denovo¶

Bindings for protocols::rna::denovo namespace

class pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoPoseInitializer¶

Bases: pybind11_object

Object used in RNA_FragmentMonteCarlo to handle setup of pose & fold-tree, and: jump changes.

initialize_for_de_novo_protocol(*args, **kwargs)¶

Overloaded function.

initialize_for_de_novo_protocol(self: pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoPoseInitializer, pose: pyrosetta.rosetta.core.pose.Pose) -> None
initialize_for_de_novo_protocol(self: pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoPoseInitializer, pose: pyrosetta.rosetta.core.pose.Pose, ignore_secstruct: bool) -> None

“classic” setup, used in denovo protocol. Note: changes pose (virtualizes phosphate).: and requires later call of setup_fold_tree_and_jumps_and_variants

C++: protocols::rna::denovo::RNA_DeNovoPoseInitializer::initialize_for_de_novo_protocol(class core::pose::Pose &, const bool) –> void

model_with_density(self: pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoPoseInitializer) → bool¶: C++: protocols::rna::denovo::RNA_DeNovoPoseInitializer::model_with_density() const –> bool

new_fold_tree_initializer(self: pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoPoseInitializer) → bool¶: C++: protocols::rna::denovo::RNA_DeNovoPoseInitializer::new_fold_tree_initializer() const –> bool

rna_params(self: pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoPoseInitializer) → pyrosetta.rosetta.core.import_pose.RNA_DeNovoParameters¶: C++: protocols::rna::denovo::RNA_DeNovoPoseInitializer::rna_params() const –> const class core::import_pose::RNA_DeNovoParameters &

set_bps_moves(self: pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoPoseInitializer, setting: bool) → None¶: C++: protocols::rna::denovo::RNA_DeNovoPoseInitializer::set_bps_moves(const bool &) –> void

set_center_jumps_in_single_stranded(self: pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoPoseInitializer, setting: bool) → None¶: C++: protocols::rna::denovo::RNA_DeNovoPoseInitializer::set_center_jumps_in_single_stranded(const bool &) –> void

set_dock_chunks_res(self: pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoPoseInitializer, dock_chunks_res: pyrosetta.rosetta.utility.vector1_unsigned_long) → None¶: C++: protocols::rna::denovo::RNA_DeNovoPoseInitializer::set_dock_chunks_res(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

set_dock_each_chunk(self: pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoPoseInitializer, setting: bool) → None¶: C++: protocols::rna::denovo::RNA_DeNovoPoseInitializer::set_dock_each_chunk(const bool &) –> void

set_dock_each_chunk_per_chain(self: pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoPoseInitializer, setting: bool) → None¶: C++: protocols::rna::denovo::RNA_DeNovoPoseInitializer::set_dock_each_chunk_per_chain(const bool &) –> void

set_model_with_density(self: pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoPoseInitializer, setting: bool) → None¶: C++: protocols::rna::denovo::RNA_DeNovoPoseInitializer::set_model_with_density(const bool &) –> void

set_new_fold_tree_initializer(self: pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoPoseInitializer, setting: bool) → None¶: C++: protocols::rna::denovo::RNA_DeNovoPoseInitializer::set_new_fold_tree_initializer(const bool &) –> void

set_root_at_first_rigid_body(self: pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoPoseInitializer, setting: bool) → None¶: C++: protocols::rna::denovo::RNA_DeNovoPoseInitializer::set_root_at_first_rigid_body(const bool) –> void

setup_chainbreak_variants(self: pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoPoseInitializer, pose: pyrosetta.rosetta.core.pose.Pose, atom_level_domain_map: pyrosetta.rosetta.core.pose.toolbox.AtomLevelDomainMap) → None¶: C++: protocols::rna::denovo::RNA_DeNovoPoseInitializer::setup_chainbreak_variants(class core::pose::Pose &, class std::shared_ptr<class core::pose::toolbox::AtomLevelDomainMap>) const –> void

setup_fold_tree_and_jumps_and_variants(*args, **kwargs)¶

Overloaded function.

setup_fold_tree_and_jumps_and_variants(self: pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoPoseInitializer, pose: pyrosetta.rosetta.core.pose.Pose, rna_jump_mover: pyrosetta.rosetta.core.import_pose.RNA_JumpMover, atom_level_domain_map: pyrosetta.rosetta.core.pose.toolbox.AtomLevelDomainMap, rna_chunk_library: pyrosetta.rosetta.core.import_pose.libraries.RNA_ChunkLibrary) -> None
setup_fold_tree_and_jumps_and_variants(self: pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoPoseInitializer, pose: pyrosetta.rosetta.core.pose.Pose, rna_jump_mover: pyrosetta.rosetta.core.import_pose.RNA_JumpMover, atom_level_domain_map: pyrosetta.rosetta.core.pose.toolbox.AtomLevelDomainMap, rna_chunk_library: pyrosetta.rosetta.core.import_pose.libraries.RNA_ChunkLibrary, enumerate: bool) -> None

C++: protocols::rna::denovo::RNA_DeNovoPoseInitializer::setup_fold_tree_and_jumps_and_variants(class core::pose::Pose &, const class core::import_pose::RNA_JumpMover &, class std::shared_ptr<class core::pose::toolbox::AtomLevelDomainMap>, const class core::import_pose::libraries::RNA_ChunkLibrary &, const bool &) const –> void

setup_fold_tree_and_jumps_and_variants(self: pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoPoseInitializer, pose: pyrosetta.rosetta.core.pose.Pose) -> None

C++: protocols::rna::denovo::RNA_DeNovoPoseInitializer::setup_fold_tree_and_jumps_and_variants(class core::pose::Pose &) const –> void

class pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol¶

Bases: Mover

The RNA de novo structure modeling protocol

align_and_output_to_silent_file(self: pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol, pose: pyrosetta.rosetta.core.pose.Pose, silent_file: str, out_file_tag: str) → None¶: C++: protocols::rna::denovo::RNA_DeNovoProtocol::align_and_output_to_silent_file(class core::pose::Pose &, const std::string &, const std::string &) const –> void

apply(self: pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Apply the RNA denovo modeling protocol to the input pose

C++: protocols::rna::denovo::RNA_DeNovoProtocol::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol, : pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol) → pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol¶: C++: protocols::rna::denovo::RNA_DeNovoProtocol::operator=(const class protocols::rna::denovo::RNA_DeNovoProtocol &) –> class protocols::rna::denovo::RNA_DeNovoProtocol &

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.rna.denovo.RNA_DeNovoProtocol) → pyrosetta.rosetta.protocols.moves.Mover¶

Clone this object

C++: protocols::rna::denovo::RNA_DeNovoProtocol::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.rna.denovo.RNA_DeNovoProtocol) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::rna::denovo::RNA_DeNovoProtocol::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.rna.denovo.RNA_DeNovoProtocol) → str¶: C++: protocols::rna::denovo::RNA_DeNovoProtocol::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 mover_name() → str¶: C++: protocols::rna::denovo::RNA_DeNovoProtocol::mover_name() –> std::string

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

options(self: pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol) → pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions¶: C++: protocols::rna::denovo::RNA_DeNovoProtocol::options() const –> class std::shared_ptr<const class core::import_pose::options::RNA_DeNovoProtocolOptions>

output_to_silent_file(*args, **kwargs)¶

Overloaded function.

output_to_silent_file(self: pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol, pose: pyrosetta.rosetta.core.pose.Pose, silent_file: str, out_file_tag: str) -> None
output_to_silent_file(self: pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol, pose: pyrosetta.rosetta.core.pose.Pose, silent_file: str, out_file_tag: str, score_only: bool) -> None

C++: protocols::rna::denovo::RNA_DeNovoProtocol::output_to_silent_file(class core::pose::Pose &, const std::string &, const std::string &, const bool) const –> void

parse_my_tag(self: pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::rna::denovo::RNA_DeNovoProtocol::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::rna::denovo::RNA_DeNovoProtocol::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None¶: C++: protocols::rna::denovo::RNA_DeNovoProtocol::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

rna_fragment_monte_carlo(self: pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol) → protocols::rna::denovo::RNA_FragmentMonteCarlo¶: C++: protocols::rna::denovo::RNA_DeNovoProtocol::rna_fragment_monte_carlo() const –> class std::shared_ptr<const class protocols::rna::denovo::RNA_FragmentMonteCarlo>

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_refine_pose_list(self: pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol, setting: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t) → None¶: C++: protocols::rna::denovo::RNA_DeNovoProtocol::set_refine_pose_list(const class utility::vector1<class std::shared_ptr<class core::pose::Pose>, class std::allocator<class std::shared_ptr<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.rna.denovo.RNA_DeNovoProtocol) -> None
show(self: pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol, output: pyrosetta.rosetta.std.ostream) -> None

C++: protocols::rna::denovo::RNA_DeNovoProtocol::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.rna.denovo.RNA_DeNovoProtocolCreator¶

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocolCreator, : pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocolCreator) → pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocolCreator¶: C++: protocols::rna::denovo::RNA_DeNovoProtocolCreator::operator=(const class protocols::rna::denovo::RNA_DeNovoProtocolCreator &) –> class protocols::rna::denovo::RNA_DeNovoProtocolCreator &

create_mover(self: pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocolCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::rna::denovo::RNA_DeNovoProtocolCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocolCreator) → str¶: C++: protocols::rna::denovo::RNA_DeNovoProtocolCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocolCreator, xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::rna::denovo::RNA_DeNovoProtocolCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.rna.denovo.RNA_FragmentMonteCarlo¶

Bases: Mover

align_pose(*args, **kwargs)¶

Overloaded function.

align_pose(self: pyrosetta.rosetta.protocols.rna.denovo.RNA_FragmentMonteCarlo, pose: pyrosetta.rosetta.core.pose.Pose) -> None
align_pose(self: pyrosetta.rosetta.protocols.rna.denovo.RNA_FragmentMonteCarlo, pose: pyrosetta.rosetta.core.pose.Pose, verbose: bool) -> None

C++: protocols::rna::denovo::RNA_FragmentMonteCarlo::align_pose(class core::pose::Pose &, const bool) const –> void

all_lores_score_final(self: pyrosetta.rosetta.protocols.rna.denovo.RNA_FragmentMonteCarlo) → pyrosetta.rosetta.std.list_double_t¶: C++: protocols::rna::denovo::RNA_FragmentMonteCarlo::all_lores_score_final() const –> const class std::list<double, class std::allocator<double> > &

apply(self: pyrosetta.rosetta.protocols.rna.denovo.RNA_FragmentMonteCarlo, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Apply the loop-rebuild protocol to the input pose

C++: protocols::rna::denovo::RNA_FragmentMonteCarlo::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::operator=(const class protocols::moves::Mover &) –> class protocols::moves::Mover &

atom_level_domain_map(self: pyrosetta.rosetta.protocols.rna.denovo.RNA_FragmentMonteCarlo) → pyrosetta.rosetta.core.pose.toolbox.AtomLevelDomainMap¶: C++: protocols::rna::denovo::RNA_FragmentMonteCarlo::atom_level_domain_map() const –> class std::shared_ptr<const class core::pose::toolbox::AtomLevelDomainMap>

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>

get_additional_output(self: pyrosetta.rosetta.protocols.rna.denovo.RNA_FragmentMonteCarlo) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::rna::denovo::RNA_FragmentMonteCarlo::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.rna.denovo.RNA_FragmentMonteCarlo) → str¶: C++: protocols::rna::denovo::RNA_FragmentMonteCarlo::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_rmsd_no_superimpose(self: pyrosetta.rosetta.protocols.rna.denovo.RNA_FragmentMonteCarlo, pose: pyrosetta.rosetta.core.pose.Pose) → float¶: C++: protocols::rna::denovo::RNA_FragmentMonteCarlo::get_rmsd_no_superimpose(const class core::pose::Pose &) const –> double

get_rmsd_stems_no_superimpose(self: pyrosetta.rosetta.protocols.rna.denovo.RNA_FragmentMonteCarlo, pose: pyrosetta.rosetta.core.pose.Pose) → float¶: C++: protocols::rna::denovo::RNA_FragmentMonteCarlo::get_rmsd_stems_no_superimpose(const class core::pose::Pose &) const –> 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 > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

loop_modeling(self: pyrosetta.rosetta.protocols.rna.denovo.RNA_FragmentMonteCarlo) → bool¶: C++: protocols::rna::denovo::RNA_FragmentMonteCarlo::loop_modeling() const –> bool

lores_pose(self: pyrosetta.rosetta.protocols.rna.denovo.RNA_FragmentMonteCarlo) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::rna::denovo::RNA_FragmentMonteCarlo::lores_pose() –> class std::shared_ptr<class core::pose::Pose>

lores_score_early(self: pyrosetta.rosetta.protocols.rna.denovo.RNA_FragmentMonteCarlo) → float¶: C++: protocols::rna::denovo::RNA_FragmentMonteCarlo::lores_score_early() const –> double

lores_score_final(self: pyrosetta.rosetta.protocols.rna.denovo.RNA_FragmentMonteCarlo) → float¶: C++: protocols::rna::denovo::RNA_FragmentMonteCarlo::lores_score_final() const –> double

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

outputter(self: pyrosetta.rosetta.protocols.rna.denovo.RNA_FragmentMonteCarlo) → protocols::rna::denovo::output::RNA_FragmentMonteCarloOutputter¶: C++: protocols::rna::denovo::RNA_FragmentMonteCarlo::outputter() const –> class std::shared_ptr<class protocols::rna::denovo::output::RNA_FragmentMonteCarloOutputter>

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.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static 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

rna_base_pair_handler(self: pyrosetta.rosetta.protocols.rna.denovo.RNA_FragmentMonteCarlo) → pyrosetta.rosetta.core.import_pose.RNA_BasePairHandler¶: C++: protocols::rna::denovo::RNA_FragmentMonteCarlo::rna_base_pair_handler() const –> class std::shared_ptr<const class core::import_pose::RNA_BasePairHandler>

rna_chunk_library(self: pyrosetta.rosetta.protocols.rna.denovo.RNA_FragmentMonteCarlo) → pyrosetta.rosetta.core.import_pose.libraries.RNA_ChunkLibrary¶: C++: protocols::rna::denovo::RNA_FragmentMonteCarlo::rna_chunk_library() const –> class std::shared_ptr<const class core::import_pose::libraries::RNA_ChunkLibrary>

rna_loop_closer(self: pyrosetta.rosetta.protocols.rna.denovo.RNA_FragmentMonteCarlo) → protocols::rna::movers::RNA_LoopCloser¶: C++: protocols::rna::denovo::RNA_FragmentMonteCarlo::rna_loop_closer() const –> class std::shared_ptr<const class protocols::rna::movers::RNA_LoopCloser>

set_all_lores_score_final(self: pyrosetta.rosetta.protocols.rna.denovo.RNA_FragmentMonteCarlo, setting: pyrosetta.rosetta.std.list_double_t) → None¶: C++: protocols::rna::denovo::RNA_FragmentMonteCarlo::set_all_lores_score_final(const class std::list<double, class std::allocator<double> > &) –> 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_denovo_scorefxn(self: pyrosetta.rosetta.protocols.rna.denovo.RNA_FragmentMonteCarlo, setting: pyrosetta.rosetta.core.scoring.ScoreFunction) → None¶: C++: protocols::rna::denovo::RNA_FragmentMonteCarlo::set_denovo_scorefxn(class std::shared_ptr<const class core::scoring::ScoreFunction>) –> void

set_hires_scorefxn(self: pyrosetta.rosetta.protocols.rna.denovo.RNA_FragmentMonteCarlo, setting: pyrosetta.rosetta.core.scoring.ScoreFunction) → None¶: C++: protocols::rna::denovo::RNA_FragmentMonteCarlo::set_hires_scorefxn(class std::shared_ptr<const class core::scoring::ScoreFunction>) –> 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_is_rna_and_protein(self: pyrosetta.rosetta.protocols.rna.denovo.RNA_FragmentMonteCarlo, setting: bool) → None¶: C++: protocols::rna::denovo::RNA_FragmentMonteCarlo::set_is_rna_and_protein(const bool &) –> 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_out_file_tag(self: pyrosetta.rosetta.protocols.rna.denovo.RNA_FragmentMonteCarlo, setting: str) → None¶: C++: protocols::rna::denovo::RNA_FragmentMonteCarlo::set_out_file_tag(const std::string &) –> void

set_outputter(self: pyrosetta.rosetta.protocols.rna.denovo.RNA_FragmentMonteCarlo, setting: protocols::rna::denovo::output::RNA_FragmentMonteCarloOutputter) → None¶: C++: protocols::rna::denovo::RNA_FragmentMonteCarlo::set_outputter(const class std::shared_ptr<class protocols::rna::denovo::output::RNA_FragmentMonteCarloOutputter> &) –> void

set_refine_pose(self: pyrosetta.rosetta.protocols.rna.denovo.RNA_FragmentMonteCarlo, setting: bool) → None¶: C++: protocols::rna::denovo::RNA_FragmentMonteCarlo::set_refine_pose(const bool) –> void

set_rna_base_pair_handler(self: pyrosetta.rosetta.protocols.rna.denovo.RNA_FragmentMonteCarlo, setting: pyrosetta.rosetta.core.import_pose.RNA_BasePairHandler) → None¶: C++: protocols::rna::denovo::RNA_FragmentMonteCarlo::set_rna_base_pair_handler(class std::shared_ptr<const class core::import_pose::RNA_BasePairHandler>) –> void

set_rna_de_novo_pose_initializer(self: pyrosetta.rosetta.protocols.rna.denovo.RNA_FragmentMonteCarlo, setting: pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoPoseInitializer) → None¶: C++: protocols::rna::denovo::RNA_FragmentMonteCarlo::set_rna_de_novo_pose_initializer(class std::shared_ptr<const class protocols::rna::denovo::RNA_DeNovoPoseInitializer>) –> 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_user_input_chunk_initialization_library(self: pyrosetta.rosetta.protocols.rna.denovo.RNA_FragmentMonteCarlo, setting: pyrosetta.rosetta.core.import_pose.libraries.RNA_ChunkLibrary) → None¶: C++: protocols::rna::denovo::RNA_FragmentMonteCarlo::set_user_input_chunk_initialization_library(class std::shared_ptr<const class core::import_pose::libraries::RNA_ChunkLibrary>) –> void

set_user_input_chunk_library(self: pyrosetta.rosetta.protocols.rna.denovo.RNA_FragmentMonteCarlo, setting: pyrosetta.rosetta.core.import_pose.libraries.RNA_ChunkLibrary) → None¶: C++: protocols::rna::denovo::RNA_FragmentMonteCarlo::set_user_input_chunk_library(class std::shared_ptr<const class core::import_pose::libraries::RNA_ChunkLibrary>) –> void

set_vdw_grid(self: pyrosetta.rosetta.protocols.rna.denovo.RNA_FragmentMonteCarlo, setting: protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker) → None¶: C++: protocols::rna::denovo::RNA_FragmentMonteCarlo::set_vdw_grid(class std::shared_ptr<class protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker>) –> void

show(self: pyrosetta.rosetta.protocols.rna.denovo.RNA_FragmentMonteCarlo, output: pyrosetta.rosetta.std.ostream) → None¶: C++: protocols::rna::denovo::RNA_FragmentMonteCarlo::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.rna.denovo.check_base_pair(pose: pyrosetta.rosetta.core.pose.Pose, struct_type: pyrosetta.rosetta.ObjexxFCL.FArray1D_int_t) → None¶: C++: protocols::rna::denovo::check_base_pair(class core::pose::Pose &, class ObjexxFCL::FArray1D<int> &) –> void

pyrosetta.rosetta.protocols.rna.denovo.classify_base_pairs_lores(pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_core_pose_rna_BasePair¶: C++: protocols::rna::denovo::classify_base_pairs_lores(const class core::pose::Pose &) –> class utility::vector1<class core::pose::rna::BasePair, class std::allocator<class core::pose::rna::BasePair> >

pyrosetta.rosetta.protocols.rna.denovo.create_rna_vall_torsions(*args, **kwargs)¶

Overloaded function.

create_rna_vall_torsions(pose: pyrosetta.rosetta.core.pose.Pose, torsions_out: pyrosetta.rosetta.utility.io.ozstream, exclude_res_list: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

C++: protocols::rna::denovo::create_rna_vall_torsions(class core::pose::Pose &, class utility::io::ozstream &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

create_rna_vall_torsions(pose: pyrosetta.rosetta.core.pose.Pose, outfile: str, exclude_res_list: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

C++: protocols::rna::denovo::create_rna_vall_torsions(class core::pose::Pose &, const std::string &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

pyrosetta.rosetta.protocols.rna.denovo.delete_non_protein_from_pose(pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::rna::denovo::delete_non_protein_from_pose(class core::pose::Pose &) –> void

pyrosetta.rosetta.protocols.rna.denovo.ensure_phosphate_nomenclature_matches_mini(pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::rna::denovo::ensure_phosphate_nomenclature_matches_mini(class core::pose::Pose &) –> void

pyrosetta.rosetta.protocols.rna.denovo.export_packer_results(*args, **kwargs)¶

Overloaded function.

export_packer_results(results: pyrosetta.rosetta.utility.vector1_std_pair_double_std_string_t, pose_list: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, outfile: str) -> None
export_packer_results(results: pyrosetta.rosetta.utility.vector1_std_pair_double_std_string_t, pose_list: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, outfile: str, dumo: bool) -> None

C++: protocols::rna::denovo::export_packer_results(class utility::vector1<struct std::pair<double, std::string >, class std::allocator<struct std::pair<double, std::string > > > &, class utility::vector1<class std::shared_ptr<class core::pose::Pose>, class std::allocator<class std::shared_ptr<class core::pose::Pose> > >, class std::shared_ptr<class core::scoring::ScoreFunction> &, const std::string &, const bool) –> void

pyrosetta.rosetta.protocols.rna.denovo.figure_out_base_pair_partner(*args, **kwargs)¶

Overloaded function.

figure_out_base_pair_partner(pose: pyrosetta.rosetta.core.pose.Pose, partner: pyrosetta.rosetta.std.map_unsigned_long_unsigned_long) -> None
figure_out_base_pair_partner(pose: pyrosetta.rosetta.core.pose.Pose, partner: pyrosetta.rosetta.std.map_unsigned_long_unsigned_long, strict: bool) -> None

C++: protocols::rna::denovo::figure_out_base_pair_partner(class core::pose::Pose &, class std::map<unsigned long, unsigned long, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, unsigned long> > > &, const bool) –> void

pyrosetta.rosetta.protocols.rna.denovo.get_moving_res(pose: pyrosetta.rosetta.core.pose.Pose, atom_level_domain_map: pyrosetta.rosetta.core.pose.toolbox.AtomLevelDomainMap) → pyrosetta.rosetta.utility.vector1_unsigned_long¶: C++: protocols::rna::denovo::get_moving_res(const class core::pose::Pose &, class std::shared_ptr<const class core::pose::toolbox::AtomLevelDomainMap>) –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

pyrosetta.rosetta.protocols.rna.denovo.get_residues_within_dist_of_RNA(pose: pyrosetta.rosetta.core.pose.Pose, dist_cutoff: float) → pyrosetta.rosetta.utility.vector1_unsigned_long¶: C++: protocols::rna::denovo::get_residues_within_dist_of_RNA(const class core::pose::Pose &, const double &) –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

pyrosetta.rosetta.protocols.rna.denovo.get_rna_hires_scorefxn(*args, **kwargs)¶

Overloaded function.

get_rna_hires_scorefxn() -> pyrosetta.rosetta.core.scoring.ScoreFunction
get_rna_hires_scorefxn(include_protein_terms: bool) -> pyrosetta.rosetta.core.scoring.ScoreFunction

C++: protocols::rna::denovo::get_rna_hires_scorefxn(const bool &) –> class std::shared_ptr<class core::scoring::ScoreFunction>

pyrosetta.rosetta.protocols.rna.denovo.get_rnp_docking_fold_tree(*args, **kwargs)¶

Overloaded function.

get_rnp_docking_fold_tree(pose: pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.core.kinematics.FoldTree
get_rnp_docking_fold_tree(pose: pyrosetta.rosetta.core.pose.Pose, with_density: bool) -> pyrosetta.rosetta.core.kinematics.FoldTree

C++: protocols::rna::denovo::get_rnp_docking_fold_tree(const class core::pose::Pose &, const bool &) –> class core::kinematics::FoldTree

pyrosetta.rosetta.protocols.rna.denovo.involved_in_phosphate_torsion(atomname: str) → bool¶: C++: protocols::rna::denovo::involved_in_phosphate_torsion(const std::string &) –> bool

pyrosetta.rosetta.protocols.rna.denovo.is_num_in_list(i: int, list: pyrosetta.rosetta.utility.vector1_unsigned_long) → bool¶: C++: protocols::rna::denovo::is_num_in_list(const unsigned long, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> bool

pyrosetta.rosetta.protocols.rna.denovo.let_rigid_body_jumps_move(*args, **kwargs)¶

Overloaded function.

let_rigid_body_jumps_move(movemap: pyrosetta.rosetta.core.kinematics.MoveMap, pose: pyrosetta.rosetta.core.pose.Pose) -> bool
let_rigid_body_jumps_move(movemap: pyrosetta.rosetta.core.kinematics.MoveMap, pose: pyrosetta.rosetta.core.pose.Pose, move_first_rigid_body: bool) -> bool
let_rigid_body_jumps_move(movemap: pyrosetta.rosetta.core.kinematics.MoveMap, pose: pyrosetta.rosetta.core.pose.Pose, move_first_rigid_body: bool, allow_first_rigid_body: bool) -> bool

C++: protocols::rna::denovo::let_rigid_body_jumps_move(class core::kinematics::MoveMap &, const class core::pose::Pose &, const bool &, const bool &) –> bool

pyrosetta.rosetta.protocols.rna.denovo.possible_root(f: pyrosetta.rosetta.core.kinematics.FoldTree, n: int) → bool¶: C++: protocols::rna::denovo::possible_root(const class core::kinematics::FoldTree &, const unsigned long &) –> bool

pyrosetta.rosetta.protocols.rna.denovo.print_hbonds(pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::rna::denovo::print_hbonds(class core::pose::Pose &) –> void

pyrosetta.rosetta.protocols.rna.denovo.print_internal_coords(pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::rna::denovo::print_internal_coords(const class core::pose::Pose &) –> void

pyrosetta.rosetta.protocols.rna.denovo.setup_coarse_chainbreak_constraints(pose: pyrosetta.rosetta.core.pose.Pose, n: int) → None¶: C++: protocols::rna::denovo::setup_coarse_chainbreak_constraints(class core::pose::Pose &, const unsigned long &) –> void

pyrosetta.rosetta.protocols.rna.denovo.translate_virtual_anchor_to_first_rigid_body(pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::rna::denovo::translate_virtual_anchor_to_first_rigid_body(class core::pose::Pose &) –> void

pyrosetta.rosetta.protocols.rna.denovo.virtualize_bulges(input_pose: pyrosetta.rosetta.core.pose.Pose, in_allow_bulge_res_list: pyrosetta.rosetta.utility.vector1_unsigned_long, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, tag: str, allow_pre_virtualize: bool, allow_consecutive_bulges: bool, verbose: bool) → int¶: C++: protocols::rna::denovo::virtualize_bulges(class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const class std::shared_ptr<const class core::scoring::ScoreFunction> &, const std::string &, const bool, const bool, const bool) –> unsigned long