switches

Bindings for protocols::switches namespace

class pyrosetta.rosetta.protocols.switches.GraftSwitchMover

Bases: pyrosetta.rosetta.protocols.moves.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_std_allocator_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_std_allocator_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: 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.

  1. show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None

  2. 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.

  1. type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

  1. 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: pyrosetta.rosetta.protocols.moves.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: utility::tag::XMLSchemaDefinition) None

C++: protocols::switches::GraftSwitchMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void