color_change(class core::pose::Pose &) –> 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_ensemble_trial_counters(self: pyrosetta.rosetta.protocols.docking.DockingLowResEnsemble) None ¶
C++: protocols::docking::DockingLowResEnsemble::reset_ensemble_trial_counters() –> void
- reset_rb_trial_counters(self: pyrosetta.rosetta.protocols.docking.DockingLowRes) None ¶
C++: protocols::docking::DockingLowRes::reset_rb_trial_counters() –> void
- 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
- rigid_body_trial(self: pyrosetta.rosetta.protocols.docking.DockingLowRes, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
Perform a cycle of rigid-body Monte Carlo moves
C++: protocols::docking::DockingLowRes::rigid_body_trial(class core::pose::Pose &) –> 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_default(self: pyrosetta.rosetta.protocols.docking.DockingLowRes) None ¶
Assigns default values to primitive members
C++: protocols::docking::DockingLowRes::set_default() –> void
- set_ensemble1(self: pyrosetta.rosetta.protocols.docking.DockingLowResEnsemble, ensemble1: pyrosetta.rosetta.protocols.docking.DockingEnsemble) None ¶
C++: protocols::docking::DockingLowResEnsemble::set_ensemble1(class std::shared_ptr<class protocols::docking::DockingEnsemble>) –> void
- set_ensemble2(self: pyrosetta.rosetta.protocols.docking.DockingLowResEnsemble, ensemble2: pyrosetta.rosetta.protocols.docking.DockingEnsemble) None ¶
C++: protocols::docking::DockingLowResEnsemble::set_ensemble2(class std::shared_ptr<class protocols::docking::DockingEnsemble>) –> void
- set_inner_cycles(self: pyrosetta.rosetta.protocols.docking.DockingLowRes, inner_cycles: int) None ¶
C++: protocols::docking::DockingLowRes::set_inner_cycles(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_outer_cycles(self: pyrosetta.rosetta.protocols.docking.DockingLowRes, outer_cycles: int) None ¶
C++: protocols::docking::DockingLowRes::set_outer_cycles(unsigned long) –> void
- set_rb_trial(self: pyrosetta.rosetta.protocols.docking.DockingLowRes, rb_trial_in: protocols::moves::TrialMover) None ¶
C++: protocols::docking::DockingLowRes::set_rb_trial(class std::shared_ptr<class protocols::moves::TrialMover>) –> void
- set_rot_magnitude(self: pyrosetta.rosetta.protocols.docking.DockingLowRes, rot_magnitude: float) None ¶
C++: protocols::docking::DockingLowRes::set_rot_magnitude(double) –> void
- set_scorefxn(self: pyrosetta.rosetta.protocols.docking.DockingLowRes, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) None ¶
C++: protocols::docking::DockingLowRes::set_scorefxn(class std::shared_ptr<const class core::scoring::ScoreFunction>) –> void
- set_trans_magnitude(self: pyrosetta.rosetta.protocols.docking.DockingLowRes, trans_magnitude: float) None ¶
C++: protocols::docking::DockingLowRes::set_trans_magnitude(double) –> void
- set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) None ¶
Set the ‘type’ string
C++: protocols::moves::Mover::set_type(const std::string &) –> void
- show(*args, **kwargs)¶
Overloaded function.
show(self: pyrosetta.rosetta.protocols.docking.DockingLowResEnsemble) -> None
show(self: pyrosetta.rosetta.protocols.docking.DockingLowResEnsemble, out: pyrosetta.rosetta.std.ostream) -> None
C++: protocols::docking::DockingLowResEnsemble::show(std::ostream &) const –> void
- sync_magnitudes_with_flags(self: pyrosetta.rosetta.protocols.docking.DockingLowRes) None ¶
C++: protocols::docking::DockingLowRes::sync_magnitudes_with_flags() –> void
- sync_objects_with_flags(self: pyrosetta.rosetta.protocols.docking.DockingLowRes) None ¶
Instantiates non-primitive members based on the value of the primitive members
C++: protocols::docking::DockingLowRes::sync_objects_with_flags() –> 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
- try_all_conformers(self: pyrosetta.rosetta.protocols.docking.DockingLowResEnsemble, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::docking::DockingLowResEnsemble::try_all_conformers(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.docking.DockingLowResFilter¶
Bases:
Filter
Low-resolution (centroid-mode) filter for docking. Checks (1) at least some contact is being made between docking partners,
clashes are limited so partners are not overlapping
and (3) constraints, if present, are met
- apply(self: pyrosetta.rosetta.protocols.docking.DockingLowResFilter, pose: pyrosetta.rosetta.core.pose.Pose) bool ¶
add docking constraints
C++: protocols::docking::DockingLowResFilter::apply(const class core::pose::Pose &) const –> bool
- clear(self: pyrosetta.rosetta.protocols.filters.Filter) None ¶
used to clear internal variables if needed. Using fresh_instance is preferred since it’s a pure virtual
C++: protocols::filters::Filter::clear() –> void
- clone(self: pyrosetta.rosetta.protocols.docking.DockingLowResFilter) pyrosetta.rosetta.protocols.filters.Filter ¶
C++: protocols::docking::DockingLowResFilter::clone() const –> class std::shared_ptr<class protocols::filters::Filter>
- fresh_instance(self: pyrosetta.rosetta.protocols.docking.DockingLowResFilter) pyrosetta.rosetta.protocols.filters.Filter ¶
C++: protocols::docking::DockingLowResFilter::fresh_instance() const –> class std::shared_ptr<class protocols::filters::Filter>
- get_type(self: pyrosetta.rosetta.protocols.filters.Filter) str ¶
C++: protocols::filters::Filter::get_type() const –> std::string
- get_user_defined_name(self: pyrosetta.rosetta.protocols.filters.Filter) str ¶
C++: protocols::filters::Filter::get_user_defined_name() const –> std::string
- name(self: pyrosetta.rosetta.protocols.filters.Filter) str ¶
C++: protocols::filters::Filter::name() const –> std::string
- parse_my_tag(self: pyrosetta.rosetta.protocols.filters.Filter, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None ¶
Called by FilterFactory when constructing new Filter. Takes care of the specific mover’s parsing.
C++: protocols::filters::Filter::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- provide_citation_info(self: pyrosetta.rosetta.protocols.filters.Filter, : 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 filters wishing to provide citation information.
C++: protocols::filters::Filter::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void
- report(self: pyrosetta.rosetta.protocols.docking.DockingLowResFilter, out: pyrosetta.rosetta.std.ostream, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::docking::DockingLowResFilter::report(std::ostream &, const class core::pose::Pose &) const –> void
- report_sm(self: pyrosetta.rosetta.protocols.filters.Filter, : pyrosetta.rosetta.core.pose.Pose) float ¶
C++: protocols::filters::Filter::report_sm(const class core::pose::Pose &) const –> double
- score(self: pyrosetta.rosetta.protocols.filters.Filter, pose: pyrosetta.rosetta.core.pose.Pose) float ¶
C++: protocols::filters::Filter::score(class core::pose::Pose &) –> double
- set_use_constraints(*args, **kwargs)¶
Overloaded function.
set_use_constraints(self: pyrosetta.rosetta.protocols.docking.DockingLowResFilter, flag: bool) -> None
set_use_constraints(self: pyrosetta.rosetta.protocols.docking.DockingLowResFilter, flag: bool, cutoff: float) -> None
C++: protocols::docking::DockingLowResFilter::set_use_constraints(bool, double) –> void
- set_user_defined_name(self: pyrosetta.rosetta.protocols.filters.Filter, name: str) None ¶
C++: protocols::filters::Filter::set_user_defined_name(const std::string &) –> void
- class pyrosetta.rosetta.protocols.docking.DockingPrepackProtocol¶
Bases:
DockingHighRes
- add_additional_task_operaration(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, task_operation: pyrosetta.rosetta.core.pack.task.operation.TaskOperation) None ¶
C++: protocols::docking::DockingHighRes::add_additional_task_operaration(class std::shared_ptr<class core::pack::task::operation::TaskOperation>) –> void
- apply(self: pyrosetta.rosetta.protocols.docking.DockingPrepackProtocol, : pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::docking::DockingPrepackProtocol::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.docking.DockingPrepackProtocol, : pyrosetta.rosetta.protocols.docking.DockingPrepackProtocol) pyrosetta.rosetta.protocols.docking.DockingPrepackProtocol ¶
C++: protocols::docking::DockingPrepackProtocol::operator=(const class protocols::docking::DockingPrepackProtocol &) –> class protocols::docking::DockingPrepackProtocol &
- clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) None ¶
Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.
clear_info is called by jd2 before calling apply
C++: protocols::moves::Mover::clear_info() –> void
- clone(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
Return a clone of the Mover object.
C++: protocols::moves::Mover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>
- create(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>
- fresh_instance(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
Generates a new Mover object freshly created with the default ctor.
C++: protocols::moves::Mover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>
- get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose ¶
fpd
Mechanism by which a mover may return multiple output poses from a single input pose.
Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.
C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>
- get_additional_task_operarations(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_task_operation_TaskOperation_t ¶
C++: protocols::docking::DockingHighRes::get_additional_task_operarations() –> class utility::vector1<class std::shared_ptr<class core::pack::task::operation::TaskOperation>, class std::allocator<class std::shared_ptr<class core::pack::task::operation::TaskOperation> > >
- 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.docking.DockingPrepackProtocol) str ¶
C++: protocols::docking::DockingPrepackProtocol::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_partners(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) str ¶
C++: protocols::docking::DockingHighRes::get_partners() const –> std::string
- get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>
- get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t ¶
C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>
- get_type(self: pyrosetta.rosetta.protocols.moves.Mover) str ¶
C++: protocols::moves::Mover::get_type() const –> std::string
- ignore_default_task(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) bool ¶
C++: protocols::docking::DockingHighRes::ignore_default_task() –> bool
- info(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.list_std_string_t ¶
non-const accessor
C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &
- last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) float ¶
C++: protocols::moves::Mover::last_proposal_density_ratio() –> double
- movable_jumps(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) pyrosetta.rosetta.utility.vector1_int ¶
C++: protocols::docking::DockingHighRes::movable_jumps() –> class utility::vector1<int, class std::allocator<int> > &
- static mover_name() str ¶
C++: protocols::docking::DockingPrepackProtocol::mover_name() –> std::string
- static name() str ¶
C++: protocols::moves::Mover::name() –> std::string
- parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None ¶
Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.
C++: protocols::moves::Mover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- partners(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) str ¶
C++: protocols::docking::DockingHighRes::partners() –> std::string
- provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None ¶
- Provide citations to the passed CitationCollectionList
Subclasses should add the info for themselves and any other classes they use.
The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.
C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void
- static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None ¶
C++: protocols::docking::DockingPrepackProtocol::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
- rt_min(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) bool ¶
C++: protocols::docking::DockingHighRes::rt_min() –> bool
- sc_min(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) bool ¶
C++: protocols::docking::DockingHighRes::sc_min() –> bool
- score_and_output(self: pyrosetta.rosetta.protocols.docking.DockingPrepackProtocol, filename: str, : pyrosetta.rosetta.core.pose.Pose) None ¶
Scores and outputs the pose - jd2 compatible.
C++: protocols::docking::DockingPrepackProtocol::score_and_output(std::string, class core::pose::Pose &) –> void
- scorefxn(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) pyrosetta.rosetta.core.scoring.ScoreFunction ¶
C++: protocols::docking::DockingHighRes::scorefxn() const –> class std::shared_ptr<class core::scoring::ScoreFunction>
- scorefxn_pack(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) pyrosetta.rosetta.core.scoring.ScoreFunction ¶
C++: protocols::docking::DockingHighRes::scorefxn_pack() const –> class std::shared_ptr<class core::scoring::ScoreFunction>
- set_additional_task_operarations(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, additional_task_operations: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_task_operation_TaskOperation_t) None ¶
C++: protocols::docking::DockingHighRes::set_additional_task_operarations(class utility::vector1<class std::shared_ptr<class core::pack::task::operation::TaskOperation>, class std::allocator<class std::shared_ptr<class core::pack::task::operation::TaskOperation> > >) –> 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_dock_ppk(self: pyrosetta.rosetta.protocols.docking.DockingPrepackProtocol, dock_ppk: bool) None ¶
C++: protocols::docking::DockingPrepackProtocol::set_dock_ppk(bool) –> void
- set_ignore_default_task(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, ignore_default_task: bool) None ¶
C++: protocols::docking::DockingHighRes::set_ignore_default_task(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_interface_definition_task_operation(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, interface_definition: protocols::simple_task_operations::InterfaceTaskOperation) None ¶
C++: protocols::docking::DockingHighRes::set_interface_definition_task_operation(class std::shared_ptr<class protocols::simple_task_operations::InterfaceTaskOperation>) –> void
- set_movable_jumps(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, movable_jumps: pyrosetta.rosetta.utility.vector1_int) None ¶
C++: protocols::docking::DockingHighRes::set_movable_jumps(class utility::vector1<int, class std::allocator<int> >) –> 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_partners(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, partners: str) None ¶
C++: protocols::docking::DockingHighRes::set_partners(std::string) –> void
- set_rt_min(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, rt_min: bool) None ¶
C++: protocols::docking::DockingHighRes::set_rt_min(bool) –> void
- set_sc_min(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, sc_min: bool) None ¶
C++: protocols::docking::DockingHighRes::set_sc_min(bool) –> void
- set_scorefxn(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) None ¶
C++: protocols::docking::DockingHighRes::set_scorefxn(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void
- set_scorefxn_pack(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, scorefxn_pack: pyrosetta.rosetta.core.scoring.ScoreFunction) None ¶
C++: protocols::docking::DockingHighRes::set_scorefxn_pack(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void
- set_task_factory(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, tf: pyrosetta.rosetta.core.pack.task.TaskFactory) None ¶
C++: protocols::docking::DockingHighRes::set_task_factory(class std::shared_ptr<const class core::pack::task::TaskFactory>) –> void
- set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) None ¶
Set the ‘type’ string
C++: protocols::moves::Mover::set_type(const std::string &) –> void
- setup_defaults(self: pyrosetta.rosetta.protocols.docking.DockingPrepackProtocol) None ¶
Assigns default values to members
C++: protocols::docking::DockingPrepackProtocol::setup_defaults() –> void
- setup_pack_operation_movers(self: pyrosetta.rosetta.protocols.docking.DockingPrepackProtocol) None ¶
Instantiates and configures movers used by DockingPrepackProtocol
C++: protocols::docking::DockingPrepackProtocol::setup_pack_operation_movers() –> void
- show(*args, **kwargs)¶
Overloaded function.
show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None
Outputs details about the Mover, including current settings.
C++: protocols::moves::Mover::show(std::ostream &) const –> void
- task_factory(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) pyrosetta.rosetta.core.pack.task.TaskFactory ¶
C++: protocols::docking::DockingHighRes::task_factory() –> class std::shared_ptr<const class core::pack::task::TaskFactory>
- 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.docking.DockingPrepackProtocolCreator¶
Bases:
MoverCreator
- assign(self: pyrosetta.rosetta.protocols.docking.DockingPrepackProtocolCreator, : pyrosetta.rosetta.protocols.docking.DockingPrepackProtocolCreator) pyrosetta.rosetta.protocols.docking.DockingPrepackProtocolCreator ¶
C++: protocols::docking::DockingPrepackProtocolCreator::operator=(const class protocols::docking::DockingPrepackProtocolCreator &) –> class protocols::docking::DockingPrepackProtocolCreator &
- create_mover(self: pyrosetta.rosetta.protocols.docking.DockingPrepackProtocolCreator) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::docking::DockingPrepackProtocolCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>
- keyname(self: pyrosetta.rosetta.protocols.docking.DockingPrepackProtocolCreator) str ¶
C++: protocols::docking::DockingPrepackProtocolCreator::keyname() const –> std::string
- class pyrosetta.rosetta.protocols.docking.DockingProtocol¶
Bases:
Mover
This is the standard RosettaDock protocol
RosettaDock protocol based on [refs…Gray2003, Wang2005, Chaudhury 2007 … ]
- add_additional_low_resolution_step(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, additional_low_resolution_mover: pyrosetta.rosetta.protocols.moves.Mover) None ¶
C++: protocols::docking::DockingProtocol::add_additional_low_resolution_step(class std::shared_ptr<class protocols::moves::Mover>) –> void
- add_additional_task_operaration(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, task_operation: pyrosetta.rosetta.core.pack.task.operation.TaskOperation) None ¶
C++: protocols::docking::DockingProtocol::add_additional_task_operaration(class std::shared_ptr<class core::pack::task::operation::TaskOperation>) –> void
- add_jump(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, jump_number: int) None ¶
C++: protocols::docking::DockingProtocol::add_jump(const unsigned long) –> void
- apply(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::docking::DockingProtocol::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, rhs: pyrosetta.rosetta.protocols.docking.DockingProtocol) pyrosetta.rosetta.protocols.docking.DockingProtocol ¶
assignment operator
C++: protocols::docking::DockingProtocol::operator=(const class protocols::docking::DockingProtocol &) –> class protocols::docking::DockingProtocol &
- 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.docking.DockingProtocol) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::docking::DockingProtocol::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>
- docking_highres_mover(self: pyrosetta.rosetta.protocols.docking.DockingProtocol) pyrosetta.rosetta.protocols.docking.DockingHighRes ¶
C++: protocols::docking::DockingProtocol::docking_highres_mover() const –> class std::shared_ptr<const class protocols::docking::DockingHighRes>
- docking_lowres_mover(self: pyrosetta.rosetta.protocols.docking.DockingProtocol) pyrosetta.rosetta.protocols.docking.DockingLowRes ¶
C++: protocols::docking::DockingProtocol::docking_lowres_mover() const –> class std::shared_ptr<const class protocols::docking::DockingLowRes>
- fresh_instance(self: pyrosetta.rosetta.protocols.docking.DockingProtocol) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::docking::DockingProtocol::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_additional_task_operarations(self: pyrosetta.rosetta.protocols.docking.DockingProtocol) pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_task_operation_TaskOperation_t ¶
C++: protocols::docking::DockingProtocol::get_additional_task_operarations() –> class utility::vector1<class std::shared_ptr<class core::pack::task::operation::TaskOperation>, class std::allocator<class std::shared_ptr<class core::pack::task::operation::TaskOperation> > >
- 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_highres_scorefxn(self: pyrosetta.rosetta.protocols.docking.DockingProtocol) pyrosetta.rosetta.core.scoring.ScoreFunction ¶
C++: protocols::docking::DockingProtocol::get_highres_scorefxn() const –> class std::shared_ptr<const class core::scoring::ScoreFunction>
- 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.docking.DockingProtocol) str ¶
C++: protocols::docking::DockingProtocol::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
- movable_jumps(self: pyrosetta.rosetta.protocols.docking.DockingProtocol) pyrosetta.rosetta.utility.vector1_int ¶
returns ref to the jumps vector for docking
C++: protocols::docking::DockingProtocol::movable_jumps() –> class utility::vector1<int, class std::allocator<int> > &
- static mover_name() str ¶
C++: protocols::docking::DockingProtocol::mover_name() –> std::string
- static name() str ¶
C++: protocols::moves::Mover::name() –> std::string
- parse_my_tag(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None ¶
C++: protocols::docking::DockingProtocol::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- partners(self: pyrosetta.rosetta.protocols.docking.DockingProtocol) str ¶
returns the docking partners chain identifiers
C++: protocols::docking::DockingProtocol::partners() const –> std::string
- perturber(self: pyrosetta.rosetta.protocols.docking.DockingProtocol) pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation ¶
C++: protocols::docking::DockingProtocol::perturber() const –> class std::shared_ptr<const class protocols::docking::DockingInitialPerturbation>
- provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None ¶
- Provide citations to the passed CitationCollectionList
Subclasses should add the info for themselves and any other classes they use.
The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.
C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void
- static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None ¶
C++: protocols::docking::DockingProtocol::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void
- static register_options() None ¶
Associates relevant options with the DockingProtocol class
C++: protocols::docking::DockingProtocol::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.docking.DockingProtocol) bool ¶
This mover retains state such that a fresh version is needed if the input Pose is about to change
C++: protocols::docking::DockingProtocol::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_additional_task_operarations(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, additional_task_operations: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_task_operation_TaskOperation_t) None ¶
C++: protocols::docking::DockingProtocol::set_additional_task_operarations(class utility::vector1<class std::shared_ptr<class core::pack::task::operation::TaskOperation>, class std::allocator<class std::shared_ptr<class core::pack::task::operation::TaskOperation> > >) –> void
- set_autofoldtree(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, autofoldtree: bool) None ¶
C++: protocols::docking::DockingProtocol::set_autofoldtree(const bool) –> void
- set_cst_weight(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, cst_weight: float) None ¶
C++: protocols::docking::DockingProtocol::set_cst_weight(const 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_default(self: pyrosetta.rosetta.protocols.docking.DockingProtocol) None ¶
Assigns default values to primitive members
C++: protocols::docking::DockingProtocol::set_default() –> void
- set_design(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, design: bool) None ¶
C++: protocols::docking::DockingProtocol::set_design(const bool) –> void
- set_dock_min(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, dock_min: bool) None ¶
C++: protocols::docking::DockingProtocol::set_dock_min(const bool) –> void
- set_docking_highres_mover(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, docking_highres_mover: pyrosetta.rosetta.protocols.docking.DockingHighRes) None ¶
C++: protocols::docking::DockingProtocol::set_docking_highres_mover(class std::shared_ptr<class protocols::docking::DockingHighRes>) –> void
- set_docking_local_refine(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, docking_local_refine: bool) None ¶
C++: protocols::docking::DockingProtocol::set_docking_local_refine(const bool) –> void
- set_ensemble1(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, ensemble1: str) None ¶
C++: protocols::docking::DockingProtocol::set_ensemble1(const std::string &) –> void
- set_ensemble2(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, ensemble2: str) None ¶
C++: protocols::docking::DockingProtocol::set_ensemble2(const std::string &) –> void
- set_highres_scorefxn(*args, **kwargs)¶
Overloaded function.
set_highres_scorefxn(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, docking_scorefxn_high: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None
- Sets the score function that will be used in the high-resolution phase.
The same score function will be used for evaluating moves, packing and discriminating
C++: protocols::docking::DockingProtocol::set_highres_scorefxn(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void
set_highres_scorefxn(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, docking_scorefxn_high: pyrosetta.rosetta.core.scoring.ScoreFunction, docking_scorefxn_pack: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None
- Sets the score function that will be used in the high-resolution phase.
The first scorefunction will be used for evaluating moves and discriminating, the second will be used for packing
C++: protocols::docking::DockingProtocol::set_highres_scorefxn(class std::shared_ptr<class core::scoring::ScoreFunction>, class std::shared_ptr<class core::scoring::ScoreFunction>) –> void
set_highres_scorefxn(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, docking_scorefxn_high: pyrosetta.rosetta.core.scoring.ScoreFunction, docking_scorefxn_pack: pyrosetta.rosetta.core.scoring.ScoreFunction, docking_scorefxn_output: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None
- Sets the score function that will be used in the high-resolution phase.
The first scorefunction will be used for evaluating moves, the second will be used for packing and the third for discriminating
C++: protocols::docking::DockingProtocol::set_highres_scorefxn(class std::shared_ptr<class core::scoring::ScoreFunction>, class std::shared_ptr<class core::scoring::ScoreFunction>, class std::shared_ptr<class core::scoring::ScoreFunction>) –> void
- set_ignore_default_docking_task(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, ignore_default_docking_task: bool) None ¶
C++: protocols::docking::DockingProtocol::set_ignore_default_docking_task(const bool) –> void
- set_inner_cycles(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, inner_cycles: int) None ¶
C++: protocols::docking::DockingProtocol::set_inner_cycles(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_interface_definition_task_operation(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, interface_definition: protocols::simple_task_operations::InterfaceTaskOperation) None ¶
C++: protocols::docking::DockingProtocol::set_interface_definition_task_operation(class std::shared_ptr<class protocols::simple_task_operations::InterfaceTaskOperation>) –> void
- set_low_res_protocol_only(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, low_res_protocol_only: bool) None ¶
C++: protocols::docking::DockingProtocol::set_low_res_protocol_only(const bool) –> void
- set_lowres_scorefxn(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, docking_scorefxn_low: pyrosetta.rosetta.core.scoring.ScoreFunction) None ¶
Sets the score function that will be used in the low-resolution phase
C++: protocols::docking::DockingProtocol::set_lowres_scorefxn(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void
- set_movable_jumps(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, jump_numbers: pyrosetta.rosetta.utility.vector1_int) None ¶
C++: protocols::docking::DockingProtocol::set_movable_jumps(const class utility::vector1<int, class std::allocator<int> >) –> void
- set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe
C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void
- set_no_filters(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, no_filters: bool) None ¶
C++: protocols::docking::DockingProtocol::set_no_filters(bool) –> void
- set_outer_cycles(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, outer_cycles: int) None ¶
C++: protocols::docking::DockingProtocol::set_outer_cycles(unsigned long) –> void
- set_partners(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, partners: str) None ¶
C++: protocols::docking::DockingProtocol::set_partners(const std::string &) –> void
- set_recover_sidechains_filename(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, file: str) None ¶
C++: protocols::docking::DockingProtocol::set_recover_sidechains_filename(const std::string &) –> void
- set_reporting(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, report: bool) None ¶
C++: protocols::docking::DockingProtocol::set_reporting(bool) –> void
- set_rt_min(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, rt_min: bool) None ¶
C++: protocols::docking::DockingProtocol::set_rt_min(bool) –> void
- set_sc_min(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, sc_min: bool) None ¶
C++: protocols::docking::DockingProtocol::set_sc_min(bool) –> void
- set_task_factory(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, task_factory: pyrosetta.rosetta.core.pack.task.TaskFactory) None ¶
C++: protocols::docking::DockingProtocol::set_task_factory(class std::shared_ptr<class core::pack::task::TaskFactory>) –> void
- set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) None ¶
Set the ‘type’ string
C++: protocols::moves::Mover::set_type(const std::string &) –> void
- set_use_constraints(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, use_csts: bool) None ¶
C++: protocols::docking::DockingProtocol::set_use_constraints(const bool) –> void
- set_use_legacy_protocol(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, use_legacy_protocol: bool) None ¶
C++: protocols::docking::DockingProtocol::set_use_legacy_protocol(const bool) –> void
- show(*args, **kwargs)¶
Overloaded function.
show(self: pyrosetta.rosetta.protocols.docking.DockingProtocol) -> None
show(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, out: pyrosetta.rosetta.std.ostream) -> None
C++: protocols::docking::DockingProtocol::show(std::ostream &) const –> void
- sync_objects_with_flags(self: pyrosetta.rosetta.protocols.docking.DockingProtocol) None ¶
Instantiates non-primitive members based on the value of the primitive members
C++: protocols::docking::DockingProtocol::sync_objects_with_flags() –> void
- task_factory(self: pyrosetta.rosetta.protocols.docking.DockingProtocol) pyrosetta.rosetta.core.pack.task.TaskFactory ¶
C++: protocols::docking::DockingProtocol::task_factory() –> const class core::pack::task::TaskFactory &
- 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
- to_all_atom(self: pyrosetta.rosetta.protocols.docking.DockingProtocol) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::docking::DockingProtocol::to_all_atom() const –> class std::shared_ptr<const class protocols::moves::Mover>
- to_centroid(self: pyrosetta.rosetta.protocols.docking.DockingProtocol) protocols::simple_moves::SwitchResidueTypeSetMover ¶
C++: protocols::docking::DockingProtocol::to_centroid() const –> class std::shared_ptr<const class protocols::simple_moves::SwitchResidueTypeSetMover>
- 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.docking.DockingProtocolCreator¶
Bases:
MoverCreator
- assign(self: pyrosetta.rosetta.protocols.docking.DockingProtocolCreator, : pyrosetta.rosetta.protocols.docking.DockingProtocolCreator) pyrosetta.rosetta.protocols.docking.DockingProtocolCreator ¶
C++: protocols::docking::DockingProtocolCreator::operator=(const class protocols::docking::DockingProtocolCreator &) –> class protocols::docking::DockingProtocolCreator &
- create_mover(self: pyrosetta.rosetta.protocols.docking.DockingProtocolCreator) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::docking::DockingProtocolCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>
- keyname(self: pyrosetta.rosetta.protocols.docking.DockingProtocolCreator) str ¶
C++: protocols::docking::DockingProtocolCreator::keyname() const –> std::string
- class pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact¶
Bases:
Mover
Contrary to the name, slides things apart first, then together. OK for proteins, bad for ligands (because they may escape the pocket permanently).
- apply(self: pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::docking::DockingSlideIntoContact::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact, : pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact) pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact ¶
C++: protocols::docking::DockingSlideIntoContact::operator=(const class protocols::docking::DockingSlideIntoContact &) –> class protocols::docking::DockingSlideIntoContact &
- 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.docking.DockingSlideIntoContact) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::docking::DockingSlideIntoContact::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.docking.DockingSlideIntoContact) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::docking::DockingSlideIntoContact::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_jump_num(self: pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact) int ¶
C++: protocols::docking::DockingSlideIntoContact::get_jump_num() const –> unsigned long
- 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.docking.DockingSlideIntoContact) str ¶
C++: protocols::docking::DockingSlideIntoContact::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::docking::DockingSlideIntoContact::mover_name() –> std::string
- static name() str ¶
C++: protocols::moves::Mover::name() –> std::string
- parse_my_tag(self: pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None ¶
C++: protocols::docking::DockingSlideIntoContact::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None ¶
- Provide citations to the passed CitationCollectionList
Subclasses should add the info for themselves and any other classes they use.
The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.
C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void
- static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None ¶
C++: protocols::docking::DockingSlideIntoContact::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
- set_use_delta(self: pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact, setting: bool) None ¶
C++: protocols::docking::DockingSlideIntoContact::set_use_delta(bool) –> void
- show(*args, **kwargs)¶
Overloaded function.
show(self: pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact) -> None
show(self: pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact, output: pyrosetta.rosetta.std.ostream) -> None
C++: protocols::docking::DockingSlideIntoContact::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.docking.DockingSlideIntoContactCreator¶
Bases:
MoverCreator
- assign(self: pyrosetta.rosetta.protocols.docking.DockingSlideIntoContactCreator, : pyrosetta.rosetta.protocols.docking.DockingSlideIntoContactCreator) pyrosetta.rosetta.protocols.docking.DockingSlideIntoContactCreator ¶
C++: protocols::docking::DockingSlideIntoContactCreator::operator=(const class protocols::docking::DockingSlideIntoContactCreator &) –> class protocols::docking::DockingSlideIntoContactCreator &
- create_mover(self: pyrosetta.rosetta.protocols.docking.DockingSlideIntoContactCreator) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::docking::DockingSlideIntoContactCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>
- keyname(self: pyrosetta.rosetta.protocols.docking.DockingSlideIntoContactCreator) str ¶
C++: protocols::docking::DockingSlideIntoContactCreator::keyname() const –> std::string
- class pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover¶
Bases:
Mover
This mover approximates one docking partner as an ellipsoid and docks the other partner along a random normal to said ellipsoid; sliding the partners into contact is necessary to complete this docking move.
- apply(self: pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover, : pyrosetta.rosetta.core.pose.Pose) None ¶
Applies EllipsoidalRandomizationMover mover.
C++: protocols::docking::EllipsoidalRandomizationMover::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover, : pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover) pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover ¶
C++: protocols::docking::EllipsoidalRandomizationMover::operator=(const class protocols::docking::EllipsoidalRandomizationMover &) –> class protocols::docking::EllipsoidalRandomizationMover &
- calculate_axes(self: pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover, : pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.numeric.xyzMatrix_double_t ¶
Calculates ellipsoid axes from atomic coordinates.
C++: protocols::docking::EllipsoidalRandomizationMover::calculate_axes(class core::pose::Pose &) –> class numeric::xyzMatrix<double>
- calculate_geometry(self: pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover, : pyrosetta.rosetta.core.pose.Pose) Tuple[pyrosetta.rosetta.numeric.xyzMatrix_double_t, pyrosetta.rosetta.numeric.xyzVector_double_t] ¶
Defines geometry required for docking move.
C++: protocols::docking::EllipsoidalRandomizationMover::calculate_geometry(class core::pose::Pose &) –> struct std::pair<class numeric::xyzMatrix<double>, class numeric::xyzVector<double> >
- calculate_plane_axes(self: pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover, : pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.utility.vector1_numeric_xyzVector_double_t ¶
Calculates two vectors defining a plane at the docking interface.
C++: protocols::docking::EllipsoidalRandomizationMover::calculate_plane_axes(class core::pose::Pose &) –> class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > >
- 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.docking.EllipsoidalRandomizationMover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::docking::EllipsoidalRandomizationMover::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.docking.EllipsoidalRandomizationMover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::docking::EllipsoidalRandomizationMover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>
- get_a_axis(self: pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover) float ¶
C++: protocols::docking::EllipsoidalRandomizationMover::get_a_axis() const –> double
- 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_b_axis(self: pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover) float ¶
C++: protocols::docking::EllipsoidalRandomizationMover::get_b_axis() const –> double
- get_c_axis(self: pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover) float ¶
C++: protocols::docking::EllipsoidalRandomizationMover::get_c_axis() 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_interface_residues(self: pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover, pose_in: pyrosetta.rosetta.core.pose.Pose, interface_distence_cutoff: float, autofoldtree: bool) pyrosetta.rosetta.utility.vector1_bool ¶
Identifies residues at interface of docking partners.
C++: protocols::docking::EllipsoidalRandomizationMover::get_interface_residues(class core::pose::Pose &, double, bool) –> class utility::vector1<bool, class std::allocator<bool> >
- 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.docking.EllipsoidalRandomizationMover) str ¶
Returns mover name.
C++: protocols::docking::EllipsoidalRandomizationMover::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_nbr_atom_centroid(self: pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover) pyrosetta.rosetta.numeric.xyzVector_double_t ¶
C++: protocols::docking::EllipsoidalRandomizationMover::get_nbr_atom_centroid() const –> class numeric::xyzVector<double>
- get_nbr_atom_non_ellipsoid_centroid(self: pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover) pyrosetta.rosetta.numeric.xyzVector_double_t ¶
C++: protocols::docking::EllipsoidalRandomizationMover::get_nbr_atom_non_ellipsoid_centroid() const –> class numeric::xyzVector<double>
- get_normal_to_plane(self: pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover) pyrosetta.rosetta.numeric.xyzVector_double_t ¶
C++: protocols::docking::EllipsoidalRandomizationMover::get_normal_to_plane() const –> class numeric::xyzVector<double>
- get_partner_residue_start_stop(self: pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover, : pyrosetta.rosetta.core.pose.Pose, : bool) pyrosetta.rosetta.utility.vector1_unsigned_long ¶
Identifies first and last residues of a docking partner.
C++: protocols::docking::EllipsoidalRandomizationMover::get_partner_residue_start_stop(class core::pose::Pose &, bool) –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >
- get_random_point_on_ellipsoid(self: pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover) pyrosetta.rosetta.numeric.xyzVector_double_t ¶
C++: protocols::docking::EllipsoidalRandomizationMover::get_random_point_on_ellipsoid() const –> class numeric::xyzVector<double>
- get_rotation_matrix(self: pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover, : pyrosetta.rosetta.numeric.xyzVector_double_t, : pyrosetta.rosetta.numeric.xyzVector_double_t) pyrosetta.rosetta.numeric.xyzMatrix_double_t ¶
Calculates a rotation matrix to superimpose source vector to target vector.
C++: protocols::docking::EllipsoidalRandomizationMover::get_rotation_matrix(class numeric::xyzVector<double>, class numeric::xyzVector<double>) –> class numeric::xyzMatrix<double>
- 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_slide_axis(self: pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover) pyrosetta.rosetta.numeric.xyzVector_double_t ¶
Get the axis for sliding partners into contact.
C++: protocols::docking::EllipsoidalRandomizationMover::get_slide_axis() const –> class numeric::xyzVector<double>
- get_spin_center(self: pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover) pyrosetta.rosetta.numeric.xyzVector_double_t ¶
Get the point about which to spin the docking partner.
C++: protocols::docking::EllipsoidalRandomizationMover::get_spin_center() const –> class numeric::xyzVector<double>
- get_type(self: pyrosetta.rosetta.protocols.moves.Mover) str ¶
C++: protocols::moves::Mover::get_type() const –> std::string
- info(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.list_std_string_t ¶
non-const accessor
C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &
- init_from_options(self: pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover) None ¶
Initializes data members from options.
C++: protocols::docking::EllipsoidalRandomizationMover::init_from_options() –> void
- inward_normal_to_plane(self: pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover, : pyrosetta.rosetta.utility.vector1_numeric_xyzVector_double_t) pyrosetta.rosetta.numeric.xyzVector_double_t ¶
Calculates normal vector from a plane at the docking interface.
C++: protocols::docking::EllipsoidalRandomizationMover::inward_normal_to_plane(class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > >) –> class numeric::xyzVector<double>
- 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
- normal_to_ellipsoid(self: pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover, : pyrosetta.rosetta.numeric.xyzVector_double_t) pyrosetta.rosetta.numeric.xyzVector_double_t ¶
Calculates normal vector to a point on ellipsoid.
C++: protocols::docking::EllipsoidalRandomizationMover::normal_to_ellipsoid(class numeric::xyzVector<double>) –> class numeric::xyzVector<double>
- 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
- point_on_ellipsoid(self: pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover, : pyrosetta.rosetta.numeric.xyzMatrix_double_t) pyrosetta.rosetta.numeric.xyzVector_double_t ¶
Selects a random point on ellipsoid surface.
C++: protocols::docking::EllipsoidalRandomizationMover::point_on_ellipsoid(class numeric::xyzMatrix<double>) –> class numeric::xyzVector<double>
- 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
- recalculate_z_coordinate(self: pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover, : pyrosetta.rosetta.numeric.xyzVector_double_t) float ¶
Calculates 3rd coordinate of a point on ellipsoid surface given first 2 coordinates.
C++: protocols::docking::EllipsoidalRandomizationMover::recalculate_z_coordinate(class numeric::xyzVector<double>) –> double
- 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_default(self: pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover) None ¶
Sets up the default values for the object including the movemap and minimization type.
C++: protocols::docking::EllipsoidalRandomizationMover::set_default() –> void
- set_foldtree(self: pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover, : pyrosetta.rosetta.core.pose.Pose) None ¶
Sets pose fold tree based on -partners flag.
C++: protocols::docking::EllipsoidalRandomizationMover::set_foldtree(class core::pose::Pose &) –> 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_partners(self: pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover, : str) None ¶
Set the partners_ string.
C++: protocols::docking::EllipsoidalRandomizationMover::set_partners(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.docking.EllipsoidalRandomizationMover) -> None
show(self: pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover, output: pyrosetta.rosetta.std.ostream) -> None
Generates string representation of EllipsoidalRandomizationMover.
C++: protocols::docking::EllipsoidalRandomizationMover::show(std::ostream &) const –> void
- single_beta_sample(self: pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover, : float, : float) float ¶
Returns a sample from a beta distribution.
C++: protocols::docking::EllipsoidalRandomizationMover::single_beta_sample(double, double) –> double
- 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 &
Bases:
Mover
C++: protocols::docking::EnsureExclusivelySharedJumpMover::apply(class core::pose::Pose &) –> void
C++: protocols::docking::EnsureExclusivelySharedJumpMover::operator=(const class protocols::docking::EnsureExclusivelySharedJumpMover &) –> class protocols::docking::EnsureExclusivelySharedJumpMover &
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
C++: protocols::docking::EnsureExclusivelySharedJumpMover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>
C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>
C++: protocols::docking::EnsureExclusivelySharedJumpMover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>
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>
C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>
- 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
C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>
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
C++: protocols::docking::EnsureExclusivelySharedJumpMover::get_name() const –> std::string
C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>
C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>
C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>
C++: protocols::moves::Mover::get_type() const –> std::string
non-const accessor
C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &
C++: protocols::moves::Mover::last_proposal_density_ratio() –> double
C++: protocols::docking::EnsureExclusivelySharedJumpMover::mover_name() –> std::string
C++: protocols::moves::Mover::name() –> std::string
C++: protocols::docking::EnsureExclusivelySharedJumpMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- 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
C++: protocols::docking::EnsureExclusivelySharedJumpMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void
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
- 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
- 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
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
ExclusivelySharedJumpSelector selects the jump that builds ALL and ONLY the residues selected by this selector (getter)
C++: protocols::docking::EnsureExclusivelySharedJumpMover::selector() const –> class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>
C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void
C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void
setter for poses contained for rms
C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void
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
ExclusivelySharedJumpSelector selects the jump that builds ALL and ONLY the residues selected by this selector (setter)
C++: protocols::docking::EnsureExclusivelySharedJumpMover::set_selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void
Set the ‘type’ string
C++: protocols::moves::Mover::set_type(const std::string &) –> void
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
- : 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
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 &
Bases:
MoverCreator
C++: protocols::docking::EnsureExclusivelySharedJumpMoverCreator::operator=(const class protocols::docking::EnsureExclusivelySharedJumpMoverCreator &) –> class protocols::docking::EnsureExclusivelySharedJumpMoverCreator &
C++: protocols::docking::EnsureExclusivelySharedJumpMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>
C++: protocols::docking::EnsureExclusivelySharedJumpMoverCreator::keyname() const –> std::string
C++: protocols::docking::EnsureExclusivelySharedJumpMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void
- class pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact¶
Bases:
Mover
Slides docking partners together by monitoring fa_rep.
If partners are already touching, no change is made. Separation will be 1A or less after calling this function.
- apply(self: pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::docking::FaDockingSlideIntoContact::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact, : pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact) pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact ¶
C++: protocols::docking::FaDockingSlideIntoContact::operator=(const class protocols::docking::FaDockingSlideIntoContact &) –> class protocols::docking::FaDockingSlideIntoContact &
- clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) None ¶
Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.
clear_info is called by jd2 before calling apply
C++: protocols::moves::Mover::clear_info() –> void
- clone(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
Return a clone of the Mover object.
C++: protocols::moves::Mover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>
- create(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>
- fresh_instance(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
Generates a new Mover object freshly created with the default ctor.
C++: protocols::moves::Mover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>
- get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose ¶
fpd
Mechanism by which a mover may return multiple output poses from a single input pose.
Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.
C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>
- get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) protocols::jobdist::BasicJob ¶
C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>
- get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) str ¶
- A tag is a unique identifier used to identify structures produced
by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.
C++: protocols::moves::Mover::get_current_tag() const –> std::string
- get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose ¶
C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>
- get_jump_num(self: pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact) int ¶
C++: protocols::docking::FaDockingSlideIntoContact::get_jump_num() const –> unsigned long
- 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.docking.FaDockingSlideIntoContact) str ¶
C++: protocols::docking::FaDockingSlideIntoContact::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_tolerance(self: pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact) float ¶
C++: protocols::docking::FaDockingSlideIntoContact::get_tolerance() const –> double
- get_type(self: pyrosetta.rosetta.protocols.moves.Mover) str ¶
C++: protocols::moves::Mover::get_type() const –> std::string
- info(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.list_std_string_t ¶
non-const accessor
C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &
- last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) float ¶
C++: protocols::moves::Mover::last_proposal_density_ratio() –> double
- static 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.docking.FaDockingSlideIntoContact) -> None
show(self: pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact, output: pyrosetta.rosetta.std.ostream) -> None
C++: protocols::docking::FaDockingSlideIntoContact::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.docking.InterfaceSidechainMinMover¶
Bases:
SidechainMinMover
- add_additional_task_operaration(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, task_operation: pyrosetta.rosetta.core.pack.task.operation.TaskOperation) None ¶
C++: protocols::docking::DockingHighRes::add_additional_task_operaration(class std::shared_ptr<class core::pack::task::operation::TaskOperation>) –> void
- apply(self: pyrosetta.rosetta.protocols.docking.InterfaceSidechainMinMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::docking::InterfaceSidechainMinMover::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.docking.InterfaceSidechainMinMover, : pyrosetta.rosetta.protocols.docking.InterfaceSidechainMinMover) pyrosetta.rosetta.protocols.docking.InterfaceSidechainMinMover ¶
C++: protocols::docking::InterfaceSidechainMinMover::operator=(const class protocols::docking::InterfaceSidechainMinMover &) –> class protocols::docking::InterfaceSidechainMinMover &
- clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) None ¶
Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.
clear_info is called by jd2 before calling apply
C++: protocols::moves::Mover::clear_info() –> void
- clone(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
Return a clone of the Mover object.
C++: protocols::moves::Mover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>
- create(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>
- fresh_instance(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
Generates a new Mover object freshly created with the default ctor.
C++: protocols::moves::Mover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>
- get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose ¶
fpd
Mechanism by which a mover may return multiple output poses from a single input pose.
Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.
C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>
- get_additional_task_operarations(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_task_operation_TaskOperation_t ¶
C++: protocols::docking::DockingHighRes::get_additional_task_operarations() –> class utility::vector1<class std::shared_ptr<class core::pack::task::operation::TaskOperation>, class std::allocator<class std::shared_ptr<class core::pack::task::operation::TaskOperation> > >
- 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.docking.InterfaceSidechainMinMover) str ¶
C++: protocols::docking::InterfaceSidechainMinMover::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_partners(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) str ¶
C++: protocols::docking::DockingHighRes::get_partners() const –> std::string
- get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>
- get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t ¶
C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>
- get_type(self: pyrosetta.rosetta.protocols.moves.Mover) str ¶
C++: protocols::moves::Mover::get_type() const –> std::string
- ignore_default_task(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) bool ¶
C++: protocols::docking::DockingHighRes::ignore_default_task() –> bool
- info(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.list_std_string_t ¶
non-const accessor
C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &
- last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) float ¶
C++: protocols::moves::Mover::last_proposal_density_ratio() –> double
- movable_jumps(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) pyrosetta.rosetta.utility.vector1_int ¶
C++: protocols::docking::DockingHighRes::movable_jumps() –> class utility::vector1<int, class std::allocator<int> > &
- 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
- partners(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) str ¶
C++: protocols::docking::DockingHighRes::partners() –> std::string
- 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
- rt_min(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) bool ¶
C++: protocols::docking::DockingHighRes::rt_min() –> bool
- sc_min(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) bool ¶
C++: protocols::docking::DockingHighRes::sc_min() –> bool
- scorefxn(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) pyrosetta.rosetta.core.scoring.ScoreFunction ¶
C++: protocols::docking::DockingHighRes::scorefxn() const –> class std::shared_ptr<class core::scoring::ScoreFunction>
- scorefxn_pack(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) pyrosetta.rosetta.core.scoring.ScoreFunction ¶
C++: protocols::docking::DockingHighRes::scorefxn_pack() const –> class std::shared_ptr<class core::scoring::ScoreFunction>
- set_additional_task_operarations(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, additional_task_operations: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_task_operation_TaskOperation_t) None ¶
C++: protocols::docking::DockingHighRes::set_additional_task_operarations(class utility::vector1<class std::shared_ptr<class core::pack::task::operation::TaskOperation>, class std::allocator<class std::shared_ptr<class core::pack::task::operation::TaskOperation> > >) –> 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_default(self: pyrosetta.rosetta.protocols.docking.InterfaceSidechainMinMover) None ¶
C++: protocols::docking::InterfaceSidechainMinMover::set_default() –> void
- set_ignore_default_task(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, ignore_default_task: bool) None ¶
C++: protocols::docking::DockingHighRes::set_ignore_default_task(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_interface_definition_task_operation(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, interface_definition: protocols::simple_task_operations::InterfaceTaskOperation) None ¶
C++: protocols::docking::DockingHighRes::set_interface_definition_task_operation(class std::shared_ptr<class protocols::simple_task_operations::InterfaceTaskOperation>) –> void
- set_interface_dist(self: pyrosetta.rosetta.protocols.docking.InterfaceSidechainMinMover, interface_dist: float) None ¶
C++: protocols::docking::InterfaceSidechainMinMover::set_interface_dist(double) –> void
- set_minmover(self: pyrosetta.rosetta.protocols.docking.SidechainMinMover, minmover: pyrosetta.rosetta.protocols.minimization_packing.MinMover) None ¶
C++: protocols::docking::SidechainMinMover::set_minmover(class std::shared_ptr<class protocols::minimization_packing::MinMover>) –> void
- set_movable_jumps(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, movable_jumps: pyrosetta.rosetta.utility.vector1_int) None ¶
C++: protocols::docking::DockingHighRes::set_movable_jumps(class utility::vector1<int, class std::allocator<int> >) –> 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_partners(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, partners: str) None ¶
C++: protocols::docking::DockingHighRes::set_partners(std::string) –> void
- set_rt_min(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, rt_min: bool) None ¶
C++: protocols::docking::DockingHighRes::set_rt_min(bool) –> void
- set_sc_min(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, sc_min: bool) None ¶
C++: protocols::docking::DockingHighRes::set_sc_min(bool) –> void
- set_scorefxn(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) None ¶
C++: protocols::docking::DockingHighRes::set_scorefxn(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void
- set_scorefxn_pack(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, scorefxn_pack: pyrosetta.rosetta.core.scoring.ScoreFunction) None ¶
C++: protocols::docking::DockingHighRes::set_scorefxn_pack(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void
- set_task_factory(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, tf: pyrosetta.rosetta.core.pack.task.TaskFactory) None ¶
C++: protocols::docking::DockingHighRes::set_task_factory(class std::shared_ptr<const class core::pack::task::TaskFactory>) –> void
- set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) None ¶
Set the ‘type’ string
C++: protocols::moves::Mover::set_type(const std::string &) –> void
- show(*args, **kwargs)¶
Overloaded function.
show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None
Outputs details about the Mover, including current settings.
C++: protocols::moves::Mover::show(std::ostream &) const –> void
- task_factory(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) pyrosetta.rosetta.core.pack.task.TaskFactory ¶
C++: protocols::docking::DockingHighRes::task_factory() –> class std::shared_ptr<const class core::pack::task::TaskFactory>
- 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_movemap(self: pyrosetta.rosetta.protocols.docking.SidechainMinMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::docking::SidechainMinMover::update_movemap(class core::pose::Pose &) –> void
- class pyrosetta.rosetta.protocols.docking.RigidBodyInfo¶
Bases:
pybind11_object
- add_jump(self: pyrosetta.rosetta.protocols.docking.RigidBodyInfo, : int) None ¶
C++: protocols::docking::RigidBodyInfo::add_jump(unsigned long) –> void
- assign(self: pyrosetta.rosetta.protocols.docking.RigidBodyInfo, : pyrosetta.rosetta.protocols.docking.RigidBodyInfo) pyrosetta.rosetta.protocols.docking.RigidBodyInfo ¶
C++: protocols::docking::RigidBodyInfo::operator=(const class protocols::docking::RigidBodyInfo &) –> class protocols::docking::RigidBodyInfo &
- movable_jumps(self: pyrosetta.rosetta.protocols.docking.RigidBodyInfo) pyrosetta.rosetta.utility.vector1_unsigned_long ¶
C++: protocols::docking::RigidBodyInfo::movable_jumps() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &
- class pyrosetta.rosetta.protocols.docking.SidechainMinMover¶
Bases:
DockingHighRes
- add_additional_task_operaration(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, task_operation: pyrosetta.rosetta.core.pack.task.operation.TaskOperation) None ¶
C++: protocols::docking::DockingHighRes::add_additional_task_operaration(class std::shared_ptr<class core::pack::task::operation::TaskOperation>) –> void
- apply(self: pyrosetta.rosetta.protocols.docking.SidechainMinMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::docking::SidechainMinMover::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.docking.SidechainMinMover, : pyrosetta.rosetta.protocols.docking.SidechainMinMover) pyrosetta.rosetta.protocols.docking.SidechainMinMover ¶
C++: protocols::docking::SidechainMinMover::operator=(const class protocols::docking::SidechainMinMover &) –> class protocols::docking::SidechainMinMover &
- clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) None ¶
Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.
clear_info is called by jd2 before calling apply
C++: protocols::moves::Mover::clear_info() –> void
- clone(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
Return a clone of the Mover object.
C++: protocols::moves::Mover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>
- create(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>
- fresh_instance(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
Generates a new Mover object freshly created with the default ctor.
C++: protocols::moves::Mover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>
- get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose ¶
fpd
Mechanism by which a mover may return multiple output poses from a single input pose.
Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.
C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>
- get_additional_task_operarations(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_task_operation_TaskOperation_t ¶
C++: protocols::docking::DockingHighRes::get_additional_task_operarations() –> class utility::vector1<class std::shared_ptr<class core::pack::task::operation::TaskOperation>, class std::allocator<class std::shared_ptr<class core::pack::task::operation::TaskOperation> > >
- 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.docking.SidechainMinMover) str ¶
C++: protocols::docking::SidechainMinMover::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_partners(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) str ¶
C++: protocols::docking::DockingHighRes::get_partners() const –> std::string
- get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>
- get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t ¶
C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>
- get_type(self: pyrosetta.rosetta.protocols.moves.Mover) str ¶
C++: protocols::moves::Mover::get_type() const –> std::string
- ignore_default_task(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) bool ¶
C++: protocols::docking::DockingHighRes::ignore_default_task() –> bool
- info(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.list_std_string_t ¶
non-const accessor
C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &
- last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) float ¶
C++: protocols::moves::Mover::last_proposal_density_ratio() –> double
- movable_jumps(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) pyrosetta.rosetta.utility.vector1_int ¶
C++: protocols::docking::DockingHighRes::movable_jumps() –> class utility::vector1<int, class std::allocator<int> > &
- 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
- partners(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) str ¶
C++: protocols::docking::DockingHighRes::partners() –> std::string
- 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
- rt_min(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) bool ¶
C++: protocols::docking::DockingHighRes::rt_min() –> bool
- sc_min(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) bool ¶
C++: protocols::docking::DockingHighRes::sc_min() –> bool
- scorefxn(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) pyrosetta.rosetta.core.scoring.ScoreFunction ¶
C++: protocols::docking::DockingHighRes::scorefxn() const –> class std::shared_ptr<class core::scoring::ScoreFunction>
- scorefxn_pack(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) pyrosetta.rosetta.core.scoring.ScoreFunction ¶
C++: protocols::docking::DockingHighRes::scorefxn_pack() const –> class std::shared_ptr<class core::scoring::ScoreFunction>
- set_additional_task_operarations(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, additional_task_operations: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_task_operation_TaskOperation_t) None ¶
C++: protocols::docking::DockingHighRes::set_additional_task_operarations(class utility::vector1<class std::shared_ptr<class core::pack::task::operation::TaskOperation>, class std::allocator<class std::shared_ptr<class core::pack::task::operation::TaskOperation> > >) –> 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_default(self: pyrosetta.rosetta.protocols.docking.SidechainMinMover) None ¶
Completes the setup of a default instantiation of a SideChainMinMover
C++: protocols::docking::SidechainMinMover::set_default() –> void
- set_ignore_default_task(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, ignore_default_task: bool) None ¶
C++: protocols::docking::DockingHighRes::set_ignore_default_task(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_interface_definition_task_operation(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, interface_definition: protocols::simple_task_operations::InterfaceTaskOperation) None ¶
C++: protocols::docking::DockingHighRes::set_interface_definition_task_operation(class std::shared_ptr<class protocols::simple_task_operations::InterfaceTaskOperation>) –> void
- set_minmover(self: pyrosetta.rosetta.protocols.docking.SidechainMinMover, minmover: pyrosetta.rosetta.protocols.minimization_packing.MinMover) None ¶
C++: protocols::docking::SidechainMinMover::set_minmover(class std::shared_ptr<class protocols::minimization_packing::MinMover>) –> void
- set_movable_jumps(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, movable_jumps: pyrosetta.rosetta.utility.vector1_int) None ¶
C++: protocols::docking::DockingHighRes::set_movable_jumps(class utility::vector1<int, class std::allocator<int> >) –> 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_partners(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, partners: str) None ¶
C++: protocols::docking::DockingHighRes::set_partners(std::string) –> void
- set_rt_min(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, rt_min: bool) None ¶
C++: protocols::docking::DockingHighRes::set_rt_min(bool) –> void
- set_sc_min(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, sc_min: bool) None ¶
C++: protocols::docking::DockingHighRes::set_sc_min(bool) –> void
- set_scorefxn(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) None ¶
C++: protocols::docking::DockingHighRes::set_scorefxn(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void
- set_scorefxn_pack(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, scorefxn_pack: pyrosetta.rosetta.core.scoring.ScoreFunction) None ¶
C++: protocols::docking::DockingHighRes::set_scorefxn_pack(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void
- set_task_factory(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, tf: pyrosetta.rosetta.core.pack.task.TaskFactory) None ¶
C++: protocols::docking::DockingHighRes::set_task_factory(class std::shared_ptr<const class core::pack::task::TaskFactory>) –> void
- set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) None ¶
Set the ‘type’ string
C++: protocols::moves::Mover::set_type(const std::string &) –> void
- show(*args, **kwargs)¶
Overloaded function.
show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None
Outputs details about the Mover, including current settings.
C++: protocols::moves::Mover::show(std::ostream &) const –> void
- task_factory(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) pyrosetta.rosetta.core.pack.task.TaskFactory ¶
C++: protocols::docking::DockingHighRes::task_factory() –> class std::shared_ptr<const class core::pack::task::TaskFactory>
- 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_movemap(self: pyrosetta.rosetta.protocols.docking.SidechainMinMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::docking::SidechainMinMover::update_movemap(class core::pose::Pose &) –> void
- class pyrosetta.rosetta.protocols.docking.SlideIntoContact¶
Bases:
Mover
More general function for low-res or highres DockingSlideIntoContact
- Both DockingSlideIntoContact and FaDockingSlideIntoContact have their
issues and are not as general as they could be; they should be a single class, not two; since they are called quite often, I am rewriting the class for now and will replace it’s use later on
Contrary to the name, slides things apart first, then together. OK for proteins, bad for ligands (because they may escape the pocket permanently).
- apply(self: pyrosetta.rosetta.protocols.docking.SlideIntoContact, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::docking::SlideIntoContact::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.docking.SlideIntoContact, : pyrosetta.rosetta.protocols.docking.SlideIntoContact) pyrosetta.rosetta.protocols.docking.SlideIntoContact ¶
C++: protocols::docking::SlideIntoContact::operator=(const class protocols::docking::SlideIntoContact &) –> class protocols::docking::SlideIntoContact &
- clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) None ¶
Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.
clear_info is called by jd2 before calling apply
C++: protocols::moves::Mover::clear_info() –> void
- clone(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
Return a clone of the Mover object.
C++: protocols::moves::Mover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>
- create(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>
- fresh_instance(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
Generates a new Mover object freshly created with the default ctor.
C++: protocols::moves::Mover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>
- get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose ¶
fpd
Mechanism by which a mover may return multiple output poses from a single input pose.
Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.
C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>
- get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) protocols::jobdist::BasicJob ¶
C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>
- get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) str ¶
- A tag is a unique identifier used to identify structures produced
by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.
C++: protocols::moves::Mover::get_current_tag() const –> std::string
- get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose ¶
C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>
- get_jump_num(self: pyrosetta.rosetta.protocols.docking.SlideIntoContact) int ¶
C++: protocols::docking::SlideIntoContact::get_jump_num() const –> unsigned long
- 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.docking.SlideIntoContact) str ¶
C++: protocols::docking::SlideIntoContact::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_sfxn_name(self: pyrosetta.rosetta.protocols.docking.SlideIntoContact) str ¶
C++: protocols::docking::SlideIntoContact::get_sfxn_name() const –> std::string
- get_stepsize(self: pyrosetta.rosetta.protocols.docking.SlideIntoContact) float ¶
C++: protocols::docking::SlideIntoContact::get_stepsize() const –> double
- get_type(self: pyrosetta.rosetta.protocols.moves.Mover) str ¶
C++: protocols::moves::Mover::get_type() const –> std::string
- info(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.list_std_string_t ¶
non-const accessor
C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &
- last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) float ¶
C++: protocols::moves::Mover::last_proposal_density_ratio() –> double
- move_apart_first(self: pyrosetta.rosetta.protocols.docking.SlideIntoContact, yesno: bool) None ¶
C++: protocols::docking::SlideIntoContact::move_apart_first(bool) –> void
- 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
- scorefunction(self: pyrosetta.rosetta.protocols.docking.SlideIntoContact, sfxn_name: str, scoretype_for_sliding: str) None ¶
scorefunction and scoreterm used for evaluating closeness of partners
C++: protocols::docking::SlideIntoContact::scorefunction(std::string, std::string) –> 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_starting_rep(self: pyrosetta.rosetta.protocols.docking.SlideIntoContact, starting_rep: float) None ¶
C++: protocols::docking::SlideIntoContact::set_starting_rep(double) –> void
- set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) None ¶
Set the ‘type’ string
C++: protocols::moves::Mover::set_type(const std::string &) –> void
- show(*args, **kwargs)¶
Overloaded function.
show(self: pyrosetta.rosetta.protocols.docking.SlideIntoContact) -> None
show(self: pyrosetta.rosetta.protocols.docking.SlideIntoContact, output: pyrosetta.rosetta.std.ostream) -> None
C++: protocols::docking::SlideIntoContact::show(std::ostream &) const –> void
- slide_axis(self: pyrosetta.rosetta.protocols.docking.SlideIntoContact, slide_axis: pyrosetta.rosetta.numeric.xyzVector_double_t) None ¶
C++: protocols::docking::SlideIntoContact::slide_axis(const class numeric::xyzVector<double> &) –> void
- stepsize(self: pyrosetta.rosetta.protocols.docking.SlideIntoContact, stepsize: float) None ¶
C++: protocols::docking::SlideIntoContact::stepsize(double) –> 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 &
- vary_stepsize(self: pyrosetta.rosetta.protocols.docking.SlideIntoContact, yesno: bool) None ¶
C++: protocols::docking::SlideIntoContact::vary_stepsize(bool) –> void
- class pyrosetta.rosetta.protocols.docking.TemperedDocking¶
Bases:
Mover
allows docking using simulated or parallel tempering
- add_jump(self: pyrosetta.rosetta.protocols.docking.TemperedDocking, jump_number: int) None ¶
C++: protocols::docking::TemperedDocking::add_jump(const long) –> void
- apply(self: pyrosetta.rosetta.protocols.docking.TemperedDocking, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::docking::TemperedDocking::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.docking.TemperedDocking, rhs: pyrosetta.rosetta.protocols.docking.TemperedDocking) pyrosetta.rosetta.protocols.docking.TemperedDocking ¶
assignment operator
C++: protocols::docking::TemperedDocking::operator=(const class protocols::docking::TemperedDocking &) –> class protocols::docking::TemperedDocking &
- 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.docking.TemperedDocking) pyrosetta.rosetta.protocols.moves.Mover ¶
clone
C++: protocols::docking::TemperedDocking::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.docking.TemperedDocking) str ¶
returns the docking partners chain identifiers
C++: protocols::docking::TemperedDocking::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
- movable_jumps(self: pyrosetta.rosetta.protocols.docking.TemperedDocking) pyrosetta.rosetta.utility.vector1_int ¶
C++: protocols::docking::TemperedDocking::movable_jumps() –> class utility::vector1<int, class std::allocator<int> > &
- static name() str ¶
C++: protocols::moves::Mover::name() –> std::string
- parse_my_tag(self: pyrosetta.rosetta.protocols.docking.TemperedDocking, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None ¶
C++: protocols::docking::TemperedDocking::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- partners(self: pyrosetta.rosetta.protocols.docking.TemperedDocking) str ¶
C++: protocols::docking::TemperedDocking::partners() const –> std::string
- 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 ¶
Associates relevant options with the TemperedDocking class
C++: protocols::docking::TemperedDocking::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_autofoldtree(self: pyrosetta.rosetta.protocols.docking.TemperedDocking, setting: bool) None ¶
@ return const ref to the jumps vector for docking
C++: protocols::docking::TemperedDocking::set_autofoldtree(bool) –> void
- set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) None ¶
C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void
- set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) None ¶
C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void
- set_defaults(self: pyrosetta.rosetta.protocols.docking.TemperedDocking) None ¶
Assigns default values to primitive members
C++: protocols::docking::TemperedDocking::set_defaults() –> void
- set_highres_scorefxn(*args, **kwargs)¶
Overloaded function.
set_highres_scorefxn(self: pyrosetta.rosetta.protocols.docking.TemperedDocking, docking_scorefxn_high: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None
- Sets the score function that will be used in the high-resolution phase.
The same score function will be used for evaluating moves, packing and discriminating
C++: protocols::docking::TemperedDocking::set_highres_scorefxn(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void
set_highres_scorefxn(self: pyrosetta.rosetta.protocols.docking.TemperedDocking, docking_scorefxn_high: pyrosetta.rosetta.core.scoring.ScoreFunction, docking_scorefxn_pack: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None
- Sets the score function that will be used in the high-resolution phase.
The first scorefunction will be used for evaluating moves and discriminating, the second will be used for packing
C++: protocols::docking::TemperedDocking::set_highres_scorefxn(class std::shared_ptr<const class core::scoring::ScoreFunction>, class std::shared_ptr<const class core::scoring::ScoreFunction>) –> void
set_highres_scorefxn(self: pyrosetta.rosetta.protocols.docking.TemperedDocking, docking_scorefxn_high: pyrosetta.rosetta.core.scoring.ScoreFunction, docking_scorefxn_pack: pyrosetta.rosetta.core.scoring.ScoreFunction, docking_scorefxn_output: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None
- Sets the score function that will be used in the high-resolution phase.
The first scorefunction will be used for evaluating moves, the second will be used for packing and the third for discriminating
C++: protocols::docking::TemperedDocking::set_highres_scorefxn(class std::shared_ptr<const class core::scoring::ScoreFunction>, class std::shared_ptr<const class core::scoring::ScoreFunction>, class std::shared_ptr<const class core::scoring::ScoreFunction>) –> 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_lowres_scorefxn(self: pyrosetta.rosetta.protocols.docking.TemperedDocking, docking_scorefxn_low: pyrosetta.rosetta.core.scoring.ScoreFunction) None ¶
Sets the score function that will be used in the low-resolution phase
C++: protocols::docking::TemperedDocking::set_lowres_scorefxn(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void
- set_movable_jumps(self: pyrosetta.rosetta.protocols.docking.TemperedDocking, setting: pyrosetta.rosetta.utility.vector1_int) None ¶
C++: protocols::docking::TemperedDocking::set_movable_jumps(const class utility::vector1<int, class std::allocator<int> > &) –> 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_partners(self: pyrosetta.rosetta.protocols.docking.TemperedDocking, setting: str) None ¶
C++: protocols::docking::TemperedDocking::set_partners(const std::string &) –> void
- set_sc_min(self: pyrosetta.rosetta.protocols.docking.TemperedDocking, sc_min: bool) None ¶
C++: protocols::docking::TemperedDocking::set_sc_min(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
- set_use_constraints(self: pyrosetta.rosetta.protocols.docking.TemperedDocking, setting: bool) None ¶
C++: protocols::docking::TemperedDocking::set_use_constraints(bool) –> void
- show(*args, **kwargs)¶
Overloaded function.
show(self: pyrosetta.rosetta.protocols.docking.TemperedDocking) -> None
show(self: pyrosetta.rosetta.protocols.docking.TemperedDocking, out: pyrosetta.rosetta.std.ostream) -> None
C++: protocols::docking::TemperedDocking::show(std::ostream &) const –> void
- sync_objects_with_flags(self: pyrosetta.rosetta.protocols.docking.TemperedDocking) None ¶
Instantiates non-primitive members based on the value of the primitive members
C++: protocols::docking::TemperedDocking::sync_objects_with_flags() –> 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
- to_centroid(self: pyrosetta.rosetta.protocols.docking.TemperedDocking) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::docking::TemperedDocking::to_centroid() const –> class std::shared_ptr<const class protocols::moves::Mover>
- 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.docking.TemperedDockingCreator¶
Bases:
MoverCreator
- assign(self: pyrosetta.rosetta.protocols.docking.TemperedDockingCreator, : pyrosetta.rosetta.protocols.docking.TemperedDockingCreator) pyrosetta.rosetta.protocols.docking.TemperedDockingCreator ¶
C++: protocols::docking::TemperedDockingCreator::operator=(const class protocols::docking::TemperedDockingCreator &) –> class protocols::docking::TemperedDockingCreator &
- create_mover(self: pyrosetta.rosetta.protocols.docking.TemperedDockingCreator) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::docking::TemperedDockingCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>
- keyname(self: pyrosetta.rosetta.protocols.docking.TemperedDockingCreator) str ¶
C++: protocols::docking::TemperedDockingCreator::keyname() const –> std::string
- static mover_name() str ¶
C++: protocols::docking::TemperedDockingCreator::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
- pyrosetta.rosetta.protocols.docking.calc_CAPRI_rank(pose: pyrosetta.rosetta.core.pose.Pose, native_pose: pyrosetta.rosetta.core.pose.Pose, dock_scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, movable_jumps: pyrosetta.rosetta.utility.vector1_int) int ¶
C++: protocols::docking::calc_CAPRI_rank(const class core::pose::Pose &, const class core::pose::Pose &, const class std::shared_ptr<const class core::scoring::ScoreFunction>, const class utility::vector1<int, class std::allocator<int> >) –> unsigned long
- pyrosetta.rosetta.protocols.docking.calc_CA_Irmsd(pose: pyrosetta.rosetta.core.pose.Pose, native_pose: pyrosetta.rosetta.core.pose.Pose, dock_scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, movable_jumps: pyrosetta.rosetta.utility.vector1_int) float ¶
calcluates the CA-atom RMSD of all residues within 5A of the interface at superposition along those same atoms
C++: protocols::docking::calc_CA_Irmsd(const class core::pose::Pose &, const class core::pose::Pose &, const class std::shared_ptr<const class core::scoring::ScoreFunction>, const class utility::vector1<int, class std::allocator<int> >) –> double
- pyrosetta.rosetta.protocols.docking.calc_Fnat(*args, **kwargs)¶
Overloaded function.
calc_Fnat(pose: pyrosetta.rosetta.core.pose.Pose, native_pose: pyrosetta.rosetta.core.pose.Pose, dock_scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, movable_jumps: pyrosetta.rosetta.utility.vector1_int) -> float
- Calculates the fraction of native contacts recovered between the input and native pose. A native-contact is defined
as defined by a residue from one partner being within 5A of a residue from the other partner in the native structure
C++: protocols::docking::calc_Fnat(const class core::pose::Pose &, const class core::pose::Pose &, const class std::shared_ptr<const class core::scoring::ScoreFunction>, const class utility::vector1<int, class std::allocator<int> >) –> double
calc_Fnat(pose: pyrosetta.rosetta.core.pose.Pose, list_file: str, movable_jumps: pyrosetta.rosetta.utility.vector1_int) -> float
Calculates the fraction of native contacts from the given native contacts pair list
C++: protocols::docking::calc_Fnat(const class core::pose::Pose &, const std::string &, const class utility::vector1<int, class std::allocator<int> >) –> double
- pyrosetta.rosetta.protocols.docking.calc_Fnonnat(*args, **kwargs)¶
Overloaded function.
calc_Fnonnat(pose: pyrosetta.rosetta.core.pose.Pose, native_pose: pyrosetta.rosetta.core.pose.Pose, dock_scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, movable_jumps: pyrosetta.rosetta.utility.vector1_int) -> float
- Calculates the fraction of non-native contacts recovered between the input and native pose. A native-contact is defined
as defined by a residue from one partner being within 5A of a residue from the other partner in the native structure. Fnonnat = Nnon-native-contact/Nnative_contact
C++: protocols::docking::calc_Fnonnat(const class core::pose::Pose &, const class core::pose::Pose &, const class std::shared_ptr<const class core::scoring::ScoreFunction>, const class utility::vector1<int, class std::allocator<int> >) –> double
calc_Fnonnat(pose: pyrosetta.rosetta.core.pose.Pose, list_file: str, movable_jumps: pyrosetta.rosetta.utility.vector1_int) -> float
Calculates the fraction of non-native contacts from the given native contacts pari list
C++: protocols::docking::calc_Fnonnat(const class core::pose::Pose &, const std::string &, const class utility::vector1<int, class std::allocator<int> >) –> double
- pyrosetta.rosetta.protocols.docking.calc_Irmsd(pose: pyrosetta.rosetta.core.pose.Pose, native_pose: pyrosetta.rosetta.core.pose.Pose, dock_scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, movable_jumps: pyrosetta.rosetta.utility.vector1_int) float ¶
Calculates the all-atom RMSD of all residues within 10A of the interface at superposition along those same atoms
C++: protocols::docking::calc_Irmsd(const class core::pose::Pose &, const class core::pose::Pose &, const class std::shared_ptr<const class core::scoring::ScoreFunction>, const class utility::vector1<int, class std::allocator<int> >) –> double
- pyrosetta.rosetta.protocols.docking.calc_Irmsd_legacy(pose: pyrosetta.rosetta.core.pose.Pose, native_pose: pyrosetta.rosetta.core.pose.Pose, dock_scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, movable_jumps: pyrosetta.rosetta.utility.vector1_int) float ¶
Calculates the backbone RMSD of all residues within 8A of the interface at superposition along those same atoms
C++: protocols::docking::calc_Irmsd_legacy(const class core::pose::Pose &, const class core::pose::Pose &, const class std::shared_ptr<const class core::scoring::ScoreFunction>, const class utility::vector1<int, class std::allocator<int> >) –> double
- pyrosetta.rosetta.protocols.docking.calc_Lrmsd(pose: pyrosetta.rosetta.core.pose.Pose, native_pose: pyrosetta.rosetta.core.pose.Pose, movable_jumps: pyrosetta.rosetta.utility.vector1_int) float ¶
Calculates C-alpha RMSD of the smaller partner after superposition of the larger partner
C++: protocols::docking::calc_Lrmsd(const class core::pose::Pose &, const class core::pose::Pose &, const class utility::vector1<int, class std::allocator<int> >) –> double
- pyrosetta.rosetta.protocols.docking.calc_P1rmsd(pose: pyrosetta.rosetta.core.pose.Pose, native_pose: pyrosetta.rosetta.core.pose.Pose, movable_jumps: pyrosetta.rosetta.utility.vector1_int) float ¶
Calculates C-alpha RMSD of the superimposed larger partner
- The larger partner is the fixed partner; this is mostly for
membrane proteins, where we move the partners apart, then do relax on both partners
C++: protocols::docking::calc_P1rmsd(const class core::pose::Pose &, const class core::pose::Pose &, const class utility::vector1<int, class std::allocator<int> >) –> double
- pyrosetta.rosetta.protocols.docking.calc_P2rmsd(pose: pyrosetta.rosetta.core.pose.Pose, native_pose: pyrosetta.rosetta.core.pose.Pose, movable_jumps: pyrosetta.rosetta.utility.vector1_int) float ¶
Calculates C-alpha RMSD of the superimposed smaller partner
- This calculates the RMSD of the smaller partner after superimposing it
The computed RMSD is not from the docking, but from the flexible backbone relax
C++: protocols::docking::calc_P2rmsd(const class core::pose::Pose &, const class core::pose::Pose &, const class utility::vector1<int, class std::allocator<int> >) –> double
- pyrosetta.rosetta.protocols.docking.calc_interaction_energy(pose: pyrosetta.rosetta.core.pose.Pose, dock_scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, movable_jumps: pyrosetta.rosetta.utility.vector1_int) float ¶
Calculates the difference in energy between the inputted complex, and the complex with the two partners at 500A from each other
C++: protocols::docking::calc_interaction_energy(const class core::pose::Pose &, const class std::shared_ptr<const class core::scoring::ScoreFunction>, const class utility::vector1<int, class std::allocator<int> >) –> double
- pyrosetta.rosetta.protocols.docking.calc_intf_score(pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, jump: int) float ¶
- Compute interface score between the input complex and complex with
the two partners at 500A from each other
C++: protocols::docking::calc_intf_score(const class core::pose::Pose &, const class std::shared_ptr<class core::scoring::ScoreFunction>, const int) –> double
- pyrosetta.rosetta.protocols.docking.calc_res_contact(rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, dist_cutoff: float) bool ¶
C++: protocols::docking::calc_res_contact(class std::shared_ptr<class core::conformation::Residue>, class std::shared_ptr<class core::conformation::Residue>, double) –> bool
- pyrosetta.rosetta.protocols.docking.comma_separated_partner_chains(chains: str) str ¶
- Converts a string representation of the partner from the dock_partners flag to a comma-separated list of
chains that can be passed into a ChainSeletor. For example, the dock_partners flags “ABC_D” will split into two partners: “ABC” and “D”. This function will convert “ABC” to “A,B,C”.
A comma-separated list of chains (e.g. “A,B,C”)
C++: protocols::docking::comma_separated_partner_chains(const std::string &) –> std::string
- pyrosetta.rosetta.protocols.docking.move_apart(pose: pyrosetta.rosetta.core.pose.Pose, jump: int, axis: pyrosetta.rosetta.numeric.xyzVector_double_t) None ¶
C++: protocols::docking::move_apart(class core::pose::Pose &, int, const class numeric::xyzVector<double> &) –> void
- pyrosetta.rosetta.protocols.docking.move_together(pose: pyrosetta.rosetta.core.pose.Pose, jump: int, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) None ¶
C++: protocols::docking::move_together(class core::pose::Pose &, int, class std::shared_ptr<class core::scoring::ScoreFunction>) –> void
- pyrosetta.rosetta.protocols.docking.setup_foldtree(*args, **kwargs)¶
Overloaded function.
setup_foldtree(pose: pyrosetta.rosetta.core.pose.Pose, partner_chainID: str, movable_jumps: pyrosetta.rosetta.utility.vector1_int) -> None
setup_foldtree(pose: pyrosetta.rosetta.core.pose.Pose, partner_chainID: str, movable_jumps: pyrosetta.rosetta.utility.vector1_int, rand_jump_res_partner2: bool) -> None
- Setup FoldTree for docking across an interface.
The partners are described by a string for the partner chains (using pdb_chain identification) separated by “_”. The foldtree is set up such that the jump points are at the center of masses of the two partners.
C++: protocols::docking::setup_foldtree(class core::pose::Pose &, const std::string &, class utility::vector1<int, class std::allocator<int> > &, bool) –> void
setup_foldtree(pose: pyrosetta.rosetta.core.pose.Pose, partner1: pyrosetta.rosetta.utility.vector1_bool, movable_jumps: pyrosetta.rosetta.utility.vector1_int, ft: pyrosetta.rosetta.core.kinematics.FoldTree) -> None
setup_foldtree(pose: pyrosetta.rosetta.core.pose.Pose, partner1: pyrosetta.rosetta.utility.vector1_bool, movable_jumps: pyrosetta.rosetta.utility.vector1_int, ft: pyrosetta.rosetta.core.kinematics.FoldTree, rand_jump_res_partner2: bool) -> None
- Setup foldtree for docking across an interface.
The partners are described by a vector of booleans of the same length as the number of residues in the pose. The FoldTree is set up such that the jump points are at the center of masses of the two partners.
C++: protocols::docking::setup_foldtree(const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, class utility::vector1<int, class std::allocator<int> > &, class core::kinematics::FoldTree &, bool) –> void