loop¶
Bindings for protocols::relax::loop namespace
- class pyrosetta.rosetta.protocols.relax.loop.LoopRelaxMover¶
Bases:
Mover
- apply(self: pyrosetta.rosetta.protocols.relax.loop.LoopRelaxMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
- Apply the loop-relax protocol to a Pose. At the call to this function, the
loop indices originating from the loop file (which may list indices with PDB identifiers i.e. res+insertioncode+chain ) will be resolved. Until this point, the Loops object in the LoopRelaxMover cannot be used.
C++: protocols::relax::loop::LoopRelaxMover::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.relax.loop.LoopRelaxMover, : pyrosetta.rosetta.protocols.relax.loop.LoopRelaxMover) pyrosetta.rosetta.protocols.relax.loop.LoopRelaxMover ¶
C++: protocols::relax::loop::LoopRelaxMover::operator=(const class protocols::relax::loop::LoopRelaxMover &) –> class protocols::relax::loop::LoopRelaxMover &
- cen_scorefxn(self: pyrosetta.rosetta.protocols.relax.loop.LoopRelaxMover, cen_scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) None ¶
C++: protocols::relax::loop::LoopRelaxMover::cen_scorefxn(class std::shared_ptr<class core::scoring::ScoreFunction>) –> 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.relax.loop.LoopRelaxMover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::relax::loop::LoopRelaxMover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>
- cmd_line_csts(*args, **kwargs)¶
Overloaded function.
cmd_line_csts(self: pyrosetta.rosetta.protocols.relax.loop.LoopRelaxMover, setting: bool) -> None
C++: protocols::relax::loop::LoopRelaxMover::cmd_line_csts(bool) –> void
cmd_line_csts(self: pyrosetta.rosetta.protocols.relax.loop.LoopRelaxMover) -> bool
C++: protocols::relax::loop::LoopRelaxMover::cmd_line_csts() const –> bool
- compute_rmsd(*args, **kwargs)¶
Overloaded function.
compute_rmsd(self: pyrosetta.rosetta.protocols.relax.loop.LoopRelaxMover, c: bool) -> None
C++: protocols::relax::loop::LoopRelaxMover::compute_rmsd(const bool) –> void
compute_rmsd(self: pyrosetta.rosetta.protocols.relax.loop.LoopRelaxMover) -> bool
C++: protocols::relax::loop::LoopRelaxMover::compute_rmsd() const –> bool
- copy_sidechains(*args, **kwargs)¶
Overloaded function.
copy_sidechains(self: pyrosetta.rosetta.protocols.relax.loop.LoopRelaxMover, setting: bool) -> None
C++: protocols::relax::loop::LoopRelaxMover::copy_sidechains(bool) –> void
copy_sidechains(self: pyrosetta.rosetta.protocols.relax.loop.LoopRelaxMover) -> bool
C++: protocols::relax::loop::LoopRelaxMover::copy_sidechains() const –> bool
- 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>
- fa_scorefxn(self: pyrosetta.rosetta.protocols.relax.loop.LoopRelaxMover, fa_scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) None ¶
C++: protocols::relax::loop::LoopRelaxMover::fa_scorefxn(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void
- frag_libs(*args, **kwargs)¶
Overloaded function.
frag_libs(self: pyrosetta.rosetta.protocols.relax.loop.LoopRelaxMover, new_libs: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_fragment_FragSet_t) -> None
C++: protocols::relax::loop::LoopRelaxMover::frag_libs(class utility::vector1<class std::shared_ptr<class core::fragment::FragSet>, class std::allocator<class std::shared_ptr<class core::fragment::FragSet> > >) –> void
frag_libs(self: pyrosetta.rosetta.protocols.relax.loop.LoopRelaxMover) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_fragment_FragSet_t
C++: protocols::relax::loop::LoopRelaxMover::frag_libs() const –> class utility::vector1<class std::shared_ptr<class core::fragment::FragSet>, class std::allocator<class std::shared_ptr<class core::fragment::FragSet> > >
- fresh_instance(self: pyrosetta.rosetta.protocols.relax.loop.LoopRelaxMover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::relax::loop::LoopRelaxMover::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_loops(self: pyrosetta.rosetta.protocols.relax.loop.LoopRelaxMover) pyrosetta.rosetta.protocols.loops.Loops ¶
- Loops accessor. May only be retrieved after the loop indices have been resolved
in a call to apply.
C++: protocols::relax::loop::LoopRelaxMover::get_loops() –> class std::shared_ptr<class protocols::loops::Loops>
- get_name(self: pyrosetta.rosetta.protocols.relax.loop.LoopRelaxMover) str ¶
C++: protocols::relax::loop::LoopRelaxMover::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 > > &
- intermedrelax(*args, **kwargs)¶
Overloaded function.
intermedrelax(self: pyrosetta.rosetta.protocols.relax.loop.LoopRelaxMover, val: str) -> None
C++: protocols::relax::loop::LoopRelaxMover::intermedrelax(const std::string &) –> void
intermedrelax(self: pyrosetta.rosetta.protocols.relax.loop.LoopRelaxMover) -> str
C++: protocols::relax::loop::LoopRelaxMover::intermedrelax() const –> std::string
- last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) float ¶
C++: protocols::moves::Mover::last_proposal_density_ratio() –> double
- loops(self: pyrosetta.rosetta.protocols.relax.loop.LoopRelaxMover, val: pyrosetta.rosetta.protocols.loops.Loops) None ¶
- set the Loops object (with resolved indices) directly. This would override
the unresolved-indices held in the LoopsFileData if that data were set in the constructor
C++: protocols::relax::loop::LoopRelaxMover::loops(const class std::shared_ptr<class protocols::loops::Loops>) –> void
- loops_file_data(self: pyrosetta.rosetta.protocols.relax.loop.LoopRelaxMover, loopfiledata: protocols::loops::LoopsFileData) None ¶
- Set the loop file data. This will require that a Pose be presented to
the LoopRelax object before get_loops() can be called.
C++: protocols::relax::loop::LoopRelaxMover::loops_file_data(const class protocols::loops::LoopsFileData &) –> void
- static mover_name() str ¶
C++: protocols::relax::loop::LoopRelaxMover::mover_name() –> std::string
- n_rebuild_tries(*args, **kwargs)¶
Overloaded function.
n_rebuild_tries(self: pyrosetta.rosetta.protocols.relax.loop.LoopRelaxMover, setting: int) -> None
C++: protocols::relax::loop::LoopRelaxMover::n_rebuild_tries(unsigned long) –> void
n_rebuild_tries(self: pyrosetta.rosetta.protocols.relax.loop.LoopRelaxMover) -> int
C++: protocols::relax::loop::LoopRelaxMover::n_rebuild_tries() const –> unsigned long
- static name() str ¶
C++: protocols::moves::Mover::name() –> std::string
- parse_my_tag(self: pyrosetta.rosetta.protocols.relax.loop.LoopRelaxMover, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None ¶
C++: protocols::relax::loop::LoopRelaxMover::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::relax::loop::LoopRelaxMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void
- rebuild_filter(*args, **kwargs)¶
Overloaded function.
rebuild_filter(self: pyrosetta.rosetta.protocols.relax.loop.LoopRelaxMover, setting: float) -> None
C++: protocols::relax::loop::LoopRelaxMover::rebuild_filter(double) –> void
rebuild_filter(self: pyrosetta.rosetta.protocols.relax.loop.LoopRelaxMover) -> float
C++: protocols::relax::loop::LoopRelaxMover::rebuild_filter() const –> double
- refine(*args, **kwargs)¶
Overloaded function.
refine(self: pyrosetta.rosetta.protocols.relax.loop.LoopRelaxMover, val: str) -> None
C++: protocols::relax::loop::LoopRelaxMover::refine(const std::string &) –> void
refine(self: pyrosetta.rosetta.protocols.relax.loop.LoopRelaxMover) -> str
C++: protocols::relax::loop::LoopRelaxMover::refine() const –> std::string
- 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
- relax(*args, **kwargs)¶
Overloaded function.
relax(self: pyrosetta.rosetta.protocols.relax.loop.LoopRelaxMover, val: str) -> None
C++: protocols::relax::loop::LoopRelaxMover::relax(const std::string &) –> void
relax(self: pyrosetta.rosetta.protocols.relax.loop.LoopRelaxMover) -> str
C++: protocols::relax::loop::LoopRelaxMover::relax() const –> std::string
- remodel(*args, **kwargs)¶
Overloaded function.
remodel(self: pyrosetta.rosetta.protocols.relax.loop.LoopRelaxMover, val: str) -> None
C++: protocols::relax::loop::LoopRelaxMover::remodel(const std::string &) –> void
remodel(self: pyrosetta.rosetta.protocols.relax.loop.LoopRelaxMover) -> str
C++: protocols::relax::loop::LoopRelaxMover::remodel() const –> std::string
- 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
- resolve_loopfile_indices(self: pyrosetta.rosetta.protocols.relax.loop.LoopRelaxMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
Must be called before the Loops data can be read from.
C++: protocols::relax::loop::LoopRelaxMover::resolve_loopfile_indices(const class core::pose::Pose &) –> void
- scorefxns(self: pyrosetta.rosetta.protocols.relax.loop.LoopRelaxMover, cen_scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, fa_scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) None ¶
C++: protocols::relax::loop::LoopRelaxMover::scorefxns(class std::shared_ptr<class core::scoring::ScoreFunction>, class std::shared_ptr<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_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
setter for poses contained for rms
C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void
- set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe
C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void
- set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) None ¶
Set the ‘type’ string
C++: protocols::moves::Mover::set_type(const std::string &) –> void
- show(*args, **kwargs)¶
Overloaded function.
show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None
Outputs details about the Mover, including current settings.
C++: protocols::moves::Mover::show(std::ostream &) const –> void
- test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
- : Unit test support function. Apply one move to a given pose.
Allows extra test specific functions to be called before applying
C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void
- type(*args, **kwargs)¶
Overloaded function.
type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None
Set the ‘type’ string
C++: protocols::moves::Mover::type(const std::string &) –> void
type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str
Get the set ‘type’ string
C++: protocols::moves::Mover::type() const –> const std::string &
- class pyrosetta.rosetta.protocols.relax.loop.LoopRelaxMoverCreator¶
Bases:
MoverCreator
- assign(self: pyrosetta.rosetta.protocols.relax.loop.LoopRelaxMoverCreator, : pyrosetta.rosetta.protocols.relax.loop.LoopRelaxMoverCreator) pyrosetta.rosetta.protocols.relax.loop.LoopRelaxMoverCreator ¶
C++: protocols::relax::loop::LoopRelaxMoverCreator::operator=(const class protocols::relax::loop::LoopRelaxMoverCreator &) –> class protocols::relax::loop::LoopRelaxMoverCreator &
- create_mover(self: pyrosetta.rosetta.protocols.relax.loop.LoopRelaxMoverCreator) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::relax::loop::LoopRelaxMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>
- keyname(self: pyrosetta.rosetta.protocols.relax.loop.LoopRelaxMoverCreator) str ¶
C++: protocols::relax::loop::LoopRelaxMoverCreator::keyname() const –> std::string