loop_grower¶
Bindings for protocols::loop_grower namespace
- class pyrosetta.rosetta.protocols.loop_grower.DensSkeleton¶
Bases:
pybind11_object
- assign(self: pyrosetta.rosetta.protocols.loop_grower.DensSkeleton, : pyrosetta.rosetta.protocols.loop_grower.DensSkeleton) pyrosetta.rosetta.protocols.loop_grower.DensSkeleton ¶
C++: protocols::loop_grower::DensSkeleton::operator=(const class protocols::loop_grower::DensSkeleton &) –> class protocols::loop_grower::DensSkeleton &
- find_closest_occupied_point(self: pyrosetta.rosetta.protocols.loop_grower.DensSkeleton, coord: pyrosetta.rosetta.numeric.xyzVector_double_t, max_grid: int) pyrosetta.rosetta.numeric.xyzVector_int_t ¶
C++: protocols::loop_grower::DensSkeleton::find_closest_occupied_point(const class numeric::xyzVector<double> &, unsigned long) –> class numeric::xyzVector<int>
- get_density(self: pyrosetta.rosetta.protocols.loop_grower.DensSkeleton) pyrosetta.rosetta.core.scoring.electron_density.ElectronDensity ¶
C++: protocols::loop_grower::DensSkeleton::get_density() const –> const class core::scoring::electron_density::ElectronDensity &
- has_density(self: pyrosetta.rosetta.protocols.loop_grower.DensSkeleton) bool ¶
C++: protocols::loop_grower::DensSkeleton::has_density() –> bool
- load_density(self: pyrosetta.rosetta.protocols.loop_grower.DensSkeleton, filename: str, mapreso: float, gridspace: float) None ¶
C++: protocols::loop_grower::DensSkeleton::load_density(std::string, double, double) –> void
- matchAtomFast(self: pyrosetta.rosetta.protocols.loop_grower.DensSkeleton, resid: int, atomid: int, res: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose) float ¶
C++: protocols::loop_grower::DensSkeleton::matchAtomFast(unsigned long, unsigned long, class core::conformation::Residue &, class core::pose::Pose &) –> double
- shortest_path_bfs(self: pyrosetta.rosetta.protocols.loop_grower.DensSkeleton, start: pyrosetta.rosetta.numeric.xyzVector_double_t, end: pyrosetta.rosetta.numeric.xyzVector_double_t, max_length: float, max_que: int, hit_max: bool, max_grid: int) float ¶
C++: protocols::loop_grower::DensSkeleton::shortest_path_bfs(const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, double, unsigned long, bool, unsigned long) –> double
- class pyrosetta.rosetta.protocols.loop_grower.FragmentExtension¶
Bases:
Mover
- apply(self: pyrosetta.rosetta.protocols.loop_grower.FragmentExtension, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::loop_grower::FragmentExtension::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.loop_grower.FragmentExtension, : pyrosetta.rosetta.protocols.loop_grower.FragmentExtension) pyrosetta.rosetta.protocols.loop_grower.FragmentExtension ¶
C++: protocols::loop_grower::FragmentExtension::operator=(const class protocols::loop_grower::FragmentExtension &) –> class protocols::loop_grower::FragmentExtension &
- 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.loop_grower.FragmentExtension) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::loop_grower::FragmentExtension::clone() const –> class std::shared_ptr<class protocols::moves::Mover>
- cluster_fragments(self: pyrosetta.rosetta.protocols.loop_grower.FragmentExtension, fragments: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_fragment_FragSet_t, fragfilter: float) None ¶
C++: protocols::loop_grower::FragmentExtension::cluster_fragments(class utility::vector1<class std::shared_ptr<class core::fragment::FragSet>, class std::allocator<class std::shared_ptr<class core::fragment::FragSet> > > &, double) –> void
- 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.loop_grower.FragmentExtension) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::loop_grower::FragmentExtension::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.loop_grower.FragmentExtension) str ¶
C++: protocols::loop_grower::FragmentExtension::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
- get_unaligned(self: pyrosetta.rosetta.protocols.loop_grower.FragmentExtension, seqmap: pyrosetta.rosetta.core.id.SequenceMapping) pyrosetta.rosetta.utility.vector1_protocols_loops_Loop ¶
C++: protocols::loop_grower::FragmentExtension::get_unaligned(const class core::id::SequenceMapping &) const –> class utility::vector1<class protocols::loops::Loop, class std::allocator<class protocols::loops::Loop> >
- 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::loop_grower::FragmentExtension::mover_name() –> std::string
- static name() str ¶
C++: protocols::moves::Mover::name() –> std::string
- parse_my_tag(self: pyrosetta.rosetta.protocols.loop_grower.FragmentExtension, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None ¶
C++: protocols::loop_grower::FragmentExtension::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- provide_citation_info(self: pyrosetta.rosetta.protocols.loop_grower.FragmentExtension, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None ¶
Provide the citation.
C++: protocols::loop_grower::FragmentExtension::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void
- static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None ¶
C++: protocols::loop_grower::FragmentExtension::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void
- static register_options() None ¶
Overload this static method if you access options within the mover.
These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.
C++: protocols::moves::Mover::register_options() –> void
- reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) bool ¶
- Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on
each use.
C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool
- reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) bool ¶
- Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input
pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).
C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool
- reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) None ¶
resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.
C++: protocols::moves::Mover::reset_status() –> void
- set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) None ¶
C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void
- set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) None ¶
C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void
- set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
setter for poses contained for rms
C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void
- set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe
C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void
- set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) None ¶
Set the ‘type’ string
C++: protocols::moves::Mover::set_type(const std::string &) –> void
- 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.loop_grower.FragmentExtensionCreator¶
Bases:
MoverCreator
- assign(self: pyrosetta.rosetta.protocols.loop_grower.FragmentExtensionCreator, : pyrosetta.rosetta.protocols.loop_grower.FragmentExtensionCreator) pyrosetta.rosetta.protocols.loop_grower.FragmentExtensionCreator ¶
C++: protocols::loop_grower::FragmentExtensionCreator::operator=(const class protocols::loop_grower::FragmentExtensionCreator &) –> class protocols::loop_grower::FragmentExtensionCreator &
- create_mover(self: pyrosetta.rosetta.protocols.loop_grower.FragmentExtensionCreator) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::loop_grower::FragmentExtensionCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>
- keyname(self: pyrosetta.rosetta.protocols.loop_grower.FragmentExtensionCreator) str ¶
C++: protocols::loop_grower::FragmentExtensionCreator::keyname() const –> std::string
- class pyrosetta.rosetta.protocols.loop_grower.LoopComparator¶
Bases:
pybind11_object
- apply(self: pyrosetta.rosetta.protocols.loop_grower.LoopComparator, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::loop_grower::LoopComparator::apply(class core::pose::Pose &) –> void
- fill_pose(self: pyrosetta.rosetta.protocols.loop_grower.LoopComparator, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::loop_grower::LoopComparator::fill_pose(class core::pose::Pose &) –> void
- get_one_body_score(self: pyrosetta.rosetta.protocols.loop_grower.LoopComparator) float ¶
C++: protocols::loop_grower::LoopComparator::get_one_body_score() –> double
- push(self: pyrosetta.rosetta.protocols.loop_grower.LoopComparator, solutionset: pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolutionStore) None ¶
C++: protocols::loop_grower::LoopComparator::push(const class protocols::loop_grower::LoopPartialSolutionStore) –> void
- read_from_file(self: pyrosetta.rosetta.protocols.loop_grower.LoopComparator) None ¶
C++: protocols::loop_grower::LoopComparator::read_from_file() –> void
- set_assign_incomplete(self: pyrosetta.rosetta.protocols.loop_grower.LoopComparator, assign_incomplete: bool) None ¶
C++: protocols::loop_grower::LoopComparator::set_assign_incomplete(bool) –> void
- set_density_sf(self: pyrosetta.rosetta.protocols.loop_grower.LoopComparator, sf_dens: pyrosetta.rosetta.core.scoring.ScoreFunction) None ¶
C++: protocols::loop_grower::LoopComparator::set_density_sf(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void
- set_loops(self: pyrosetta.rosetta.protocols.loop_grower.LoopComparator, loops: pyrosetta.rosetta.utility.vector1_protocols_loops_Loop) None ¶
C++: protocols::loop_grower::LoopComparator::set_loops(class utility::vector1<class protocols::loops::Loop, class std::allocator<class protocols::loops::Loop> >) –> void
- set_read_from_file(self: pyrosetta.rosetta.protocols.loop_grower.LoopComparator, read_from_file: bool) None ¶
C++: protocols::loop_grower::LoopComparator::set_read_from_file(bool) –> void
- set_scores(self: pyrosetta.rosetta.protocols.loop_grower.LoopComparator, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::loop_grower::LoopComparator::set_scores(class core::pose::Pose &) –> void
- set_sequence(self: pyrosetta.rosetta.protocols.loop_grower.LoopComparator, fullength_seq: pyrosetta.rosetta.core.sequence.Sequence) None ¶
C++: protocols::loop_grower::LoopComparator::set_sequence(class std::shared_ptr<class core::sequence::Sequence>) –> void
- set_vdw_sf(self: pyrosetta.rosetta.protocols.loop_grower.LoopComparator, sf_vdw: pyrosetta.rosetta.core.scoring.ScoreFunction) None ¶
C++: protocols::loop_grower::LoopComparator::set_vdw_sf(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void
- class pyrosetta.rosetta.protocols.loop_grower.LoopGrower¶
Bases:
Mover
- GDThatonative(self: pyrosetta.rosetta.protocols.loop_grower.LoopGrower, pose: pyrosetta.rosetta.core.pose.Pose, natlow: int, nathi: int, natstoplow: int, natstarthi: int, startlow: int, stoplow: int, starthi: int, stophi: int) float ¶
C++: protocols::loop_grower::LoopGrower::GDThatonative(const class core::pose::Pose &, int, int, int, int, int, int, int, int) –> double
- RMStonative(self: pyrosetta.rosetta.protocols.loop_grower.LoopGrower, pose: pyrosetta.rosetta.core.pose.Pose, natlow: int, nathi: int, natstoplow: int, natstarthi: int, startlow: int, stoplow: int, starthi: int, stophi: int) float ¶
C++: protocols::loop_grower::LoopGrower::RMStonative(const class core::pose::Pose &, int, int, int, int, int, int, int, int) –> double
- add_fragment_csts(self: pyrosetta.rosetta.protocols.loop_grower.LoopGrower, pose: pyrosetta.rosetta.core.pose.Pose, startfasta: int, endfasta: int, natstoplow: int, natstarthi: int, startlower: int) None ¶
C++: protocols::loop_grower::LoopGrower::add_fragment_csts(class core::pose::Pose &, unsigned long, unsigned long, unsigned long, unsigned long, unsigned long) –> void
- add_user_csts(self: pyrosetta.rosetta.protocols.loop_grower.LoopGrower, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::loop_grower::LoopGrower::add_user_csts(class core::pose::Pose &) –> void
- addnativesolution(self: pyrosetta.rosetta.protocols.loop_grower.LoopGrower, solutionset: pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolutionStore, fa_pose: pyrosetta.rosetta.core.pose.Pose, cen_pose: pyrosetta.rosetta.core.pose.Pose, natlowerstart: int, natlowerstop: int, natupperstart: int, natupperstop: int, lower_pose: int, torsionrangelo: int, torsionrangehi: int) None ¶
C++: protocols::loop_grower::LoopGrower::addnativesolution(class protocols::loop_grower::LoopPartialSolutionStore &, class core::pose::Pose &, class core::pose::Pose &, int, int, int, int, int, unsigned long, unsigned long) –> void
- apply(self: pyrosetta.rosetta.protocols.loop_grower.LoopGrower, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::loop_grower::LoopGrower::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.loop_grower.LoopGrower, : pyrosetta.rosetta.protocols.loop_grower.LoopGrower) pyrosetta.rosetta.protocols.loop_grower.LoopGrower ¶
C++: protocols::loop_grower::LoopGrower::operator=(const class protocols::loop_grower::LoopGrower &) –> class protocols::loop_grower::LoopGrower &
- atomGDTha(self: pyrosetta.rosetta.protocols.loop_grower.LoopGrower, atom1: pyrosetta.rosetta.numeric.xyzVector_double_t, atom2: pyrosetta.rosetta.numeric.xyzVector_double_t, GDTha: int) None ¶
C++: protocols::loop_grower::LoopGrower::atomGDTha(class numeric::xyzVector<double>, class numeric::xyzVector<double>, unsigned long &) –> void
- check_auto_stop(self: pyrosetta.rosetta.protocols.loop_grower.LoopGrower, pose: pyrosetta.rosetta.core.pose.Pose, lower_res: int, upper_res: int) bool ¶
C++: protocols::loop_grower::LoopGrower::check_auto_stop(class core::pose::Pose &, unsigned long, unsigned long) –> bool
- check_coordinates(self: pyrosetta.rosetta.protocols.loop_grower.LoopGrower, pose: pyrosetta.rosetta.core.pose.Pose, lower_pose: int, upper_pose: int, lower_fasta: int, radius: float) int ¶
C++: protocols::loop_grower::LoopGrower::check_coordinates(class core::pose::Pose &, unsigned long, unsigned long, unsigned long, double) –> unsigned long
- 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.loop_grower.LoopGrower) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::loop_grower::LoopGrower::clone() const –> class std::shared_ptr<class protocols::moves::Mover>
- coordinate_filter(self: pyrosetta.rosetta.protocols.loop_grower.LoopGrower, solutionset: pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolutionStore, pose: pyrosetta.rosetta.core.pose.Pose, lower: bool, lower_fasta: int, upper_fasta: int, lower_pose: int, rangehi: int) None ¶
C++: protocols::loop_grower::LoopGrower::coordinate_filter(class protocols::loop_grower::LoopPartialSolutionStore &, class core::pose::Pose, bool, unsigned long, unsigned long, unsigned long, unsigned long) –> void
- 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>
- fafilter(self: pyrosetta.rosetta.protocols.loop_grower.LoopGrower, solutionset: pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolutionStore, fapose: pyrosetta.rosetta.core.pose.Pose, cenpose: pyrosetta.rosetta.core.pose.Pose, total_lower: int, torsionrangelo: int, torsionrangehi: int, cycle: int, lower_fasta: int, upper_fasta: int, lower_pose: int) None ¶
C++: protocols::loop_grower::LoopGrower::fafilter(class protocols::loop_grower::LoopPartialSolutionStore &, class core::pose::Pose &, class core::pose::Pose &, unsigned long, unsigned long, unsigned long, unsigned long, unsigned long, unsigned long, unsigned long) –> void
- fresh_instance(self: pyrosetta.rosetta.protocols.loop_grower.LoopGrower) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::loop_grower::LoopGrower::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>
- full_atom_beam(self: pyrosetta.rosetta.protocols.loop_grower.LoopGrower, solutionset: pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolutionStore, fa_pose: pyrosetta.rosetta.core.pose.Pose, cen_pose: pyrosetta.rosetta.core.pose.Pose, lower_pos: int, upper_pos: int) None ¶
C++: protocols::loop_grower::LoopGrower::full_atom_beam(class protocols::loop_grower::LoopPartialSolutionStore &, class core::pose::Pose &, class core::pose::Pose &, unsigned long, unsigned long) –> void
- getSolutionSet(self: pyrosetta.rosetta.protocols.loop_grower.LoopGrower) pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolutionStore ¶
C++: protocols::loop_grower::LoopGrower::getSolutionSet() –> class protocols::loop_grower::LoopPartialSolutionStore
- 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.loop_grower.LoopGrower) str ¶
C++: protocols::loop_grower::LoopGrower::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_resrange_hbond_energy(self: pyrosetta.rosetta.protocols.loop_grower.LoopGrower, pose: pyrosetta.rosetta.core.pose.Pose, lower: int, upper: int) float ¶
C++: protocols::loop_grower::LoopGrower::get_resrange_hbond_energy(class core::pose::Pose &, unsigned long, unsigned long) –> 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_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 > > &
- is_beta(self: pyrosetta.rosetta.protocols.loop_grower.LoopGrower, phi: float, psi: float) bool ¶
C++: protocols::loop_grower::LoopGrower::is_beta(double, double) –> bool
- last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) float ¶
C++: protocols::moves::Mover::last_proposal_density_ratio() –> double
- modifieddensity(self: pyrosetta.rosetta.protocols.loop_grower.LoopGrower, pose: pyrosetta.rosetta.core.pose.Pose, rangelo: int, rangehi: int, density_weight: float, includesheets: int) float ¶
C++: protocols::loop_grower::LoopGrower::modifieddensity(class core::pose::Pose &, unsigned long, unsigned long, double, unsigned long &) –> double
- modifiedscore(self: pyrosetta.rosetta.protocols.loop_grower.LoopGrower, fapose: pyrosetta.rosetta.core.pose.Pose, cen_pose: pyrosetta.rosetta.core.pose.Pose, rangelo: int, rangehi: int) float ¶
C++: protocols::loop_grower::LoopGrower::modifiedscore(class core::pose::Pose &, class core::pose::Pose &, unsigned long, unsigned long) –> double
- static name() str ¶
C++: protocols::moves::Mover::name() –> std::string
- nton3_hbond_score(self: pyrosetta.rosetta.protocols.loop_grower.LoopGrower, pose: pyrosetta.rosetta.core.pose.Pose) float ¶
C++: protocols::loop_grower::LoopGrower::nton3_hbond_score(class core::pose::Pose &) –> double
- parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None ¶
Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.
C++: protocols::moves::Mover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- provide_citation_info(self: pyrosetta.rosetta.protocols.loop_grower.LoopGrower, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None ¶
Provide the citation.
C++: protocols::loop_grower::LoopGrower::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void
- read_coordfile(self: pyrosetta.rosetta.protocols.loop_grower.LoopGrower) None ¶
C++: protocols::loop_grower::LoopGrower::read_coordfile() –> void
- read_from_disk(self: pyrosetta.rosetta.protocols.loop_grower.LoopGrower, solutionset: pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolutionStore, cycle: int, lower: bool, filterbeams: bool) None ¶
C++: protocols::loop_grower::LoopGrower::read_from_disk(class protocols::loop_grower::LoopPartialSolutionStore &, int &, bool &, bool) –> void
- refine_cycle(self: pyrosetta.rosetta.protocols.loop_grower.LoopGrower, pose: pyrosetta.rosetta.core.pose.Pose, cen_pose: pyrosetta.rosetta.core.pose.Pose, loop_start: int, loop_end: int, finalrefinement: bool, cycle: int, beam: int, fragment: int, is_lower: int) None ¶
C++: protocols::loop_grower::LoopGrower::refine_cycle(class core::pose::Pose &, class core::pose::Pose &, int, int, bool, int, int, int, unsigned long) –> 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
- rescoresolutionset(self: pyrosetta.rosetta.protocols.loop_grower.LoopGrower, solutionset: pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolutionStore, fa_pose: pyrosetta.rosetta.core.pose.Pose, cen_pose: pyrosetta.rosetta.core.pose.Pose, torsionrangelo: int, torsionrangehi: int) None ¶
C++: protocols::loop_grower::LoopGrower::rescoresolutionset(class protocols::loop_grower::LoopPartialSolutionStore &, class core::pose::Pose &, class core::pose::Pose &, unsigned long, unsigned long) –> 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_asymmdump(self: pyrosetta.rosetta.protocols.loop_grower.LoopGrower, asymmdump: bool) None ¶
C++: protocols::loop_grower::LoopGrower::set_asymmdump(bool) –> void
- set_auto_stop(self: pyrosetta.rosetta.protocols.loop_grower.LoopGrower, auto_stop: bool) None ¶
C++: protocols::loop_grower::LoopGrower::set_auto_stop(bool) –> void
- set_beamscorecutoff(self: pyrosetta.rosetta.protocols.loop_grower.LoopGrower, beamscorecutoff: float) None ¶
C++: protocols::loop_grower::LoopGrower::set_beamscorecutoff(double) –> void
- set_beamwidth(self: pyrosetta.rosetta.protocols.loop_grower.LoopGrower, beamwidth: int) None ¶
C++: protocols::loop_grower::LoopGrower::set_beamwidth(unsigned long) –> void
- set_cen_scorefunction(self: pyrosetta.rosetta.protocols.loop_grower.LoopGrower, sf: pyrosetta.rosetta.core.scoring.ScoreFunction) None ¶
C++: protocols::loop_grower::LoopGrower::set_cen_scorefunction(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void
- set_cenrot(self: pyrosetta.rosetta.protocols.loop_grower.LoopGrower, cenrot: bool) None ¶
C++: protocols::loop_grower::LoopGrower::set_cenrot(bool) –> void
- set_cenrot_scorefunction(self: pyrosetta.rosetta.protocols.loop_grower.LoopGrower, sf: pyrosetta.rosetta.core.scoring.ScoreFunction) None ¶
C++: protocols::loop_grower::LoopGrower::set_cenrot_scorefunction(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void
- set_chainbreak(self: pyrosetta.rosetta.protocols.loop_grower.LoopGrower, chainbreak: float) None ¶
C++: protocols::loop_grower::LoopGrower::set_chainbreak(double) –> void
- set_checksymm(self: pyrosetta.rosetta.protocols.loop_grower.LoopGrower, checksymm: bool) None ¶
C++: protocols::loop_grower::LoopGrower::set_checksymm(bool) –> void
- set_clustercheck(self: pyrosetta.rosetta.protocols.loop_grower.LoopGrower, clustercheck: bool) None ¶
C++: protocols::loop_grower::LoopGrower::set_clustercheck(bool) –> void
- set_continuous_sheets(self: pyrosetta.rosetta.protocols.loop_grower.LoopGrower, continuous_sheets: bool) None ¶
C++: protocols::loop_grower::LoopGrower::set_continuous_sheets(bool) –> void
- set_continuous_weight(self: pyrosetta.rosetta.protocols.loop_grower.LoopGrower, continuous_weight: float) None ¶
C++: protocols::loop_grower::LoopGrower::set_continuous_weight(double) –> void
- set_coordfile(self: pyrosetta.rosetta.protocols.loop_grower.LoopGrower, coordfile: str) None ¶
C++: protocols::loop_grower::LoopGrower::set_coordfile(std::string) –> void
- set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) None ¶
C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void
- set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) None ¶
C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void
- set_debug(self: pyrosetta.rosetta.protocols.loop_grower.LoopGrower, debug: bool) None ¶
C++: protocols::loop_grower::LoopGrower::set_debug(bool) –> void
- set_direction(self: pyrosetta.rosetta.protocols.loop_grower.LoopGrower, direction: int) None ¶
C++: protocols::loop_grower::LoopGrower::set_direction(unsigned long) –> void
- set_dumpbeam(self: pyrosetta.rosetta.protocols.loop_grower.LoopGrower, dumpbeam: bool) None ¶
C++: protocols::loop_grower::LoopGrower::set_dumpbeam(bool) –> void
- set_dumperrors(self: pyrosetta.rosetta.protocols.loop_grower.LoopGrower, dumperrors: bool) None ¶
C++: protocols::loop_grower::LoopGrower::set_dumperrors(bool) –> void
- set_dumpfinalbeam(self: pyrosetta.rosetta.protocols.loop_grower.LoopGrower, dumpfinalbeam: bool) None ¶
C++: protocols::loop_grower::LoopGrower::set_dumpfinalbeam(bool) –> void
- set_dumprms(self: pyrosetta.rosetta.protocols.loop_grower.LoopGrower, dumprms: bool) None ¶
C++: protocols::loop_grower::LoopGrower::set_dumprms(bool) –> void
- set_fafilter(self: pyrosetta.rosetta.protocols.loop_grower.LoopGrower, fafilter: bool) None ¶
C++: protocols::loop_grower::LoopGrower::set_fafilter(bool) –> void
- set_famin(self: pyrosetta.rosetta.protocols.loop_grower.LoopGrower, famin: bool) None ¶
C++: protocols::loop_grower::LoopGrower::set_famin(bool) –> void
- set_filterbeams(self: pyrosetta.rosetta.protocols.loop_grower.LoopGrower, filterbeams: str) None ¶
C++: protocols::loop_grower::LoopGrower::set_filterbeams(std::string) –> void
- set_filterprevious(self: pyrosetta.rosetta.protocols.loop_grower.LoopGrower, filterprevious: bool) None ¶
C++: protocols::loop_grower::LoopGrower::set_filterprevious(bool) –> void
- set_fragmelt(self: pyrosetta.rosetta.protocols.loop_grower.LoopGrower, fragmelt: int) None ¶
C++: protocols::loop_grower::LoopGrower::set_fragmelt(unsigned long) –> void
- set_fragtrials(self: pyrosetta.rosetta.protocols.loop_grower.LoopGrower, fragtrials: int) None ¶
C++: protocols::loop_grower::LoopGrower::set_fragtrials(unsigned long) –> void
- set_greedy(self: pyrosetta.rosetta.protocols.loop_grower.LoopGrower, greedy: bool) None ¶
C++: protocols::loop_grower::LoopGrower::set_greedy(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_loopnumber(self: pyrosetta.rosetta.protocols.loop_grower.LoopGrower, loopnumber: int) None ¶
C++: protocols::loop_grower::LoopGrower::set_loopnumber(unsigned long) –> void
- set_master_beam_cutoff(self: pyrosetta.rosetta.protocols.loop_grower.LoopGrower, master_beam_cutoff: float) None ¶
C++: protocols::loop_grower::LoopGrower::set_master_beam_cutoff(double) –> void
- set_master_beam_width(self: pyrosetta.rosetta.protocols.loop_grower.LoopGrower, master_beam_width: int) None ¶
C++: protocols::loop_grower::LoopGrower::set_master_beam_width(unsigned long) –> void
- set_minimize(self: pyrosetta.rosetta.protocols.loop_grower.LoopGrower, minimize: bool) None ¶
C++: protocols::loop_grower::LoopGrower::set_minimize(bool) –> void
- set_minmelt(self: pyrosetta.rosetta.protocols.loop_grower.LoopGrower, minmelt: int) None ¶
C++: protocols::loop_grower::LoopGrower::set_minmelt(unsigned long) –> void
- set_native(self: pyrosetta.rosetta.protocols.loop_grower.LoopGrower, native: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::loop_grower::LoopGrower::set_native(class std::shared_ptr<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_nativegrow(self: pyrosetta.rosetta.protocols.loop_grower.LoopGrower, nativegrow: bool) None ¶
C++: protocols::loop_grower::LoopGrower::set_nativegrow(bool) –> void
- set_pack_min_cycles(self: pyrosetta.rosetta.protocols.loop_grower.LoopGrower, pack_min_cycles: int) None ¶
C++: protocols::loop_grower::LoopGrower::set_pack_min_cycles(unsigned long) –> void
- set_parametercheck(self: pyrosetta.rosetta.protocols.loop_grower.LoopGrower, parametercheck: bool) None ¶
C++: protocols::loop_grower::LoopGrower::set_parametercheck(bool) –> void
- set_pcount(self: pyrosetta.rosetta.protocols.loop_grower.LoopGrower, parallelcount: int) None ¶
C++: protocols::loop_grower::LoopGrower::set_pcount(unsigned long) –> void
- set_readbeams(self: pyrosetta.rosetta.protocols.loop_grower.LoopGrower, readbeams: bool) None ¶
C++: protocols::loop_grower::LoopGrower::set_readbeams(bool) –> void
- set_rephasemap(self: pyrosetta.rosetta.protocols.loop_grower.LoopGrower, rephasemap: bool) None ¶
C++: protocols::loop_grower::LoopGrower::set_rephasemap(bool) –> void
- set_rescorebeams(self: pyrosetta.rosetta.protocols.loop_grower.LoopGrower, rescorebeams: bool) None ¶
C++: protocols::loop_grower::LoopGrower::set_rescorebeams(bool) –> void
- set_rmscutoff(self: pyrosetta.rosetta.protocols.loop_grower.LoopGrower, rmscutoff: float) None ¶
C++: protocols::loop_grower::LoopGrower::set_rmscutoff(double) –> void
- set_rmswindow(self: pyrosetta.rosetta.protocols.loop_grower.LoopGrower, rmswindow: int) None ¶
C++: protocols::loop_grower::LoopGrower::set_rmswindow(unsigned long) –> void
- set_samplesheets(self: pyrosetta.rosetta.protocols.loop_grower.LoopGrower, samplesheets: bool) None ¶
C++: protocols::loop_grower::LoopGrower::set_samplesheets(bool) –> void
- set_sc_scale(self: pyrosetta.rosetta.protocols.loop_grower.LoopGrower, sc_scale: float) None ¶
C++: protocols::loop_grower::LoopGrower::set_sc_scale(double) –> void
- set_scorefunction(self: pyrosetta.rosetta.protocols.loop_grower.LoopGrower, sf: pyrosetta.rosetta.core.scoring.ScoreFunction) None ¶
C++: protocols::loop_grower::LoopGrower::set_scorefunction(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void
- set_sheet_tolerance(self: pyrosetta.rosetta.protocols.loop_grower.LoopGrower, sheet_tolerance: float) None ¶
C++: protocols::loop_grower::LoopGrower::set_sheet_tolerance(double) –> void
- set_sheetbonus(self: pyrosetta.rosetta.protocols.loop_grower.LoopGrower, sheetbonus: float) None ¶
C++: protocols::loop_grower::LoopGrower::set_sheetbonus(double) –> void
- set_sheetcriteria(self: pyrosetta.rosetta.protocols.loop_grower.LoopGrower, sheetcriteria: int) None ¶
C++: protocols::loop_grower::LoopGrower::set_sheetcriteria(unsigned long) –> void
- set_skeletonfile(self: pyrosetta.rosetta.protocols.loop_grower.LoopGrower, skeletonfile: str) None ¶
C++: protocols::loop_grower::LoopGrower::set_skeletonfile(std::string) –> void
- set_steps(self: pyrosetta.rosetta.protocols.loop_grower.LoopGrower, steps: int) None ¶
C++: protocols::loop_grower::LoopGrower::set_steps(unsigned long) –> void
- set_storedbeams(self: pyrosetta.rosetta.protocols.loop_grower.LoopGrower, storedbeams: str) None ¶
C++: protocols::loop_grower::LoopGrower::set_storedbeams(std::string) –> void
- set_trackfragments(self: pyrosetta.rosetta.protocols.loop_grower.LoopGrower, trackfragments: bool) None ¶
C++: protocols::loop_grower::LoopGrower::set_trackfragments(bool) –> void
- set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) None ¶
Set the ‘type’ string
C++: protocols::moves::Mover::set_type(const std::string &) –> void
- set_windowdensweight(self: pyrosetta.rosetta.protocols.loop_grower.LoopGrower, windowdensweight: float) None ¶
C++: protocols::loop_grower::LoopGrower::set_windowdensweight(double) –> void
- set_writebeams(self: pyrosetta.rosetta.protocols.loop_grower.LoopGrower, writebeams: bool) None ¶
C++: protocols::loop_grower::LoopGrower::set_writebeams(bool) –> void
- set_writelps(self: pyrosetta.rosetta.protocols.loop_grower.LoopGrower, writelps: bool) None ¶
C++: protocols::loop_grower::LoopGrower::set_writelps(bool) –> void
- sheetscore(self: pyrosetta.rosetta.protocols.loop_grower.LoopGrower, fapose: pyrosetta.rosetta.core.pose.Pose, cen_pose: pyrosetta.rosetta.core.pose.Pose, rangelo: int, rangehi: int) float ¶
C++: protocols::loop_grower::LoopGrower::sheetscore(class core::pose::Pose &, class core::pose::Pose &, unsigned long, unsigned long) –> double
- 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
- single_grow(self: pyrosetta.rosetta.protocols.loop_grower.LoopGrower, pose: pyrosetta.rosetta.core.pose.Pose, pose_cen: pyrosetta.rosetta.core.pose.Pose, solutionset: pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolutionStore, restypes_pose: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_chemical_ResidueType_t, restypes_pos_cen: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_chemical_ResidueType_t, lower_pose: int, upper_pose: int, upper_term: int, lower_fasta: int, upper_fasta: int, torsionrangelo: int, torsionrangehi: int, insert_lower: bool, initial_melt_left: int, is_cterm: bool, is_nterm: bool, cycle: int, n_to_insert: int) float ¶
C++: protocols::loop_grower::LoopGrower::single_grow(class core::pose::Pose &, class core::pose::Pose &, class protocols::loop_grower::LoopPartialSolutionStore &, const class utility::vector1<class std::shared_ptr<const class core::chemical::ResidueType>, class std::allocator<class std::shared_ptr<const class core::chemical::ResidueType> > > &, const class utility::vector1<class std::shared_ptr<const class core::chemical::ResidueType>, class std::allocator<class std::shared_ptr<const class core::chemical::ResidueType> > > &, unsigned long, unsigned long, unsigned long, int, int, unsigned long, unsigned long, bool, unsigned long, bool, bool, unsigned long, int) –> double
- store_sheets(self: pyrosetta.rosetta.protocols.loop_grower.LoopGrower, pose: pyrosetta.rosetta.core.pose.Pose, lps: pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolution) None ¶
C++: protocols::loop_grower::LoopGrower::store_sheets(class core::pose::Pose &, class protocols::loop_grower::LoopPartialSolution &) –> 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 &
- update_and_writelps(self: pyrosetta.rosetta.protocols.loop_grower.LoopGrower, solutionset: pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolutionStore, fa_pose: pyrosetta.rosetta.core.pose.Pose, pose_cen: pyrosetta.rosetta.core.pose.Pose, restypes_pose: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_chemical_ResidueType_t, restypes_pose_cen: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_chemical_ResidueType_t, lower_pose: int, upper_pose: int, is_nterm: bool, is_cterm: bool, fasta_range_low: int, fasta_range_hi: int, pose_range_low: int, pose_range_hi: int, torsionrangelo: int, torsionrangehi: int, tgt_jump: int, update_pose: bool) None ¶
C++: protocols::loop_grower::LoopGrower::update_and_writelps(class protocols::loop_grower::LoopPartialSolutionStore &, class core::pose::Pose &, class core::pose::Pose &, class utility::vector1<class std::shared_ptr<const class core::chemical::ResidueType>, class std::allocator<class std::shared_ptr<const class core::chemical::ResidueType> > > &, class utility::vector1<class std::shared_ptr<const class core::chemical::ResidueType>, class std::allocator<class std::shared_ptr<const class core::chemical::ResidueType> > > &, int, int, bool, bool, unsigned long, unsigned long, unsigned long, unsigned long, int, int, int, bool) –> void
- update_fragment_library_pointers(self: pyrosetta.rosetta.protocols.loop_grower.LoopGrower) None ¶
C++: protocols::loop_grower::LoopGrower::update_fragment_library_pointers() –> void
- update_to_stored(self: pyrosetta.rosetta.protocols.loop_grower.LoopGrower, growpose: pyrosetta.rosetta.core.pose.Pose, growpose_cen: pyrosetta.rosetta.core.pose.Pose, restypes_pose: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_chemical_ResidueType_t, restypes_pose_cen: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_chemical_ResidueType_t, lower_pose: int, upper_pose: int, lower_fasta: int, upper_fasta: int, newreslow: int, newreshi: int, is_cterm: bool, is_nterm: bool) None ¶
C++: protocols::loop_grower::LoopGrower::update_to_stored(class core::pose::Pose &, class core::pose::Pose &, const class utility::vector1<class std::shared_ptr<const class core::chemical::ResidueType>, class std::allocator<class std::shared_ptr<const class core::chemical::ResidueType> > > &, const class utility::vector1<class std::shared_ptr<const class core::chemical::ResidueType>, class std::allocator<class std::shared_ptr<const class core::chemical::ResidueType> > > &, int &, int &, int &, int &, unsigned long, unsigned long, bool, bool) –> void
- write_to_disk(self: pyrosetta.rosetta.protocols.loop_grower.LoopGrower, solutionset: pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolutionStore, step: int, added_lower: int, added_upper: int, filteronly: bool, lower: bool) None ¶
C++: protocols::loop_grower::LoopGrower::write_to_disk(class protocols::loop_grower::LoopPartialSolutionStore, unsigned long, unsigned long, unsigned long, bool, bool) –> void
- class pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolution¶
Bases:
pybind11_object
- add_sheets(self: pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolution, pose: pyrosetta.rosetta.core.pose.Pose, takeoffres: int, totalres: int) None ¶
C++: protocols::loop_grower::LoopPartialSolution::add_sheets(class core::pose::Pose &, unsigned long, unsigned long) –> void
- apply(*args, **kwargs)¶
Overloaded function.
apply(self: pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolution, pose: pyrosetta.rosetta.core.pose.Pose, range1lo: int, range1hi: int, range2lo: int, range2hi: int) -> None
C++: protocols::loop_grower::LoopPartialSolution::apply(class core::pose::Pose &, int, int, int, int) –> void
apply(self: pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolution, pose: pyrosetta.rosetta.core.pose.Pose, range1lo: int, range1hi: int) -> None
C++: protocols::loop_grower::LoopPartialSolution::apply(class core::pose::Pose &, int, int) –> void
- apply_sheets(self: pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolution, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::loop_grower::LoopPartialSolution::apply_sheets(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolution, : pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolution) pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolution ¶
C++: protocols::loop_grower::LoopPartialSolution::operator=(const class protocols::loop_grower::LoopPartialSolution &) –> class protocols::loop_grower::LoopPartialSolution &
- get_backbone(self: pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolution) pyrosetta.rosetta.utility.vector1_utility_vector1_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t ¶
C++: protocols::loop_grower::LoopPartialSolution::get_backbone() const –> class utility::vector1<class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > >, class std::allocator<class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > > > >
- get_bonus_score(self: pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolution) float ¶
C++: protocols::loop_grower::LoopPartialSolution::get_bonus_score() const –> double
- get_calphas(self: pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolution) pyrosetta.rosetta.utility.vector1_numeric_xyzVector_double_t ¶
C++: protocols::loop_grower::LoopPartialSolution::get_calphas() const –> class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > >
- get_gdt(self: pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolution) float ¶
C++: protocols::loop_grower::LoopPartialSolution::get_gdt() const –> double
- get_history(self: pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolution) pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t ¶
C++: protocols::loop_grower::LoopPartialSolution::get_history() –> class utility::vector1<struct std::pair<unsigned long, unsigned long>, class std::allocator<struct std::pair<unsigned long, unsigned long> > >
- get_id(self: pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolution) str ¶
C++: protocols::loop_grower::LoopPartialSolution::get_id() –> std::string
- get_rms(self: pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolution) float ¶
C++: protocols::loop_grower::LoopPartialSolution::get_rms() const –> double
- get_score(self: pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolution) float ¶
C++: protocols::loop_grower::LoopPartialSolution::get_score() const –> double
- max_calpha_distance(self: pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolution, : pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolution, fragmelt: int, total_lower: int, takeoffonly: bool, full_loop: bool, lower: bool) float ¶
C++: protocols::loop_grower::LoopPartialSolution::max_calpha_distance(const class protocols::loop_grower::LoopPartialSolution &, unsigned long, unsigned long, bool, bool, bool) const –> double
- partialrms(self: pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolution, : pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolution, fragmelt: int, total_lower: int, takeoffonly: bool, rmswindow: int) float ¶
C++: protocols::loop_grower::LoopPartialSolution::partialrms(const class protocols::loop_grower::LoopPartialSolution &, int, int, bool, int) const –> double
- push_back_backbone(self: pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolution, backbone: pyrosetta.rosetta.utility.vector1_numeric_xyzVector_double_t) None ¶
C++: protocols::loop_grower::LoopPartialSolution::push_back_backbone(class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > >) –> void
- push_back_restorsions(self: pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolution, restorsions: pyrosetta.rosetta.protocols.loop_grower.ResTorsions) None ¶
C++: protocols::loop_grower::LoopPartialSolution::push_back_restorsions(struct protocols::loop_grower::ResTorsions) –> void
- push_back_sheet(self: pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolution, sheet: pyrosetta.rosetta.protocols.loop_grower.SheetPositions) None ¶
C++: protocols::loop_grower::LoopPartialSolution::push_back_sheet(struct protocols::loop_grower::SheetPositions) –> void
- set_bonus_score(self: pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolution, bonus: float) None ¶
C++: protocols::loop_grower::LoopPartialSolution::set_bonus_score(double) –> void
- set_centerofmass(self: pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolution) None ¶
C++: protocols::loop_grower::LoopPartialSolution::set_centerofmass() –> void
- set_coordinates(self: pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolution, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::loop_grower::LoopPartialSolution::set_coordinates(class core::pose::Pose &) –> void
- set_gdt(self: pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolution, GDT: float) None ¶
C++: protocols::loop_grower::LoopPartialSolution::set_gdt(double) –> void
- set_history(*args, **kwargs)¶
Overloaded function.
set_history(self: pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolution, history: pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t, newfrag: Tuple[int, int]) -> None
C++: protocols::loop_grower::LoopPartialSolution::set_history(class utility::vector1<struct std::pair<unsigned long, unsigned long>, class std::allocator<struct std::pair<unsigned long, unsigned long> > >, struct std::pair<unsigned long, unsigned long>) –> void
set_history(self: pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolution, history: pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t) -> None
C++: protocols::loop_grower::LoopPartialSolution::set_history(class utility::vector1<struct std::pair<unsigned long, unsigned long>, class std::allocator<struct std::pair<unsigned long, unsigned long> > >) –> void
- set_id(self: pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolution, id: str) None ¶
C++: protocols::loop_grower::LoopPartialSolution::set_id(std::string) –> void
- set_ids(self: pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolution, ids: pyrosetta.rosetta.utility.vector1_core_id_AtomID) None ¶
C++: protocols::loop_grower::LoopPartialSolution::set_ids(class utility::vector1<class core::id::AtomID, class std::allocator<class core::id::AtomID> >) –> void
- set_positions(self: pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolution, positions: pyrosetta.rosetta.utility.vector1_numeric_xyzVector_double_t) None ¶
C++: protocols::loop_grower::LoopPartialSolution::set_positions(class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > >) –> void
- set_rms(self: pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolution, RMS: float) None ¶
C++: protocols::loop_grower::LoopPartialSolution::set_rms(double) –> void
- set_score(self: pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolution, score: float) None ¶
C++: protocols::loop_grower::LoopPartialSolution::set_score(double) –> void
- size(self: pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolution) float ¶
C++: protocols::loop_grower::LoopPartialSolution::size() –> double
- store_coordinates(self: pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolution, pose: pyrosetta.rosetta.core.pose.Pose, reslow: int, reshigh: int, lower_fasta: int) None ¶
C++: protocols::loop_grower::LoopPartialSolution::store_coordinates(const class core::pose::Pose &, int, int, unsigned long) –> void
- store_sheetpositions(self: pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolution, pose: pyrosetta.rosetta.core.pose.Pose, rangelo: int, rangehi: int, jumpid: int, basres: int) None ¶
C++: protocols::loop_grower::LoopPartialSolution::store_sheetpositions(class core::pose::Pose &, unsigned long, unsigned long, unsigned long, unsigned long) –> void
- write_beam(self: pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolution, outbeam: pyrosetta.rosetta.std.ostream) None ¶
C++: protocols::loop_grower::LoopPartialSolution::write_beam(std::ostream &) –> void
- write_beam_lps(self: pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolution, lpsfile: pyrosetta.rosetta.std.ostream) None ¶
C++: protocols::loop_grower::LoopPartialSolution::write_beam_lps(std::ostream &) –> void
- class pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolutionStore¶
Bases:
pybind11_object
- assign(self: pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolutionStore, : pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolutionStore) pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolutionStore ¶
C++: protocols::loop_grower::LoopPartialSolutionStore::operator=(const class protocols::loop_grower::LoopPartialSolutionStore &) –> class protocols::loop_grower::LoopPartialSolutionStore &
- clear(self: pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolutionStore) None ¶
C++: protocols::loop_grower::LoopPartialSolutionStore::clear() –> void
- cluster_check(self: pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolutionStore, nearnativelps: pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolution, pose: pyrosetta.rosetta.core.pose.Pose, total_lower: int, lower_res: int, upper_res: int) None ¶
C++: protocols::loop_grower::LoopPartialSolutionStore::cluster_check(class protocols::loop_grower::LoopPartialSolution, class core::pose::Pose &, unsigned long, unsigned long, unsigned long) –> void
- diversityfilter(self: pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolutionStore, maxbeamsize: int, total_lower: int) None ¶
C++: protocols::loop_grower::LoopPartialSolutionStore::diversityfilter(unsigned long, unsigned long) –> void
- filter(self: pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolutionStore, pose: pyrosetta.rosetta.core.pose.Pose, maxbeam: int, total_lower: int, lower_res: int, upper_res: int, cycle: int) None ¶
C++: protocols::loop_grower::LoopPartialSolutionStore::filter(class core::pose::Pose &, unsigned long, unsigned long, unsigned long, unsigned long, unsigned long) –> void
- filterprevious(self: pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolutionStore, lps: pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolution, total_lower: int, fragmelt: int, rmscutoff: float, masterbeamwidth: int) bool ¶
C++: protocols::loop_grower::LoopPartialSolutionStore::filterprevious(class protocols::loop_grower::LoopPartialSolution, unsigned long, unsigned long, double, unsigned long) –> bool
- get_cutpoint(self: pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolutionStore) int ¶
C++: protocols::loop_grower::LoopPartialSolutionStore::get_cutpoint() –> unsigned long
- get_filteronly_solutions(self: pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolutionStore) pyrosetta.rosetta.utility.vector1_protocols_loop_grower_LoopPartialSolution ¶
C++: protocols::loop_grower::LoopPartialSolutionStore::get_filteronly_solutions() –> class utility::vector1<class protocols::loop_grower::LoopPartialSolution, class std::allocator<class protocols::loop_grower::LoopPartialSolution> >
- get_lower_fasta(self: pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolutionStore) int ¶
C++: protocols::loop_grower::LoopPartialSolutionStore::get_lower_fasta() –> unsigned long
- get_lower_pose(self: pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolutionStore) int ¶
C++: protocols::loop_grower::LoopPartialSolutionStore::get_lower_pose() –> unsigned long
- get_solutions(self: pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolutionStore) pyrosetta.rosetta.utility.vector1_protocols_loop_grower_LoopPartialSolution ¶
C++: protocols::loop_grower::LoopPartialSolutionStore::get_solutions() –> class utility::vector1<class protocols::loop_grower::LoopPartialSolution, class std::allocator<class protocols::loop_grower::LoopPartialSolution> >
- get_upper_fasta(self: pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolutionStore) int ¶
C++: protocols::loop_grower::LoopPartialSolutionStore::get_upper_fasta() –> unsigned long
- get_upper_pose(self: pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolutionStore) int ¶
C++: protocols::loop_grower::LoopPartialSolutionStore::get_upper_pose() –> unsigned long
- is_empty(self: pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolutionStore) bool ¶
C++: protocols::loop_grower::LoopPartialSolutionStore::is_empty() –> bool
- parametercheck_filter(self: pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolutionStore, pose: pyrosetta.rosetta.core.pose.Pose, fragmelt: int, total_lower: int, lower_res: int, upper_res: int, rmswindow: int, dump_beam: bool, totalreqbeam: int, totalreqmaxbeam: int, totalreqscorecut: float, writebeams: bool, cycle: int, parallelcount: int) None ¶
C++: protocols::loop_grower::LoopPartialSolutionStore::parametercheck_filter(class core::pose::Pose &, unsigned long, unsigned long, unsigned long, unsigned long, unsigned long, bool, unsigned long &, unsigned long &, double &, bool, unsigned long, unsigned long) –> void
- push(self: pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolutionStore, pose: pyrosetta.rosetta.core.pose.Pose, new_entry: pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolution, fragmelt: int, beamscorecutoff: float, total_lower: int, lower: bool, dump_errors: bool, RMS: float, lower_res: int, upper_res: int) None ¶
C++: protocols::loop_grower::LoopPartialSolutionStore::push(class core::pose::Pose &, const class protocols::loop_grower::LoopPartialSolution &, unsigned long, double, unsigned long, bool, bool, double, unsigned long, unsigned long) –> void
- report_rms_and_scores(self: pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolutionStore, rangelo: int, rangehi: int) None ¶
C++: protocols::loop_grower::LoopPartialSolutionStore::report_rms_and_scores(unsigned long, unsigned long) –> void
- set_cutpoint(self: pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolutionStore, cutpoint: int) None ¶
C++: protocols::loop_grower::LoopPartialSolutionStore::set_cutpoint(unsigned long) –> void
- set_fastas(self: pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolutionStore, lower: int, upper: int) None ¶
C++: protocols::loop_grower::LoopPartialSolutionStore::set_fastas(unsigned long, unsigned long) –> void
- set_filterprevious(self: pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolutionStore, filterprevious: bool) None ¶
C++: protocols::loop_grower::LoopPartialSolutionStore::set_filterprevious(bool) –> void
- set_poses(self: pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolutionStore, lower: int, upper: int) None ¶
C++: protocols::loop_grower::LoopPartialSolutionStore::set_poses(unsigned long, unsigned long) –> void
- setfilterparams(self: pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolutionStore, fragmelt: int, rmswindow: int, parallelcount: int, beamscorecutoff: float, dump_errors: bool, dump_beam: bool, writebeams: bool, clustercheck: bool, fafilter: bool, samplesheets: bool, filterprevious: bool, checksymm: bool, asymmdump: bool, dumpfinalbeam: bool) None ¶
C++: protocols::loop_grower::LoopPartialSolutionStore::setfilterparams(unsigned long, unsigned long, unsigned long, double, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool) –> void
- size(self: pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolutionStore) int ¶
C++: protocols::loop_grower::LoopPartialSolutionStore::size() –> unsigned long
- skeleton_filter(self: pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolutionStore, pose: pyrosetta.rosetta.core.pose.Pose, skeleton: pyrosetta.rosetta.protocols.loop_grower.DensSkeleton, start_res: int, stop_res: int, lower_term: int, res_gap: int) None ¶
C++: protocols::loop_grower::LoopPartialSolutionStore::skeleton_filter(class core::pose::Pose &, class protocols::loop_grower::DensSkeleton &, unsigned long, unsigned long, unsigned long, unsigned long) –> void
- sort(self: pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolutionStore) None ¶
C++: protocols::loop_grower::LoopPartialSolutionStore::sort() –> void
- sortrms(self: pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolutionStore) None ¶
C++: protocols::loop_grower::LoopPartialSolutionStore::sortrms() –> void
- store(self: pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolutionStore, new_entry: pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolution) None ¶
C++: protocols::loop_grower::LoopPartialSolutionStore::store(const class protocols::loop_grower::LoopPartialSolution &) –> void
- store_filteronly_solutions(self: pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolutionStore, filteronly: pyrosetta.rosetta.utility.vector1_protocols_loop_grower_LoopPartialSolution) None ¶
C++: protocols::loop_grower::LoopPartialSolutionStore::store_filteronly_solutions(class utility::vector1<class protocols::loop_grower::LoopPartialSolution, class std::allocator<class protocols::loop_grower::LoopPartialSolution> >) –> void
- writelpsstore(self: pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolutionStore, loopid: int, jobid: int) None ¶
C++: protocols::loop_grower::LoopPartialSolutionStore::writelpsstore(unsigned long, unsigned long) –> void
- zscoretransform(self: pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolutionStore) None ¶
C++: protocols::loop_grower::LoopPartialSolutionStore::zscoretransform() –> void
- class pyrosetta.rosetta.protocols.loop_grower.RMSComparator¶
Bases:
pybind11_object
- class pyrosetta.rosetta.protocols.loop_grower.ResTorsions¶
Bases:
pybind11_object
- assign(self: pyrosetta.rosetta.protocols.loop_grower.ResTorsions, : pyrosetta.rosetta.protocols.loop_grower.ResTorsions) pyrosetta.rosetta.protocols.loop_grower.ResTorsions ¶
C++: protocols::loop_grower::ResTorsions::operator=(const struct protocols::loop_grower::ResTorsions &) –> struct protocols::loop_grower::ResTorsions &
- property chi1_¶
- property chi2_¶
- property chi3_¶
- property chi4_¶
- property nchi_¶
- property omega_¶
- property phi_¶
- property psi_¶
- class pyrosetta.rosetta.protocols.loop_grower.SheetPositions¶
Bases:
pybind11_object
- assign(self: pyrosetta.rosetta.protocols.loop_grower.SheetPositions, : pyrosetta.rosetta.protocols.loop_grower.SheetPositions) pyrosetta.rosetta.protocols.loop_grower.SheetPositions ¶
C++: protocols::loop_grower::SheetPositions::operator=(const struct protocols::loop_grower::SheetPositions &) –> struct protocols::loop_grower::SheetPositions &
- property baseres_¶
- property jumpid_¶
- property residues_¶
- property rotation_¶
- property translation_¶
- class pyrosetta.rosetta.protocols.loop_grower.SheetSampler¶
Bases:
Mover
- alignPerfectCA(self: pyrosetta.rosetta.protocols.loop_grower.SheetSampler, pose: pyrosetta.rosetta.core.pose.Pose, moving: int, ref: int) None ¶
C++: protocols::loop_grower::SheetSampler::alignPerfectCA(class core::pose::Pose &, unsigned long, unsigned long) –> void
- alignStrand(self: pyrosetta.rosetta.protocols.loop_grower.SheetSampler, pose: pyrosetta.rosetta.core.pose.Pose, ref: int, moving: int, strand_start: int, strand_size: int) None ¶
C++: protocols::loop_grower::SheetSampler::alignStrand(class core::pose::Pose &, unsigned long, unsigned long, unsigned long, unsigned long) –> void
- apply(self: pyrosetta.rosetta.protocols.loop_grower.SheetSampler, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::loop_grower::SheetSampler::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.loop_grower.SheetSampler, : pyrosetta.rosetta.protocols.loop_grower.SheetSampler) pyrosetta.rosetta.protocols.loop_grower.SheetSampler ¶
C++: protocols::loop_grower::SheetSampler::operator=(const class protocols::loop_grower::SheetSampler &) –> class protocols::loop_grower::SheetSampler &
- 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>
- generate_jump_frags(self: pyrosetta.rosetta.protocols.loop_grower.SheetSampler, pose: pyrosetta.rosetta.core.pose.Pose, jump_nr: int, orientation: int, pleating: int, all_frames: pyrosetta.rosetta.core.fragment.FrameList) None ¶
C++: protocols::loop_grower::SheetSampler::generate_jump_frags(const class core::pose::Pose &, unsigned long, int, int, class core::fragment::FrameList &) –> void
- 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.loop_grower.SheetSampler) str ¶
C++: protocols::loop_grower::SheetSampler::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 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.loop_grower.SheetSampler, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None ¶
Provide the citation.
C++: protocols::loop_grower::SheetSampler::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void
- static register_options() None ¶
Overload this static method if you access options within the mover.
These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.
C++: protocols::moves::Mover::register_options() –> void
- reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) bool ¶
- Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on
each use.
C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool
- reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) bool ¶
- Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input
pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).
C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool
- reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) None ¶
resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.
C++: protocols::moves::Mover::reset_status() –> void
- set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) None ¶
C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void
- set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) None ¶
C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void
- set_ideal_sheets(self: pyrosetta.rosetta.protocols.loop_grower.SheetSampler, ideal_sheets: bool) None ¶
C++: protocols::loop_grower::SheetSampler::set_ideal_sheets(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_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_sf(self: pyrosetta.rosetta.protocols.loop_grower.SheetSampler, newsf: pyrosetta.rosetta.core.scoring.ScoreFunction) None ¶
C++: protocols::loop_grower::SheetSampler::set_sf(class std::shared_ptr<class core::scoring::ScoreFunction>) –> 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
- sheethbonds(self: pyrosetta.rosetta.protocols.loop_grower.SheetSampler, pose: pyrosetta.rosetta.core.pose.Pose, lower: int, upper: int) float ¶
C++: protocols::loop_grower::SheetSampler::sheethbonds(class core::pose::Pose &, unsigned long, unsigned long) –> double
- 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 &
- pyrosetta.rosetta.protocols.loop_grower.transform_res_to_subunit(pose: pyrosetta.rosetta.core.pose.Pose, xformed: pyrosetta.rosetta.core.conformation.Residue, symmcopy: int) None ¶
C++: protocols::loop_grower::transform_res_to_subunit(class core::pose::Pose &, class std::shared_ptr<class core::conformation::Residue>, unsigned long) –> void
- pyrosetta.rosetta.protocols.loop_grower.transform_to_closest_symmunit(cen_pose: pyrosetta.rosetta.core.pose.Pose, fa_pose: pyrosetta.rosetta.core.pose.Pose, lower_pose: int) None ¶
C++: protocols::loop_grower::transform_to_closest_symmunit(class core::pose::Pose &, class core::pose::Pose &, unsigned long) –> void