switches¶
Bindings for protocols::switches namespace
- class pyrosetta.rosetta.protocols.switches.GraftSwitchMover¶
Bases:
Mover
A protocols::moves::Mover that grafts a sequence onto the terminal helix of a helical-bundle monomer. Utilizes SimpleThreadingMover alongside
- add_sequence(self: pyrosetta.rosetta.protocols.switches.GraftSwitchMover, seq: str) None ¶
C++: protocols::switches::GraftSwitchMover::add_sequence(std::string) –> void
- apply(self: pyrosetta.rosetta.protocols.switches.GraftSwitchMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
- Grafts, minimizes, and scores functional sequences grafted
onto LOCKR type de novo protien switches
C++: protocols::switches::GraftSwitchMover::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.switches.GraftSwitchMover, : pyrosetta.rosetta.protocols.switches.GraftSwitchMover) pyrosetta.rosetta.protocols.switches.GraftSwitchMover ¶
C++: protocols::switches::GraftSwitchMover::operator=(const class protocols::switches::GraftSwitchMover &) –> class protocols::switches::GraftSwitchMover &
- 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.switches.GraftSwitchMover) pyrosetta.rosetta.protocols.moves.Mover ¶
required in the context of the parser/scripting scheme
C++: protocols::switches::GraftSwitchMover::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.switches.GraftSwitchMover) pyrosetta.rosetta.protocols.moves.Mover ¶
required in the context of the parser/scripting scheme
C++: protocols::switches::GraftSwitchMover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>
- get_additional_output(self: pyrosetta.rosetta.protocols.switches.GraftSwitchMover) pyrosetta.rosetta.core.pose.Pose ¶
C++: protocols::switches::GraftSwitchMover::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.switches.GraftSwitchMover) str ¶
C++: protocols::switches::GraftSwitchMover::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_output_list(self: pyrosetta.rosetta.protocols.switches.GraftSwitchMover) pyrosetta.rosetta.std.list_utility_vector1_unsigned_long_std_allocator_unsigned_long_t ¶
C++: protocols::switches::GraftSwitchMover::get_output_list() –> class std::list<class utility::vector1<unsigned long, class std::allocator<unsigned long> >, class std::allocator<class utility::vector1<unsigned long, class std::allocator<unsigned long> > > >
- get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>
- get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t ¶
C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>
- get_type(self: pyrosetta.rosetta.protocols.moves.Mover) str ¶
C++: protocols::moves::Mover::get_type() const –> std::string
- info(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.list_std_string_t ¶
non-const accessor
C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &
- 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::switches::GraftSwitchMover::mover_name() –> std::string
- static name() str ¶
C++: protocols::moves::Mover::name() –> std::string
- parse_my_tag(self: pyrosetta.rosetta.protocols.switches.GraftSwitchMover, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None ¶
parse XML (specifically in the context of the parser/scripting scheme)
C++: protocols::switches::GraftSwitchMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- parse_score_function(self: pyrosetta.rosetta.protocols.switches.GraftSwitchMover, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None ¶
parse “scorefxn” XML option (can be employed virtually by derived Packing movers)
C++: protocols::switches::GraftSwitchMover::parse_score_function(class std::shared_ptr<const class utility::tag::Tag>, const class basic::datacache::DataMap &) –> void
- parse_task_operations(self: pyrosetta.rosetta.protocols.switches.GraftSwitchMover, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None ¶
parse “task_operations” XML option (can be employed virtually by derived Packing movers)
C++: protocols::switches::GraftSwitchMover::parse_task_operations(class std::shared_ptr<const class utility::tag::Tag>, const class basic::datacache::DataMap &) –> void
- provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None ¶
- Provide citations to the passed CitationCollectionList
Subclasses should add the info for themselves and any other classes they use.
The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.
C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void
- static provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) None ¶
C++: protocols::switches::GraftSwitchMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void
- static register_options() None ¶
Overload this static method if you access options within the mover.
These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.
C++: protocols::moves::Mover::register_options() –> void
- reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) bool ¶
- Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on
each use.
C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool
- reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) bool ¶
- Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input
pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).
C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool
- reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) None ¶
resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.
C++: protocols::moves::Mover::reset_status() –> void
- score_function(self: pyrosetta.rosetta.protocols.switches.GraftSwitchMover, sf: pyrosetta.rosetta.core.scoring.ScoreFunction) None ¶
Sets the ScoreFunction to <sf>
- example(s):
graftmover.score_function(scorefxn)
C++: protocols::switches::GraftSwitchMover::score_function(class std::shared_ptr<const class core::scoring::ScoreFunction>) –> void
- set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) None ¶
C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void
- set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) None ¶
C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void
- set_end_graft(self: pyrosetta.rosetta.protocols.switches.GraftSwitchMover, end: int) None ¶
C++: protocols::switches::GraftSwitchMover::set_end_graft(unsigned long) –> void
- set_important_residues(self: pyrosetta.rosetta.protocols.switches.GraftSwitchMover, residue_list: pyrosetta.rosetta.utility.vector1_unsigned_long) None ¶
C++: protocols::switches::GraftSwitchMover::set_important_residues(class utility::vector1<unsigned long, class std::allocator<unsigned long> >) –> void
- set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
setter for poses contained for rms
C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void
- set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe
C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void
- set_pack_min(self: pyrosetta.rosetta.protocols.switches.GraftSwitchMover, input: bool) None ¶
C++: protocols::switches::GraftSwitchMover::set_pack_min(bool) –> void
- set_pack_neighbors(self: pyrosetta.rosetta.protocols.switches.GraftSwitchMover, input: bool) None ¶
C++: protocols::switches::GraftSwitchMover::set_pack_neighbors(bool) –> void
- set_start_graft(self: pyrosetta.rosetta.protocols.switches.GraftSwitchMover, start: int) None ¶
C++: protocols::switches::GraftSwitchMover::set_start_graft(unsigned long) –> void
- set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) None ¶
Set the ‘type’ string
C++: protocols::moves::Mover::set_type(const std::string &) –> void
- show(*args, **kwargs)¶
Overloaded function.
show(self: pyrosetta.rosetta.protocols.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.switches.GraftSwitchMover, tf: pyrosetta.rosetta.core.pack.task.TaskFactory) None ¶
Sets the TaskFactory to <tf>
- example(s):
graftmover.task_factory(task_design)
C++: protocols::switches::GraftSwitchMover::task_factory(class std::shared_ptr<const class core::pack::task::TaskFactory>) –> void
- test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
- : Unit test support function. Apply one move to a given pose.
Allows extra test specific functions to be called before applying
C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void
- type(*args, **kwargs)¶
Overloaded function.
type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None
Set the ‘type’ string
C++: protocols::moves::Mover::type(const std::string &) –> void
type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str
Get the set ‘type’ string
C++: protocols::moves::Mover::type() const –> const std::string &
- class pyrosetta.rosetta.protocols.switches.GraftSwitchMoverCreator¶
Bases:
MoverCreator
- assign(self: pyrosetta.rosetta.protocols.switches.GraftSwitchMoverCreator, : pyrosetta.rosetta.protocols.switches.GraftSwitchMoverCreator) pyrosetta.rosetta.protocols.switches.GraftSwitchMoverCreator ¶
C++: protocols::switches::GraftSwitchMoverCreator::operator=(const class protocols::switches::GraftSwitchMoverCreator &) –> class protocols::switches::GraftSwitchMoverCreator &
- create_mover(self: pyrosetta.rosetta.protocols.switches.GraftSwitchMoverCreator) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::switches::GraftSwitchMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>
- keyname(self: pyrosetta.rosetta.protocols.switches.GraftSwitchMoverCreator) str ¶
C++: protocols::switches::GraftSwitchMoverCreator::keyname() const –> std::string
- provide_xml_schema(self: pyrosetta.rosetta.protocols.switches.GraftSwitchMoverCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) None ¶
C++: protocols::switches::GraftSwitchMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void