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>