loop_grower

Bindings for protocols::loop_grower namespace

class pyrosetta.rosetta.protocols.loop_grower.DensSkeleton

Bases: pybind11_builtins.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: pyrosetta.rosetta.protocols.moves.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_std_allocator_std_string_t

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) float

C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static mover_name() str

C++: protocols::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.

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

  2. show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None
: Unit test support function. Apply one move to a given pose.

Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)

Overloaded function.

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

Set the ‘type’ string

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

  1. type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.loop_grower.FragmentExtensionCreator

Bases: pyrosetta.rosetta.protocols.moves.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

provide_xml_schema(self: pyrosetta.rosetta.protocols.loop_grower.FragmentExtensionCreator, xsd: utility::tag::XMLSchemaDefinition) None

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

class pyrosetta.rosetta.protocols.loop_grower.LoopComparator

Bases: pybind11_builtins.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: pyrosetta.rosetta.protocols.moves.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_std_allocator_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.

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

  2. show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

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.

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

Set the ‘type’ string

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

  1. type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

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

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_builtins.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.

  1. 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

  1. 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.

  1. 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

  1. 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_builtins.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_builtins.pybind11_object

class pyrosetta.rosetta.protocols.loop_grower.ResTorsions

Bases: pybind11_builtins.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_builtins.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: pyrosetta.rosetta.protocols.moves.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_std_allocator_std_string_t

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) float

C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static 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.

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

  2. show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None
: Unit test support function. Apply one move to a given pose.

Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)

Overloaded function.

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

Set the ‘type’ string

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

  1. type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

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

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