features

Bindings for protocols::features namespace

class pyrosetta.rosetta.protocols.features.AtomAtomPairFeatures

Bases: pyrosetta.rosetta.protocols.features.FeaturesReporter

assign(self: pyrosetta.rosetta.protocols.features.AtomAtomPairFeatures, : pyrosetta.rosetta.protocols.features.AtomAtomPairFeatures) pyrosetta.rosetta.protocols.features.AtomAtomPairFeatures

C++: protocols::features::AtomAtomPairFeatures::operator=(const class protocols::features::AtomAtomPairFeatures &) –> class protocols::features::AtomAtomPairFeatures &

check_relevant_residues(*args, **kwargs)

Overloaded function.

  1. check_relevant_residues(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, res1: int) -> bool

C++: protocols::features::FeaturesReporter::check_relevant_residues(const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long) const –> bool

  1. check_relevant_residues(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, res1: int, res2: int) -> bool

C++: protocols::features::FeaturesReporter::check_relevant_residues(const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, unsigned long) const –> bool

  1. check_relevant_residues(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, residues: pyrosetta.rosetta.utility.vector1_unsigned_long) -> bool

C++: protocols::features::FeaturesReporter::check_relevant_residues(const class utility::vector1<bool, class std::allocator<bool> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> bool

check_relevant_residues_range(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, res1: int, res2: int) bool

C++: protocols::features::FeaturesReporter::check_relevant_residues_range(const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, unsigned long) const –> bool

static class_name() str

C++: protocols::features::AtomAtomPairFeatures::class_name() –> std::string

delete_record(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, : int, : pyrosetta.rosetta.utility.sql_database.session) None

C++: protocols::features::FeaturesReporter::delete_record(unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> void

features_reporter_dependencies(self: pyrosetta.rosetta.protocols.features.AtomAtomPairFeatures) pyrosetta.rosetta.utility.vector1_std_string

return the set of features reporters that are required to also already be extracted by the time this one is used.

C++: protocols::features::AtomAtomPairFeatures::features_reporter_dependencies() const –> class utility::vector1<std::string, class std::allocator<std::string > >

get_relevant_residues_mode(self: pyrosetta.rosetta.protocols.features.FeaturesReporter) pyrosetta.rosetta.protocols.features.RelevantResiduesMode.T

C++: protocols::features::FeaturesReporter::get_relevant_residues_mode() const –> enum protocols::features::RelevantResiduesMode::T

load_into_pose(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, : pyrosetta.rosetta.utility.sql_database.session, : int, : pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::features::FeaturesReporter::load_into_pose(class std::shared_ptr<class utility::sql_database::session>, unsigned long, class core::pose::Pose &) –> void

parse_my_tag(self: pyrosetta.rosetta.protocols.features.AtomAtomPairFeatures, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None

C++: protocols::features::AtomAtomPairFeatures::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::features::AtomAtomPairFeatures::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

report_atom_pairs(self: pyrosetta.rosetta.protocols.features.AtomAtomPairFeatures, pose: pyrosetta.rosetta.core.pose.Pose, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, struct_id: int, db_session: pyrosetta.rosetta.utility.sql_database.session) None

C++: protocols::features::AtomAtomPairFeatures::report_atom_pairs(const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> void

report_features(self: pyrosetta.rosetta.protocols.features.AtomAtomPairFeatures, pose: pyrosetta.rosetta.core.pose.Pose, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, struct_id: int, db_session: pyrosetta.rosetta.utility.sql_database.session) int

collect all the feature data for the pose

C++: protocols::features::AtomAtomPairFeatures::report_features(const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> unsigned long

schema(self: pyrosetta.rosetta.protocols.features.FeaturesReporter) str

return sql statements that sets up the appropriate tables to contain the features. This should be removed once everything has been moved to the schema generator

C++: protocols::features::FeaturesReporter::schema() const –> std::string

set_relevant_residues_mode(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, setting: pyrosetta.rosetta.protocols.features.RelevantResiduesMode.T) None

C++: protocols::features::FeaturesReporter::set_relevant_residues_mode(enum protocols::features::RelevantResiduesMode::T) –> void

type_name(self: pyrosetta.rosetta.protocols.features.AtomAtomPairFeatures) str

C++: protocols::features::AtomAtomPairFeatures::type_name() const –> std::string

write_schema_to_db(self: pyrosetta.rosetta.protocols.features.AtomAtomPairFeatures, db_session: pyrosetta.rosetta.utility.sql_database.session) None

generate the table schemas and write them to the database

C++: protocols::features::AtomAtomPairFeatures::write_schema_to_db(class std::shared_ptr<class utility::sql_database::session>) const –> void

class pyrosetta.rosetta.protocols.features.AtomAtomPairFeaturesCreator

Bases: pyrosetta.rosetta.protocols.features.FeaturesReporterCreator

creator for the AtomAtomPairFeatures class

assign(self: pyrosetta.rosetta.protocols.features.AtomAtomPairFeaturesCreator, : pyrosetta.rosetta.protocols.features.AtomAtomPairFeaturesCreator) pyrosetta.rosetta.protocols.features.AtomAtomPairFeaturesCreator

C++: protocols::features::AtomAtomPairFeaturesCreator::operator=(const class protocols::features::AtomAtomPairFeaturesCreator &) –> class protocols::features::AtomAtomPairFeaturesCreator &

create_features_reporter(self: pyrosetta.rosetta.protocols.features.AtomAtomPairFeaturesCreator) pyrosetta.rosetta.protocols.features.FeaturesReporter

C++: protocols::features::AtomAtomPairFeaturesCreator::create_features_reporter() const –> class std::shared_ptr<class protocols::features::FeaturesReporter>

provide_xml_schema(self: pyrosetta.rosetta.protocols.features.AtomAtomPairFeaturesCreator, xsd: utility::tag::XMLSchemaDefinition) None

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

type_name(self: pyrosetta.rosetta.protocols.features.AtomAtomPairFeaturesCreator) str

C++: protocols::features::AtomAtomPairFeaturesCreator::type_name() const –> std::string

class pyrosetta.rosetta.protocols.features.AtomInResidueAtomInResiduePairFeatures

Bases: pyrosetta.rosetta.protocols.features.FeaturesReporter

assign(self: pyrosetta.rosetta.protocols.features.AtomInResidueAtomInResiduePairFeatures, : pyrosetta.rosetta.protocols.features.AtomInResidueAtomInResiduePairFeatures) pyrosetta.rosetta.protocols.features.AtomInResidueAtomInResiduePairFeatures

C++: protocols::features::AtomInResidueAtomInResiduePairFeatures::operator=(const class protocols::features::AtomInResidueAtomInResiduePairFeatures &) –> class protocols::features::AtomInResidueAtomInResiduePairFeatures &

check_relevant_residues(*args, **kwargs)

Overloaded function.

  1. check_relevant_residues(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, res1: int) -> bool

C++: protocols::features::FeaturesReporter::check_relevant_residues(const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long) const –> bool

  1. check_relevant_residues(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, res1: int, res2: int) -> bool

C++: protocols::features::FeaturesReporter::check_relevant_residues(const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, unsigned long) const –> bool

  1. check_relevant_residues(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, residues: pyrosetta.rosetta.utility.vector1_unsigned_long) -> bool

C++: protocols::features::FeaturesReporter::check_relevant_residues(const class utility::vector1<bool, class std::allocator<bool> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> bool

check_relevant_residues_range(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, res1: int, res2: int) bool

C++: protocols::features::FeaturesReporter::check_relevant_residues_range(const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, unsigned long) const –> bool

static class_name() str

C++: protocols::features::AtomInResidueAtomInResiduePairFeatures::class_name() –> std::string

delete_record(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, : int, : pyrosetta.rosetta.utility.sql_database.session) None

C++: protocols::features::FeaturesReporter::delete_record(unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> void

features_reporter_dependencies(self: pyrosetta.rosetta.protocols.features.AtomInResidueAtomInResiduePairFeatures) pyrosetta.rosetta.utility.vector1_std_string

return the set of features reporters that are required to also already be extracted by the time this one is used.

C++: protocols::features::AtomInResidueAtomInResiduePairFeatures::features_reporter_dependencies() const –> class utility::vector1<std::string, class std::allocator<std::string > >

get_relevant_residues_mode(self: pyrosetta.rosetta.protocols.features.FeaturesReporter) pyrosetta.rosetta.protocols.features.RelevantResiduesMode.T

C++: protocols::features::FeaturesReporter::get_relevant_residues_mode() const –> enum protocols::features::RelevantResiduesMode::T

load_into_pose(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, : pyrosetta.rosetta.utility.sql_database.session, : int, : pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::features::FeaturesReporter::load_into_pose(class std::shared_ptr<class utility::sql_database::session>, unsigned long, class core::pose::Pose &) –> void

parse_my_tag(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None

C++: protocols::features::FeaturesReporter::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::features::AtomInResidueAtomInResiduePairFeatures::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

report_atom_pairs(self: pyrosetta.rosetta.protocols.features.AtomInResidueAtomInResiduePairFeatures, pose: pyrosetta.rosetta.core.pose.Pose, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, struct_id: int, db_session: pyrosetta.rosetta.utility.sql_database.session) None

Similar to radial density distributions defined in Lu H, Skolnick J. A distance-dependent atomic knowledge-based potential for improved protein structure selection. Proteins. 2001;44(3):223-32. Available at: http://www.ncbi.nlm.nih.gov/pubmed/11455595.

C++: protocols::features::AtomInResidueAtomInResiduePairFeatures::report_atom_pairs(const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> void

report_features(self: pyrosetta.rosetta.protocols.features.AtomInResidueAtomInResiduePairFeatures, pose: pyrosetta.rosetta.core.pose.Pose, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, struct_id: int, db_session: pyrosetta.rosetta.utility.sql_database.session) int

collect all the feature data for the pose

C++: protocols::features::AtomInResidueAtomInResiduePairFeatures::report_features(const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> unsigned long

schema(self: pyrosetta.rosetta.protocols.features.FeaturesReporter) str

return sql statements that sets up the appropriate tables to contain the features. This should be removed once everything has been moved to the schema generator

C++: protocols::features::FeaturesReporter::schema() const –> std::string

set_relevant_residues_mode(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, setting: pyrosetta.rosetta.protocols.features.RelevantResiduesMode.T) None

C++: protocols::features::FeaturesReporter::set_relevant_residues_mode(enum protocols::features::RelevantResiduesMode::T) –> void

type_name(self: pyrosetta.rosetta.protocols.features.AtomInResidueAtomInResiduePairFeatures) str

C++: protocols::features::AtomInResidueAtomInResiduePairFeatures::type_name() const –> std::string

write_schema_to_db(self: pyrosetta.rosetta.protocols.features.AtomInResidueAtomInResiduePairFeatures, db_session: pyrosetta.rosetta.utility.sql_database.session) None

generate the table schemas and write them to the database

C++: protocols::features::AtomInResidueAtomInResiduePairFeatures::write_schema_to_db(class std::shared_ptr<class utility::sql_database::session>) const –> void

class pyrosetta.rosetta.protocols.features.AtomInResidueAtomInResiduePairFeaturesCreator

Bases: pyrosetta.rosetta.protocols.features.FeaturesReporterCreator

creator for the AtomInResidueAtomInResiduePairFeatures class

assign(self: pyrosetta.rosetta.protocols.features.AtomInResidueAtomInResiduePairFeaturesCreator, : pyrosetta.rosetta.protocols.features.AtomInResidueAtomInResiduePairFeaturesCreator) pyrosetta.rosetta.protocols.features.AtomInResidueAtomInResiduePairFeaturesCreator

C++: protocols::features::AtomInResidueAtomInResiduePairFeaturesCreator::operator=(const class protocols::features::AtomInResidueAtomInResiduePairFeaturesCreator &) –> class protocols::features::AtomInResidueAtomInResiduePairFeaturesCreator &

create_features_reporter(self: pyrosetta.rosetta.protocols.features.AtomInResidueAtomInResiduePairFeaturesCreator) pyrosetta.rosetta.protocols.features.FeaturesReporter

C++: protocols::features::AtomInResidueAtomInResiduePairFeaturesCreator::create_features_reporter() const –> class std::shared_ptr<class protocols::features::FeaturesReporter>

provide_xml_schema(self: pyrosetta.rosetta.protocols.features.AtomInResidueAtomInResiduePairFeaturesCreator, xsd: utility::tag::XMLSchemaDefinition) None

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

type_name(self: pyrosetta.rosetta.protocols.features.AtomInResidueAtomInResiduePairFeaturesCreator) str

C++: protocols::features::AtomInResidueAtomInResiduePairFeaturesCreator::type_name() const –> std::string

class pyrosetta.rosetta.protocols.features.AtomTypesFeatures

Bases: pyrosetta.rosetta.protocols.features.FeaturesReporter

assign(self: pyrosetta.rosetta.protocols.features.AtomTypesFeatures, : pyrosetta.rosetta.protocols.features.AtomTypesFeatures) pyrosetta.rosetta.protocols.features.AtomTypesFeatures

C++: protocols::features::AtomTypesFeatures::operator=(const class protocols::features::AtomTypesFeatures &) –> class protocols::features::AtomTypesFeatures &

check_relevant_residues(*args, **kwargs)

Overloaded function.

  1. check_relevant_residues(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, res1: int) -> bool

C++: protocols::features::FeaturesReporter::check_relevant_residues(const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long) const –> bool

  1. check_relevant_residues(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, res1: int, res2: int) -> bool

C++: protocols::features::FeaturesReporter::check_relevant_residues(const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, unsigned long) const –> bool

  1. check_relevant_residues(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, residues: pyrosetta.rosetta.utility.vector1_unsigned_long) -> bool

C++: protocols::features::FeaturesReporter::check_relevant_residues(const class utility::vector1<bool, class std::allocator<bool> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> bool

check_relevant_residues_range(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, res1: int, res2: int) bool

C++: protocols::features::FeaturesReporter::check_relevant_residues_range(const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, unsigned long) const –> bool

static class_name() str

C++: protocols::features::AtomTypesFeatures::class_name() –> std::string

delete_record(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, : int, : pyrosetta.rosetta.utility.sql_database.session) None

C++: protocols::features::FeaturesReporter::delete_record(unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> void

features_reporter_dependencies(self: pyrosetta.rosetta.protocols.features.AtomTypesFeatures) pyrosetta.rosetta.utility.vector1_std_string

return the set of features reporters that are required to also already be extracted by the time this one is used.

C++: protocols::features::AtomTypesFeatures::features_reporter_dependencies() const –> class utility::vector1<std::string, class std::allocator<std::string > >

get_relevant_residues_mode(self: pyrosetta.rosetta.protocols.features.FeaturesReporter) pyrosetta.rosetta.protocols.features.RelevantResiduesMode.T

C++: protocols::features::FeaturesReporter::get_relevant_residues_mode() const –> enum protocols::features::RelevantResiduesMode::T

load_into_pose(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, : pyrosetta.rosetta.utility.sql_database.session, : int, : pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::features::FeaturesReporter::load_into_pose(class std::shared_ptr<class utility::sql_database::session>, unsigned long, class core::pose::Pose &) –> void

parse_my_tag(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None

C++: protocols::features::FeaturesReporter::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::features::AtomTypesFeatures::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

report_features(self: pyrosetta.rosetta.protocols.features.AtomTypesFeatures, pose: pyrosetta.rosetta.core.pose.Pose, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, struct_id: int, db_session: pyrosetta.rosetta.utility.sql_database.session) int

collect all the feature data for the pose

C++: protocols::features::AtomTypesFeatures::report_features(const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> unsigned long

schema(self: pyrosetta.rosetta.protocols.features.FeaturesReporter) str

return sql statements that sets up the appropriate tables to contain the features. This should be removed once everything has been moved to the schema generator

C++: protocols::features::FeaturesReporter::schema() const –> std::string

set_relevant_residues_mode(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, setting: pyrosetta.rosetta.protocols.features.RelevantResiduesMode.T) None

C++: protocols::features::FeaturesReporter::set_relevant_residues_mode(enum protocols::features::RelevantResiduesMode::T) –> void

type_name(self: pyrosetta.rosetta.protocols.features.AtomTypesFeatures) str

C++: protocols::features::AtomTypesFeatures::type_name() const –> std::string

write_schema_to_db(self: pyrosetta.rosetta.protocols.features.AtomTypesFeatures, db_session: pyrosetta.rosetta.utility.sql_database.session) None

generate the table schemas and write them to the database

C++: protocols::features::AtomTypesFeatures::write_schema_to_db(class std::shared_ptr<class utility::sql_database::session>) const –> void

class pyrosetta.rosetta.protocols.features.AtomTypesFeaturesCreator

Bases: pyrosetta.rosetta.protocols.features.FeaturesReporterCreator

creator for the AtomTypesFeatures class

assign(self: pyrosetta.rosetta.protocols.features.AtomTypesFeaturesCreator, : pyrosetta.rosetta.protocols.features.AtomTypesFeaturesCreator) pyrosetta.rosetta.protocols.features.AtomTypesFeaturesCreator

C++: protocols::features::AtomTypesFeaturesCreator::operator=(const class protocols::features::AtomTypesFeaturesCreator &) –> class protocols::features::AtomTypesFeaturesCreator &

create_features_reporter(self: pyrosetta.rosetta.protocols.features.AtomTypesFeaturesCreator) pyrosetta.rosetta.protocols.features.FeaturesReporter

C++: protocols::features::AtomTypesFeaturesCreator::create_features_reporter() const –> class std::shared_ptr<class protocols::features::FeaturesReporter>

provide_xml_schema(self: pyrosetta.rosetta.protocols.features.AtomTypesFeaturesCreator, xsd: utility::tag::XMLSchemaDefinition) None

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

type_name(self: pyrosetta.rosetta.protocols.features.AtomTypesFeaturesCreator) str

C++: protocols::features::AtomTypesFeaturesCreator::type_name() const –> std::string

class pyrosetta.rosetta.protocols.features.BatchFeatures

Bases: pybind11_builtins.pybind11_object

assign(self: pyrosetta.rosetta.protocols.features.BatchFeatures, : pyrosetta.rosetta.protocols.features.BatchFeatures) pyrosetta.rosetta.protocols.features.BatchFeatures

C++: protocols::features::BatchFeatures::operator=(const class protocols::features::BatchFeatures &) –> class protocols::features::BatchFeatures &

features_reporter_dependencies(self: pyrosetta.rosetta.protocols.features.BatchFeatures) pyrosetta.rosetta.utility.vector1_std_string

return the set of features reporters that are required to also already be extracted by the time this one is used.

C++: protocols::features::BatchFeatures::features_reporter_dependencies() const –> class utility::vector1<std::string, class std::allocator<std::string > >

indices(self: pyrosetta.rosetta.protocols.features.BatchFeatures) str

return sql statements that setup helpful indices on the tables

C++: protocols::features::BatchFeatures::indices() const –> std::string

report_features(self: pyrosetta.rosetta.protocols.features.BatchFeatures, batch_id: int, protocol_id: int, name: str, description: str, db_session: pyrosetta.rosetta.utility.sql_database.session) int

C++: protocols::features::BatchFeatures::report_features(unsigned long, unsigned long, std::string, std::string, class std::shared_ptr<class utility::sql_database::session>) –> unsigned long

type_name(self: pyrosetta.rosetta.protocols.features.BatchFeatures) str

return string with class name

C++: protocols::features::BatchFeatures::type_name() const –> std::string

write_schema_to_db(self: pyrosetta.rosetta.protocols.features.BatchFeatures, db_session: pyrosetta.rosetta.utility.sql_database.session, batch_id: int) None

generate the table schemas and write them to the database

C++: protocols::features::BatchFeatures::write_schema_to_db(class std::shared_ptr<class utility::sql_database::session>, unsigned long) const –> void

class pyrosetta.rosetta.protocols.features.BetaTurnDetection

Bases: pybind11_builtins.pybind11_object

all_turn_residues_are_on_the_same_chain(self: pyrosetta.rosetta.protocols.features.BetaTurnDetection, pose: pyrosetta.rosetta.core.pose.Pose, first_residue: int) bool

C++: protocols::features::BetaTurnDetection::all_turn_residues_are_on_the_same_chain(const class core::pose::Pose &, unsigned long) const –> bool

beta_turn_distance_cutoff(self: pyrosetta.rosetta.protocols.features.BetaTurnDetection) float

C++: protocols::features::BetaTurnDetection::beta_turn_distance_cutoff() const –> double

beta_turn_length(self: pyrosetta.rosetta.protocols.features.BetaTurnDetection) int

C++: protocols::features::BetaTurnDetection::beta_turn_length() const –> unsigned long

beta_turn_present(self: pyrosetta.rosetta.protocols.features.BetaTurnDetection, pose: pyrosetta.rosetta.core.pose.Pose, first_residue: int) bool

C++: protocols::features::BetaTurnDetection::beta_turn_present(const class core::pose::Pose &, unsigned long) const –> bool

beta_turn_type(self: pyrosetta.rosetta.protocols.features.BetaTurnDetection, pose: pyrosetta.rosetta.core.pose.Pose, first_residue: int) str

C++: protocols::features::BetaTurnDetection::beta_turn_type(const class core::pose::Pose &, unsigned long) const –> const std::string &

determine_ramachandran_hash(self: pyrosetta.rosetta.protocols.features.BetaTurnDetection, pose: pyrosetta.rosetta.core.pose.Pose, first_residue: int) str

C++: protocols::features::BetaTurnDetection::determine_ramachandran_hash(const class core::pose::Pose &, unsigned long) const –> std::string

determine_ramachandran_hash_for_residue_with_dihedrals(self: pyrosetta.rosetta.protocols.features.BetaTurnDetection, phi: float, psi: float, omega: float) str

C++: protocols::features::BetaTurnDetection::determine_ramachandran_hash_for_residue_with_dihedrals(double, double, double) const –> std::string

static get_conformation_to_turn_type_map() pyrosetta.rosetta.std.map_std_string_std_string

C++: protocols::features::BetaTurnDetection::get_conformation_to_turn_type_map() –> const class std::map<std::string, std::string, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, std::string > > > &

static get_valid_ramachandran_hashes() pyrosetta.rosetta.utility.vector1_std_string

C++: protocols::features::BetaTurnDetection::get_valid_ramachandran_hashes() –> const class utility::vector1<std::string, class std::allocator<std::string > > &

residue_range_is_protein(self: pyrosetta.rosetta.protocols.features.BetaTurnDetection, pose: pyrosetta.rosetta.core.pose.Pose, range_begin: int, range_end: int) bool

C++: protocols::features::BetaTurnDetection::residue_range_is_protein(const class core::pose::Pose &, unsigned long, unsigned long) const –> bool

type_name(self: pyrosetta.rosetta.protocols.features.BetaTurnDetection) str

return string with class name

C++: protocols::features::BetaTurnDetection::type_name() const –> std::string

validate_ramachandran_hash(self: pyrosetta.rosetta.protocols.features.BetaTurnDetection, rama_hash: str) None

C++: protocols::features::BetaTurnDetection::validate_ramachandran_hash(std::string &) const –> void

class pyrosetta.rosetta.protocols.features.BetaTurnDetectionFeatures

Bases: pyrosetta.rosetta.protocols.features.FeaturesReporter

assign(self: pyrosetta.rosetta.protocols.features.BetaTurnDetectionFeatures, : pyrosetta.rosetta.protocols.features.BetaTurnDetectionFeatures) pyrosetta.rosetta.protocols.features.BetaTurnDetectionFeatures

C++: protocols::features::BetaTurnDetectionFeatures::operator=(const class protocols::features::BetaTurnDetectionFeatures &) –> class protocols::features::BetaTurnDetectionFeatures &

check_relevant_residues(*args, **kwargs)

Overloaded function.

  1. check_relevant_residues(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, res1: int) -> bool

C++: protocols::features::FeaturesReporter::check_relevant_residues(const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long) const –> bool

  1. check_relevant_residues(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, res1: int, res2: int) -> bool

C++: protocols::features::FeaturesReporter::check_relevant_residues(const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, unsigned long) const –> bool

  1. check_relevant_residues(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, residues: pyrosetta.rosetta.utility.vector1_unsigned_long) -> bool

C++: protocols::features::FeaturesReporter::check_relevant_residues(const class utility::vector1<bool, class std::allocator<bool> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> bool

check_relevant_residues_range(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, res1: int, res2: int) bool

C++: protocols::features::FeaturesReporter::check_relevant_residues_range(const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, unsigned long) const –> bool

static class_name() str

C++: protocols::features::BetaTurnDetectionFeatures::class_name() –> std::string

delete_record(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, : int, : pyrosetta.rosetta.utility.sql_database.session) None

C++: protocols::features::FeaturesReporter::delete_record(unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> void

features_reporter_dependencies(self: pyrosetta.rosetta.protocols.features.BetaTurnDetectionFeatures) pyrosetta.rosetta.utility.vector1_std_string

return the set of features reporters that are required to also already be extracted by the time this one is used.

C++: protocols::features::BetaTurnDetectionFeatures::features_reporter_dependencies() const –> class utility::vector1<std::string, class std::allocator<std::string > >

get_relevant_residues_mode(self: pyrosetta.rosetta.protocols.features.FeaturesReporter) pyrosetta.rosetta.protocols.features.RelevantResiduesMode.T

C++: protocols::features::FeaturesReporter::get_relevant_residues_mode() const –> enum protocols::features::RelevantResiduesMode::T

load_into_pose(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, : pyrosetta.rosetta.utility.sql_database.session, : int, : pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::features::FeaturesReporter::load_into_pose(class std::shared_ptr<class utility::sql_database::session>, unsigned long, class core::pose::Pose &) –> void

parse_my_tag(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None

C++: protocols::features::FeaturesReporter::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::features::BetaTurnDetectionFeatures::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

report_features(self: pyrosetta.rosetta.protocols.features.BetaTurnDetectionFeatures, pose: pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.utility.vector1_bool, struct_id: int, db_session: pyrosetta.rosetta.utility.sql_database.session) int

collect all the feature data for the pose

C++: protocols::features::BetaTurnDetectionFeatures::report_features(const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> unsigned long

schema(self: pyrosetta.rosetta.protocols.features.FeaturesReporter) str

return sql statements that sets up the appropriate tables to contain the features. This should be removed once everything has been moved to the schema generator

C++: protocols::features::FeaturesReporter::schema() const –> std::string

set_relevant_residues_mode(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, setting: pyrosetta.rosetta.protocols.features.RelevantResiduesMode.T) None

C++: protocols::features::FeaturesReporter::set_relevant_residues_mode(enum protocols::features::RelevantResiduesMode::T) –> void

type_name(self: pyrosetta.rosetta.protocols.features.BetaTurnDetectionFeatures) str

C++: protocols::features::BetaTurnDetectionFeatures::type_name() const –> std::string

write_schema_to_db(self: pyrosetta.rosetta.protocols.features.BetaTurnDetectionFeatures, db_session: pyrosetta.rosetta.utility.sql_database.session) None

generate the table schemas and write them to the database

C++: protocols::features::BetaTurnDetectionFeatures::write_schema_to_db(class std::shared_ptr<class utility::sql_database::session>) const –> void

class pyrosetta.rosetta.protocols.features.BetaTurnDetectionFeaturesCreator

Bases: pyrosetta.rosetta.protocols.features.FeaturesReporterCreator

creator for the BetaTurnDetectionFeatures class

assign(self: pyrosetta.rosetta.protocols.features.BetaTurnDetectionFeaturesCreator, : pyrosetta.rosetta.protocols.features.BetaTurnDetectionFeaturesCreator) pyrosetta.rosetta.protocols.features.BetaTurnDetectionFeaturesCreator

C++: protocols::features::BetaTurnDetectionFeaturesCreator::operator=(const class protocols::features::BetaTurnDetectionFeaturesCreator &) –> class protocols::features::BetaTurnDetectionFeaturesCreator &

create_features_reporter(self: pyrosetta.rosetta.protocols.features.BetaTurnDetectionFeaturesCreator) pyrosetta.rosetta.protocols.features.FeaturesReporter

C++: protocols::features::BetaTurnDetectionFeaturesCreator::create_features_reporter() const –> class std::shared_ptr<class protocols::features::FeaturesReporter>

provide_xml_schema(self: pyrosetta.rosetta.protocols.features.BetaTurnDetectionFeaturesCreator, xsd: utility::tag::XMLSchemaDefinition) None

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

type_name(self: pyrosetta.rosetta.protocols.features.BetaTurnDetectionFeaturesCreator) str

C++: protocols::features::BetaTurnDetectionFeaturesCreator::type_name() const –> std::string

class pyrosetta.rosetta.protocols.features.ChargeChargeFeatures

Bases: pyrosetta.rosetta.protocols.features.FeaturesReporter

assign(self: pyrosetta.rosetta.protocols.features.ChargeChargeFeatures, : pyrosetta.rosetta.protocols.features.ChargeChargeFeatures) pyrosetta.rosetta.protocols.features.ChargeChargeFeatures

C++: protocols::features::ChargeChargeFeatures::operator=(const class protocols::features::ChargeChargeFeatures &) –> class protocols::features::ChargeChargeFeatures &

check_relevant_residues(*args, **kwargs)

Overloaded function.

  1. check_relevant_residues(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, res1: int) -> bool

C++: protocols::features::FeaturesReporter::check_relevant_residues(const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long) const –> bool

  1. check_relevant_residues(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, res1: int, res2: int) -> bool

C++: protocols::features::FeaturesReporter::check_relevant_residues(const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, unsigned long) const –> bool

  1. check_relevant_residues(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, residues: pyrosetta.rosetta.utility.vector1_unsigned_long) -> bool

C++: protocols::features::FeaturesReporter::check_relevant_residues(const class utility::vector1<bool, class std::allocator<bool> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> bool

check_relevant_residues_range(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, res1: int, res2: int) bool

C++: protocols::features::FeaturesReporter::check_relevant_residues_range(const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, unsigned long) const –> bool

static class_name() str

C++: protocols::features::ChargeChargeFeatures::class_name() –> std::string

delete_record(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, : int, : pyrosetta.rosetta.utility.sql_database.session) None

C++: protocols::features::FeaturesReporter::delete_record(unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> void

distance_cutoff(*args, **kwargs)

Overloaded function.

  1. distance_cutoff(self: pyrosetta.rosetta.protocols.features.ChargeChargeFeatures) -> float

C++: protocols::features::ChargeChargeFeatures::distance_cutoff() const –> double

  1. distance_cutoff(self: pyrosetta.rosetta.protocols.features.ChargeChargeFeatures, d: float) -> None

C++: protocols::features::ChargeChargeFeatures::distance_cutoff(double) –> void

features_reporter_dependencies(self: pyrosetta.rosetta.protocols.features.ChargeChargeFeatures) pyrosetta.rosetta.utility.vector1_std_string

return the set of features reporters that are required to also already be extracted by the time this one is used.

C++: protocols::features::ChargeChargeFeatures::features_reporter_dependencies() const –> class utility::vector1<std::string, class std::allocator<std::string > >

get_relevant_residues_mode(self: pyrosetta.rosetta.protocols.features.FeaturesReporter) pyrosetta.rosetta.protocols.features.RelevantResiduesMode.T

C++: protocols::features::FeaturesReporter::get_relevant_residues_mode() const –> enum protocols::features::RelevantResiduesMode::T

load_into_pose(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, : pyrosetta.rosetta.utility.sql_database.session, : int, : pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::features::FeaturesReporter::load_into_pose(class std::shared_ptr<class utility::sql_database::session>, unsigned long, class core::pose::Pose &) –> void

parse_my_tag(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None

C++: protocols::features::FeaturesReporter::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::features::ChargeChargeFeatures::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

report_features(self: pyrosetta.rosetta.protocols.features.ChargeChargeFeatures, pose: pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.utility.vector1_bool, struct_id: int, db_session: pyrosetta.rosetta.utility.sql_database.session) int

collect all the feature data for the pose

C++: protocols::features::ChargeChargeFeatures::report_features(const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> unsigned long

schema(self: pyrosetta.rosetta.protocols.features.FeaturesReporter) str

return sql statements that sets up the appropriate tables to contain the features. This should be removed once everything has been moved to the schema generator

C++: protocols::features::FeaturesReporter::schema() const –> std::string

set_relevant_residues_mode(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, setting: pyrosetta.rosetta.protocols.features.RelevantResiduesMode.T) None

C++: protocols::features::FeaturesReporter::set_relevant_residues_mode(enum protocols::features::RelevantResiduesMode::T) –> void

type_name(self: pyrosetta.rosetta.protocols.features.ChargeChargeFeatures) str

C++: protocols::features::ChargeChargeFeatures::type_name() const –> std::string

write_schema_to_db(self: pyrosetta.rosetta.protocols.features.ChargeChargeFeatures, db_session: pyrosetta.rosetta.utility.sql_database.session) None

generate the table schemas and write them to the database

C++: protocols::features::ChargeChargeFeatures::write_schema_to_db(class std::shared_ptr<class utility::sql_database::session>) const –> void

class pyrosetta.rosetta.protocols.features.ChargeChargeFeaturesCreator

Bases: pyrosetta.rosetta.protocols.features.FeaturesReporterCreator

creator for the ChargeChargeFeatures class

assign(self: pyrosetta.rosetta.protocols.features.ChargeChargeFeaturesCreator, : pyrosetta.rosetta.protocols.features.ChargeChargeFeaturesCreator) pyrosetta.rosetta.protocols.features.ChargeChargeFeaturesCreator

C++: protocols::features::ChargeChargeFeaturesCreator::operator=(const class protocols::features::ChargeChargeFeaturesCreator &) –> class protocols::features::ChargeChargeFeaturesCreator &

create_features_reporter(self: pyrosetta.rosetta.protocols.features.ChargeChargeFeaturesCreator) pyrosetta.rosetta.protocols.features.FeaturesReporter

C++: protocols::features::ChargeChargeFeaturesCreator::create_features_reporter() const –> class std::shared_ptr<class protocols::features::FeaturesReporter>

provide_xml_schema(self: pyrosetta.rosetta.protocols.features.ChargeChargeFeaturesCreator, xsd: utility::tag::XMLSchemaDefinition) None

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

type_name(self: pyrosetta.rosetta.protocols.features.ChargeChargeFeaturesCreator) str

C++: protocols::features::ChargeChargeFeaturesCreator::type_name() const –> std::string

class pyrosetta.rosetta.protocols.features.DatabaseFilter

Bases: pybind11_builtins.pybind11_object

assign(self: pyrosetta.rosetta.protocols.features.DatabaseFilter, : pyrosetta.rosetta.protocols.features.DatabaseFilter) pyrosetta.rosetta.protocols.features.DatabaseFilter

C++: protocols::features::DatabaseFilter::operator=(const class protocols::features::DatabaseFilter &) –> class protocols::features::DatabaseFilter &

class pyrosetta.rosetta.protocols.features.DatabaseJobInputter

Bases: pyrosetta.rosetta.protocols.jd2.JobInputter

This is the simplest implementation of JobInputter, which reads from -s/-l and Database files.

assign(self: pyrosetta.rosetta.protocols.features.DatabaseJobInputter, : pyrosetta.rosetta.protocols.features.DatabaseJobInputter) pyrosetta.rosetta.protocols.features.DatabaseJobInputter

C++: protocols::features::DatabaseJobInputter::operator=(const class protocols::features::DatabaseJobInputter &) –> class protocols::features::DatabaseJobInputter &

fill_jobs(self: pyrosetta.rosetta.protocols.features.DatabaseJobInputter, jobs: protocols::jd2::JobsContainer) None
this function determines what jobs exist from -in::file::silent and

-in::file::tags.

C++: protocols::features::DatabaseJobInputter::fill_jobs(class protocols::jd2::JobsContainer &) –> void

get_database_name(self: pyrosetta.rosetta.protocols.features.DatabaseJobInputter) str

Get database name

C++: protocols::features::DatabaseJobInputter::get_database_name() const –> std::string

get_database_pq_schema(self: pyrosetta.rosetta.protocols.features.DatabaseJobInputter) str

Get database postreSQL schema

C++: protocols::features::DatabaseJobInputter::get_database_pq_schema() const –> std::string

get_scorefunction(self: pyrosetta.rosetta.protocols.features.DatabaseJobInputter) pyrosetta.rosetta.core.scoring.ScoreFunction

Get score function

C++: protocols::features::DatabaseJobInputter::get_scorefunction() –> class std::shared_ptr<class core::scoring::ScoreFunction>

get_self_ptr(self: pyrosetta.rosetta.protocols.jd2.JobInputter) pyrosetta.rosetta.protocols.jd2.JobInputter

Get self owning pointers.

C++: protocols::jd2::JobInputter::get_self_ptr() –> class std::shared_ptr<class protocols::jd2::JobInputter>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.jd2.JobInputter) pyrosetta.rosetta.std.weak_ptr_protocols_jd2_JobInputter_t

Get self weak pointers.

C++: protocols::jd2::JobInputter::get_self_weak_ptr() –> class std::weak_ptr<class protocols::jd2::JobInputter>

input_source(self: pyrosetta.rosetta.protocols.features.DatabaseJobInputter) pyrosetta.rosetta.protocols.jd2.JobInputterInputSource.Enum
Return the type of input source that the DatabaseJobInputter is currently

using.

Always DATABASE.

C++: protocols::features::DatabaseJobInputter::input_source() const –> enum protocols::jd2::JobInputterInputSource::Enum

static job_inputter_input_source_to_string(source: pyrosetta.rosetta.protocols.jd2.JobInputterInputSource.Enum) str
call this with input_source() to get the input source of a

particular job inputter

C++: protocols::jd2::JobInputter::job_inputter_input_source_to_string(enum protocols::jd2::JobInputterInputSource::Enum) –> std::string

load_options_from_option_system(self: pyrosetta.rosetta.protocols.features.DatabaseJobInputter) None

load options from option sytem

C++: protocols::features::DatabaseJobInputter::load_options_from_option_system() –> void

pose_from_job(self: pyrosetta.rosetta.protocols.features.DatabaseJobInputter, pose: pyrosetta.rosetta.core.pose.Pose, job: protocols::jd2::Job) None
this function is responsible for filling the pose reference with

the pose indicated by the job. The Job object (within its InnerJob) contains a PoseCOP. This function needs to either fill the pose reference from the InnerJob or, on first demand of a pose from that InnerJob, instantiate the pose, hand off a COP to the InnerJob, and fill the reference. This implementation uses pose_from_pdb

C++: protocols::features::DatabaseJobInputter::pose_from_job(class core::pose::Pose &, class std::shared_ptr<class protocols::jd2::Job>) –> void

static register_options() None

C++: protocols::features::DatabaseJobInputter::register_options() –> void

set_database_name(self: pyrosetta.rosetta.protocols.features.DatabaseJobInputter, database_name: str) None

Set database name

C++: protocols::features::DatabaseJobInputter::set_database_name(const std::string &) –> void

set_database_pq_schema(self: pyrosetta.rosetta.protocols.features.DatabaseJobInputter, database_pq_schema: str) None

Set database postreSQL schema

C++: protocols::features::DatabaseJobInputter::set_database_pq_schema(const std::string &) –> void

set_scorefunction(self: pyrosetta.rosetta.protocols.features.DatabaseJobInputter, scorefunction: pyrosetta.rosetta.core.scoring.ScoreFunction) None

Set score function

C++: protocols::features::DatabaseJobInputter::set_scorefunction(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void

set_struct_ids_from_sql(self: pyrosetta.rosetta.protocols.features.DatabaseJobInputter, sql: pyrosetta.rosetta.utility.vector1_std_string) None

set input tags using a database SELECT command

C++: protocols::features::DatabaseJobInputter::set_struct_ids_from_sql(const class utility::vector1<std::string, class std::allocator<std::string > > &) –> void

set_struct_ids_from_strings(self: pyrosetta.rosetta.protocols.features.DatabaseJobInputter, struct_id_strings: pyrosetta.rosetta.utility.vector1_std_string) None

set struct_ids from a list of strings of integer representations

C++: protocols::features::DatabaseJobInputter::set_struct_ids_from_strings(const class utility::vector1<std::string, class std::allocator<std::string > > &) –> void

update_jobs_list(self: pyrosetta.rosetta.protocols.jd2.JobInputter, jobs: protocols::jd2::JobsContainer) None

This function is only called by certain JobInputters to update the jobs list after it has already been created.

An example case would be the LargeNstructJobInputter, which uses this function to load additional jobs after the first N have started to come back.

C++: protocols::jd2::JobInputter::update_jobs_list(class std::shared_ptr<class protocols::jd2::JobsContainer>) –> void

updates_jobs_list(self: pyrosetta.rosetta.protocols.jd2.JobInputter) bool

Does this type of JobInputter update the jobs list?

False by default. Override this function in derived classes to make it true.

C++: protocols::jd2::JobInputter::updates_jobs_list() const –> bool

class pyrosetta.rosetta.protocols.features.DatabaseJobInputterCreator

Bases: pyrosetta.rosetta.protocols.jd2.JobInputterCreator

assign(self: pyrosetta.rosetta.protocols.features.DatabaseJobInputterCreator, : pyrosetta.rosetta.protocols.features.DatabaseJobInputterCreator) pyrosetta.rosetta.protocols.features.DatabaseJobInputterCreator

C++: protocols::features::DatabaseJobInputterCreator::operator=(const class protocols::features::DatabaseJobInputterCreator &) –> class protocols::features::DatabaseJobInputterCreator &

create_JobInputter(self: pyrosetta.rosetta.protocols.features.DatabaseJobInputterCreator) pyrosetta.rosetta.protocols.jd2.JobInputter

C++: protocols::features::DatabaseJobInputterCreator::create_JobInputter() const –> class std::shared_ptr<class protocols::jd2::JobInputter>

keyname(self: pyrosetta.rosetta.protocols.features.DatabaseJobInputterCreator) str

C++: protocols::features::DatabaseJobInputterCreator::keyname() const –> std::string

class pyrosetta.rosetta.protocols.features.DatabaseJobOutputter

Bases: pyrosetta.rosetta.protocols.jd2.FileJobOutputter

this is a implementation of JobOutputter for database-based output.

add_evaluation(self: pyrosetta.rosetta.protocols.jd2.JobOutputter, : pyrosetta.rosetta.protocols.evaluation.PoseEvaluator) None

////////////////////////////// evaluator interface ////////////////////////////////////////////

C++: protocols::jd2::JobOutputter::add_evaluation(class std::shared_ptr<class protocols::evaluation::PoseEvaluator>) –> void

call_output_observers(self: pyrosetta.rosetta.protocols.jd2.JobOutputter, pose: pyrosetta.rosetta.core.pose.Pose, job: protocols::jd2::Job) None

call all output_observers

C++: protocols::jd2::JobOutputter::call_output_observers(const class core::pose::Pose &, class std::shared_ptr<class protocols::jd2::Job>) const –> void

clear_evaluators(self: pyrosetta.rosetta.protocols.jd2.JobOutputter) None

C++: protocols::jd2::JobOutputter::clear_evaluators() –> void

evaluate(self: pyrosetta.rosetta.protocols.jd2.JobOutputter, pose: pyrosetta.rosetta.core.pose.Pose, tag: str, pss: pyrosetta.rosetta.core.io.silent.SilentStruct) None

C++: protocols::jd2::JobOutputter::evaluate(class core::pose::Pose &, std::string, class core::io::silent::SilentStruct &) const –> void

evaluators(self: pyrosetta.rosetta.protocols.jd2.JobOutputter) pyrosetta.rosetta.protocols.evaluation.MetaPoseEvaluator

C++: protocols::jd2::JobOutputter::evaluators() const –> class std::shared_ptr<const class protocols::evaluation::MetaPoseEvaluator>

file(self: pyrosetta.rosetta.protocols.jd2.FileJobOutputter, job: protocols::jd2::Job, data: str) None

this function takes a string and writes it to disk (separately from Tracer output).

C++: protocols::jd2::FileJobOutputter::file(class std::shared_ptr<const class protocols::jd2::Job>, const std::string &) –> void

filename(self: pyrosetta.rosetta.protocols.jd2.JobOutputter, : protocols::jd2::Job) str

C++: protocols::jd2::JobOutputter::filename(class std::shared_ptr<const class protocols::jd2::Job>) const –> std::string

final_pose(self: pyrosetta.rosetta.protocols.features.DatabaseJobOutputter, job: protocols::jd2::Job, pose: pyrosetta.rosetta.core.pose.Pose, tag: str) None

this function outputs the final result of a job.

C++: protocols::features::DatabaseJobOutputter::final_pose(class std::shared_ptr<class protocols::jd2::Job>, const class core::pose::Pose &, const std::string &) –> void

flush(self: pyrosetta.rosetta.protocols.features.DatabaseJobOutputter) None

see parent class for explanation

C++: protocols::features::DatabaseJobOutputter::flush() –> void

get_database_name(self: pyrosetta.rosetta.protocols.features.DatabaseJobOutputter) str

Get database name

C++: protocols::features::DatabaseJobOutputter::get_database_name() const –> std::string

get_database_pq_schema(self: pyrosetta.rosetta.protocols.features.DatabaseJobOutputter) str

Get database postgresQL schema

C++: protocols::features::DatabaseJobOutputter::get_database_pq_schema() const –> std::string

job_has_completed(self: pyrosetta.rosetta.protocols.features.DatabaseJobOutputter, job: protocols::jd2::Job) bool
this function is not used for output, but it belongs here

since it needs to check the same output locations as the class normally writes to. This class checks wherever output goes to see if the job’s expected output already exists (on disk or whatever). This is the most basic form of checkpointing.

C++: protocols::features::DatabaseJobOutputter::job_has_completed(class std::shared_ptr<const class protocols::jd2::Job>) –> bool

load_options_from_option_system(self: pyrosetta.rosetta.protocols.features.DatabaseJobOutputter) None

load options from option sytem

C++: protocols::features::DatabaseJobOutputter::load_options_from_option_system() –> void

other_pose(*args, **kwargs)

Overloaded function.

  1. other_pose(self: pyrosetta.rosetta.protocols.features.DatabaseJobOutputter, job: protocols::jd2::Job, pose: pyrosetta.rosetta.core.pose.Pose, tag: str) -> None

  2. other_pose(self: pyrosetta.rosetta.protocols.features.DatabaseJobOutputter, job: protocols::jd2::Job, pose: pyrosetta.rosetta.core.pose.Pose, tag: str, copy_count: int) -> None

  3. other_pose(self: pyrosetta.rosetta.protocols.features.DatabaseJobOutputter, job: protocols::jd2::Job, pose: pyrosetta.rosetta.core.pose.Pose, tag: str, copy_count: int, score_only: bool) -> None

this function is intended for saving mid-protocol poses;

for example the final centroid structure in a combined centroid/fullatom protocol.

C++: protocols::features::DatabaseJobOutputter::other_pose(class std::shared_ptr<class protocols::jd2::Job>, const class core::pose::Pose &, const std::string &, int, bool) –> void

output_name(self: pyrosetta.rosetta.protocols.features.DatabaseJobOutputter, job: protocols::jd2::Job) str
this is the master function for determining the

unique output identifier for a job

C++: protocols::features::DatabaseJobOutputter::output_name(class std::shared_ptr<const class protocols::jd2::Job>) –> std::string

static register_options() None

C++: protocols::features::DatabaseJobOutputter::register_options() –> void

scorefile_name(self: pyrosetta.rosetta.protocols.jd2.FileJobOutputter) pyrosetta.rosetta.utility.file.FileName

C++: protocols::jd2::FileJobOutputter::scorefile_name() –> const class utility::file::FileName &

set_database_name(self: pyrosetta.rosetta.protocols.features.DatabaseJobOutputter, database_name: str) None

Set database name

C++: protocols::features::DatabaseJobOutputter::set_database_name(const std::string &) –> void

set_database_pq_schema(self: pyrosetta.rosetta.protocols.features.DatabaseJobOutputter, database_pq_schema: str) None

Set database postgreSQL schema

C++: protocols::features::DatabaseJobOutputter::set_database_pq_schema(const std::string &) –> void

set_defaults(self: pyrosetta.rosetta.protocols.jd2.FileJobOutputter) None

C++: protocols::jd2::FileJobOutputter::set_defaults() –> void

set_evaluators(self: pyrosetta.rosetta.protocols.jd2.JobOutputter, : pyrosetta.rosetta.protocols.evaluation.MetaPoseEvaluator) None

C++: protocols::jd2::JobOutputter::set_evaluators(const class protocols::evaluation::MetaPoseEvaluator &) –> void

starting_pose(self: pyrosetta.rosetta.protocols.jd2.JobOutputter, : pyrosetta.rosetta.core.pose.Pose) None
optionally pass a starting (reference) pose to a JobOutputter for later comparison

purposes and/or as interface for initializing evaluators

C++: protocols::jd2::JobOutputter::starting_pose(const class core::pose::Pose &) –> void

write_scorefile(self: pyrosetta.rosetta.protocols.jd2.FileJobOutputter) bool

C++: protocols::jd2::FileJobOutputter::write_scorefile() const –> bool

class pyrosetta.rosetta.protocols.features.DatabaseJobOutputterCreator

Bases: pyrosetta.rosetta.protocols.jd2.JobOutputterCreator

assign(self: pyrosetta.rosetta.protocols.features.DatabaseJobOutputterCreator, : pyrosetta.rosetta.protocols.features.DatabaseJobOutputterCreator) pyrosetta.rosetta.protocols.features.DatabaseJobOutputterCreator

C++: protocols::features::DatabaseJobOutputterCreator::operator=(const class protocols::features::DatabaseJobOutputterCreator &) –> class protocols::features::DatabaseJobOutputterCreator &

create_JobOutputter(self: pyrosetta.rosetta.protocols.features.DatabaseJobOutputterCreator) pyrosetta.rosetta.protocols.jd2.JobOutputter

C++: protocols::features::DatabaseJobOutputterCreator::create_JobOutputter() const –> class std::shared_ptr<class protocols::jd2::JobOutputter>

keyname(self: pyrosetta.rosetta.protocols.features.DatabaseJobOutputterCreator) str

C++: protocols::features::DatabaseJobOutputterCreator::keyname() const –> std::string

class pyrosetta.rosetta.protocols.features.DdGFeatures

Bases: pyrosetta.rosetta.protocols.features.FeaturesReporter

assign(self: pyrosetta.rosetta.protocols.features.DdGFeatures, : pyrosetta.rosetta.protocols.features.DdGFeatures) pyrosetta.rosetta.protocols.features.DdGFeatures

C++: protocols::features::DdGFeatures::operator=(const class protocols::features::DdGFeatures &) –> class protocols::features::DdGFeatures &

check_relevant_residues(*args, **kwargs)

Overloaded function.

  1. check_relevant_residues(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, res1: int) -> bool

C++: protocols::features::FeaturesReporter::check_relevant_residues(const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long) const –> bool

  1. check_relevant_residues(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, res1: int, res2: int) -> bool

C++: protocols::features::FeaturesReporter::check_relevant_residues(const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, unsigned long) const –> bool

  1. check_relevant_residues(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, residues: pyrosetta.rosetta.utility.vector1_unsigned_long) -> bool

C++: protocols::features::FeaturesReporter::check_relevant_residues(const class utility::vector1<bool, class std::allocator<bool> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> bool

check_relevant_residues_range(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, res1: int, res2: int) bool

C++: protocols::features::FeaturesReporter::check_relevant_residues_range(const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, unsigned long) const –> bool

static class_name() str

C++: protocols::features::DdGFeatures::class_name() –> std::string

delete_record(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, : int, : pyrosetta.rosetta.utility.sql_database.session) None

C++: protocols::features::FeaturesReporter::delete_record(unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> void

features_reporter_dependencies(self: pyrosetta.rosetta.protocols.features.DdGFeatures) pyrosetta.rosetta.utility.vector1_std_string

return the set of features reporters that are required to also already be extracted by the time this one is used.

C++: protocols::features::DdGFeatures::features_reporter_dependencies() const –> class utility::vector1<std::string, class std::allocator<std::string > >

get_relevant_residues_mode(self: pyrosetta.rosetta.protocols.features.FeaturesReporter) pyrosetta.rosetta.protocols.features.RelevantResiduesMode.T

C++: protocols::features::FeaturesReporter::get_relevant_residues_mode() const –> enum protocols::features::RelevantResiduesMode::T

load_into_pose(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, : pyrosetta.rosetta.utility.sql_database.session, : int, : pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::features::FeaturesReporter::load_into_pose(class std::shared_ptr<class utility::sql_database::session>, unsigned long, class core::pose::Pose &) –> void

parse_my_tag(self: pyrosetta.rosetta.protocols.features.DdGFeatures, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None

C++: protocols::features::DdGFeatures::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::features::DdGFeatures::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

report_features(self: pyrosetta.rosetta.protocols.features.DdGFeatures, pose: pyrosetta.rosetta.core.pose.Pose, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, struct_id: int, db_session: pyrosetta.rosetta.utility.sql_database.session) int

collect all the feature data for the pose

C++: protocols::features::DdGFeatures::report_features(const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> unsigned long

schema(self: pyrosetta.rosetta.protocols.features.FeaturesReporter) str

return sql statements that sets up the appropriate tables to contain the features. This should be removed once everything has been moved to the schema generator

C++: protocols::features::FeaturesReporter::schema() const –> std::string

set_relevant_residues_mode(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, setting: pyrosetta.rosetta.protocols.features.RelevantResiduesMode.T) None

C++: protocols::features::FeaturesReporter::set_relevant_residues_mode(enum protocols::features::RelevantResiduesMode::T) –> void

type_name(self: pyrosetta.rosetta.protocols.features.DdGFeatures) str

C++: protocols::features::DdGFeatures::type_name() const –> std::string

write_ddG_table_schema(self: pyrosetta.rosetta.protocols.features.DdGFeatures, db_session: pyrosetta.rosetta.utility.sql_database.session) None

C++: protocols::features::DdGFeatures::write_ddG_table_schema(class std::shared_ptr<class utility::sql_database::session>) const –> void

write_schema_to_db(self: pyrosetta.rosetta.protocols.features.DdGFeatures, db_session: pyrosetta.rosetta.utility.sql_database.session) None

generate the table schemas and write them to the database

C++: protocols::features::DdGFeatures::write_schema_to_db(class std::shared_ptr<class utility::sql_database::session>) const –> void

class pyrosetta.rosetta.protocols.features.DdGFeaturesCreator

Bases: pyrosetta.rosetta.protocols.features.FeaturesReporterCreator

creator for the DdGFeatures class

assign(self: pyrosetta.rosetta.protocols.features.DdGFeaturesCreator, : pyrosetta.rosetta.protocols.features.DdGFeaturesCreator) pyrosetta.rosetta.protocols.features.DdGFeaturesCreator

C++: protocols::features::DdGFeaturesCreator::operator=(const class protocols::features::DdGFeaturesCreator &) –> class protocols::features::DdGFeaturesCreator &

create_features_reporter(self: pyrosetta.rosetta.protocols.features.DdGFeaturesCreator) pyrosetta.rosetta.protocols.features.FeaturesReporter

C++: protocols::features::DdGFeaturesCreator::create_features_reporter() const –> class std::shared_ptr<class protocols::features::FeaturesReporter>

provide_xml_schema(self: pyrosetta.rosetta.protocols.features.DdGFeaturesCreator, xsd: utility::tag::XMLSchemaDefinition) None

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

type_name(self: pyrosetta.rosetta.protocols.features.DdGFeaturesCreator) str

C++: protocols::features::DdGFeaturesCreator::type_name() const –> std::string

class pyrosetta.rosetta.protocols.features.FeaturesReporter

Bases: pybind11_builtins.pybind11_object

assign(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, : pyrosetta.rosetta.protocols.features.FeaturesReporter) pyrosetta.rosetta.protocols.features.FeaturesReporter

C++: protocols::features::FeaturesReporter::operator=(const class protocols::features::FeaturesReporter &) –> class protocols::features::FeaturesReporter &

check_relevant_residues(*args, **kwargs)

Overloaded function.

  1. check_relevant_residues(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, res1: int) -> bool

C++: protocols::features::FeaturesReporter::check_relevant_residues(const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long) const –> bool

  1. check_relevant_residues(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, res1: int, res2: int) -> bool

C++: protocols::features::FeaturesReporter::check_relevant_residues(const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, unsigned long) const –> bool

  1. check_relevant_residues(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, residues: pyrosetta.rosetta.utility.vector1_unsigned_long) -> bool

C++: protocols::features::FeaturesReporter::check_relevant_residues(const class utility::vector1<bool, class std::allocator<bool> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> bool

check_relevant_residues_range(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, res1: int, res2: int) bool

C++: protocols::features::FeaturesReporter::check_relevant_residues_range(const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, unsigned long) const –> bool

delete_record(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, : int, : pyrosetta.rosetta.utility.sql_database.session) None

C++: protocols::features::FeaturesReporter::delete_record(unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> void

features_reporter_dependencies(self: pyrosetta.rosetta.protocols.features.FeaturesReporter) pyrosetta.rosetta.utility.vector1_std_string

return the set of features reporters that are required to also already be extracted by the time this one is used.

C++: protocols::features::FeaturesReporter::features_reporter_dependencies() const –> class utility::vector1<std::string, class std::allocator<std::string > >

get_relevant_residues_mode(self: pyrosetta.rosetta.protocols.features.FeaturesReporter) pyrosetta.rosetta.protocols.features.RelevantResiduesMode.T

C++: protocols::features::FeaturesReporter::get_relevant_residues_mode() const –> enum protocols::features::RelevantResiduesMode::T

load_into_pose(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, : pyrosetta.rosetta.utility.sql_database.session, : int, : pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::features::FeaturesReporter::load_into_pose(class std::shared_ptr<class utility::sql_database::session>, unsigned long, class core::pose::Pose &) –> void

parse_my_tag(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None

C++: protocols::features::FeaturesReporter::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

report_features(*args, **kwargs)

Overloaded function.

  1. report_features(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, : pyrosetta.rosetta.core.pose.Pose, : int, : pyrosetta.rosetta.utility.sql_database.session) -> int

collect all the feature data for the pose.

C++: protocols::features::FeaturesReporter::report_features(const class core::pose::Pose &, unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> unsigned long

  1. report_features(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.utility.vector1_bool, : int, : pyrosetta.rosetta.utility.sql_database.session) -> int

collect all the feature data for the pose.

C++: protocols::features::FeaturesReporter::report_features(const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> unsigned long

schema(self: pyrosetta.rosetta.protocols.features.FeaturesReporter) str

return sql statements that sets up the appropriate tables to contain the features. This should be removed once everything has been moved to the schema generator

C++: protocols::features::FeaturesReporter::schema() const –> std::string

set_relevant_residues_mode(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, setting: pyrosetta.rosetta.protocols.features.RelevantResiduesMode.T) None

C++: protocols::features::FeaturesReporter::set_relevant_residues_mode(enum protocols::features::RelevantResiduesMode::T) –> void

type_name(self: pyrosetta.rosetta.protocols.features.FeaturesReporter) str

C++: protocols::features::FeaturesReporter::type_name() const –> std::string

write_schema_to_db(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, db_session: pyrosetta.rosetta.utility.sql_database.session) None

Define the schema and write it to the database. This is most easily achieved using the schema_generator. Once everything has converted to the schema generator this should be made a pure virtual

C++: protocols::features::FeaturesReporter::write_schema_to_db(class std::shared_ptr<class utility::sql_database::session>) const –> void

class pyrosetta.rosetta.protocols.features.FeaturesReporterCreator

Bases: pybind11_builtins.pybind11_object

The Creator class is responsible for creating a particular mover class.

assign(self: pyrosetta.rosetta.protocols.features.FeaturesReporterCreator, : pyrosetta.rosetta.protocols.features.FeaturesReporterCreator) pyrosetta.rosetta.protocols.features.FeaturesReporterCreator

C++: protocols::features::FeaturesReporterCreator::operator=(const class protocols::features::FeaturesReporterCreator &) –> class protocols::features::FeaturesReporterCreator &

create_features_reporter(self: pyrosetta.rosetta.protocols.features.FeaturesReporterCreator) pyrosetta.rosetta.protocols.features.FeaturesReporter

C++: protocols::features::FeaturesReporterCreator::create_features_reporter() const –> class std::shared_ptr<class protocols::features::FeaturesReporter>

provide_xml_schema(self: pyrosetta.rosetta.protocols.features.FeaturesReporterCreator, xsd: utility::tag::XMLSchemaDefinition) None

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

type_name(self: pyrosetta.rosetta.protocols.features.FeaturesReporterCreator) str

C++: protocols::features::FeaturesReporterCreator::type_name() const –> std::string

class pyrosetta.rosetta.protocols.features.FeaturesReporterFactory

Bases: pyrosetta.rosetta.utility.SingletonBase_protocols_features_FeaturesReporterFactory_t

Create Features Reporters

define_features_reporter_xml_schema_group(self: pyrosetta.rosetta.protocols.features.FeaturesReporterFactory, xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::features::FeaturesReporterFactory::define_features_reporter_xml_schema_group(class utility::tag::XMLSchemaDefinition &) const –> void

factory_register(self: pyrosetta.rosetta.protocols.features.FeaturesReporterFactory, creator: pyrosetta.rosetta.protocols.features.FeaturesReporterCreator) None

C++: protocols::features::FeaturesReporterFactory::factory_register(class std::shared_ptr<const class protocols::features::FeaturesReporterCreator>) –> void

static features_reporter_xml_schema_group_name() str

C++: protocols::features::FeaturesReporterFactory::features_reporter_xml_schema_group_name() –> std::string

get_all_features_names(self: pyrosetta.rosetta.protocols.features.FeaturesReporterFactory) pyrosetta.rosetta.utility.vector1_std_string

C++: protocols::features::FeaturesReporterFactory::get_all_features_names() –> class utility::vector1<std::string, class std::allocator<std::string > >

get_features_reporter(*args, **kwargs)

Overloaded function.

  1. get_features_reporter(self: pyrosetta.rosetta.protocols.features.FeaturesReporterFactory, type_name: str) -> pyrosetta.rosetta.protocols.features.FeaturesReporter

C++: protocols::features::FeaturesReporterFactory::get_features_reporter(const std::string &) –> class std::shared_ptr<class protocols::features::FeaturesReporter>

  1. get_features_reporter(self: pyrosetta.rosetta.protocols.features.FeaturesReporterFactory, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) -> pyrosetta.rosetta.protocols.features.FeaturesReporter

convienence header for use with RosettaScripts parse_my_tag interface

C++: protocols::features::FeaturesReporterFactory::get_features_reporter(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> class std::shared_ptr<class protocols::features::FeaturesReporter>

static get_instance() protocols::features::FeaturesReporterFactory

C++: utility::SingletonBase<protocols::features::FeaturesReporterFactory>::get_instance() –> class protocols::features::FeaturesReporterFactory *

class pyrosetta.rosetta.protocols.features.GeometricSolvationFeatures

Bases: pyrosetta.rosetta.protocols.features.FeaturesReporter

assign(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, : pyrosetta.rosetta.protocols.features.FeaturesReporter) pyrosetta.rosetta.protocols.features.FeaturesReporter

C++: protocols::features::FeaturesReporter::operator=(const class protocols::features::FeaturesReporter &) –> class protocols::features::FeaturesReporter &

check_relevant_residues(*args, **kwargs)

Overloaded function.

  1. check_relevant_residues(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, res1: int) -> bool

C++: protocols::features::FeaturesReporter::check_relevant_residues(const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long) const –> bool

  1. check_relevant_residues(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, res1: int, res2: int) -> bool

C++: protocols::features::FeaturesReporter::check_relevant_residues(const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, unsigned long) const –> bool

  1. check_relevant_residues(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, residues: pyrosetta.rosetta.utility.vector1_unsigned_long) -> bool

C++: protocols::features::FeaturesReporter::check_relevant_residues(const class utility::vector1<bool, class std::allocator<bool> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> bool

check_relevant_residues_range(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, res1: int, res2: int) bool

C++: protocols::features::FeaturesReporter::check_relevant_residues_range(const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, unsigned long) const –> bool

static class_name() str

C++: protocols::features::GeometricSolvationFeatures::class_name() –> std::string

delete_record(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, : int, : pyrosetta.rosetta.utility.sql_database.session) None

C++: protocols::features::FeaturesReporter::delete_record(unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> void

features_reporter_dependencies(self: pyrosetta.rosetta.protocols.features.GeometricSolvationFeatures) pyrosetta.rosetta.utility.vector1_std_string

return the set of features reporters that are required to also already be extracted by the time this one is used.

C++: protocols::features::GeometricSolvationFeatures::features_reporter_dependencies() const –> class utility::vector1<std::string, class std::allocator<std::string > >

get_relevant_residues_mode(self: pyrosetta.rosetta.protocols.features.FeaturesReporter) pyrosetta.rosetta.protocols.features.RelevantResiduesMode.T

C++: protocols::features::FeaturesReporter::get_relevant_residues_mode() const –> enum protocols::features::RelevantResiduesMode::T

load_into_pose(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, : pyrosetta.rosetta.utility.sql_database.session, : int, : pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::features::FeaturesReporter::load_into_pose(class std::shared_ptr<class utility::sql_database::session>, unsigned long, class core::pose::Pose &) –> void

parse_my_tag(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None

C++: protocols::features::FeaturesReporter::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::features::GeometricSolvationFeatures::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

report_features(self: pyrosetta.rosetta.protocols.features.GeometricSolvationFeatures, pose: pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.utility.vector1_bool, struct_id: int, db_session: pyrosetta.rosetta.utility.sql_database.session) int

collect all the feature data for the pose

C++: protocols::features::GeometricSolvationFeatures::report_features(const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> unsigned long

schema(self: pyrosetta.rosetta.protocols.features.FeaturesReporter) str

return sql statements that sets up the appropriate tables to contain the features. This should be removed once everything has been moved to the schema generator

C++: protocols::features::FeaturesReporter::schema() const –> std::string

set_relevant_residues_mode(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, setting: pyrosetta.rosetta.protocols.features.RelevantResiduesMode.T) None

C++: protocols::features::FeaturesReporter::set_relevant_residues_mode(enum protocols::features::RelevantResiduesMode::T) –> void

type_name(self: pyrosetta.rosetta.protocols.features.GeometricSolvationFeatures) str

C++: protocols::features::GeometricSolvationFeatures::type_name() const –> std::string

write_schema_to_db(self: pyrosetta.rosetta.protocols.features.GeometricSolvationFeatures, db_session: pyrosetta.rosetta.utility.sql_database.session) None

generate the table schemas and write them to the database

C++: protocols::features::GeometricSolvationFeatures::write_schema_to_db(class std::shared_ptr<class utility::sql_database::session>) const –> void

class pyrosetta.rosetta.protocols.features.GeometricSolvationFeaturesCreator

Bases: pyrosetta.rosetta.protocols.features.FeaturesReporterCreator

creator for the GeometricSolvationFeatures class

assign(self: pyrosetta.rosetta.protocols.features.GeometricSolvationFeaturesCreator, : pyrosetta.rosetta.protocols.features.GeometricSolvationFeaturesCreator) pyrosetta.rosetta.protocols.features.GeometricSolvationFeaturesCreator

C++: protocols::features::GeometricSolvationFeaturesCreator::operator=(const class protocols::features::GeometricSolvationFeaturesCreator &) –> class protocols::features::GeometricSolvationFeaturesCreator &

create_features_reporter(self: pyrosetta.rosetta.protocols.features.GeometricSolvationFeaturesCreator) pyrosetta.rosetta.protocols.features.FeaturesReporter

C++: protocols::features::GeometricSolvationFeaturesCreator::create_features_reporter() const –> class std::shared_ptr<class protocols::features::FeaturesReporter>

provide_xml_schema(self: pyrosetta.rosetta.protocols.features.GeometricSolvationFeaturesCreator, xsd: utility::tag::XMLSchemaDefinition) None

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

type_name(self: pyrosetta.rosetta.protocols.features.GeometricSolvationFeaturesCreator) str

C++: protocols::features::GeometricSolvationFeaturesCreator::type_name() const –> std::string

class pyrosetta.rosetta.protocols.features.HBDefType

Bases: pybind11_builtins.pybind11_object

How a hydrogen bond should be defined See note for

definition_type_ below.

Members:

hbdef_NONE

hbdef_ENERGY

hbdef_AHDIST

hbdef_MAX

hbdef_AHDIST = <HBDefType.hbdef_AHDIST: 3>
hbdef_ENERGY = <HBDefType.hbdef_ENERGY: 2>
hbdef_MAX = <HBDefType.hbdef_AHDIST: 3>
hbdef_NONE = <HBDefType.hbdef_NONE: 1>
property name
class pyrosetta.rosetta.protocols.features.HBondFeatures

Bases: pyrosetta.rosetta.protocols.features.FeaturesReporter

assign(self: pyrosetta.rosetta.protocols.features.HBondFeatures, : pyrosetta.rosetta.protocols.features.HBondFeatures) pyrosetta.rosetta.protocols.features.HBondFeatures

C++: protocols::features::HBondFeatures::operator=(const class protocols::features::HBondFeatures &) –> class protocols::features::HBondFeatures &

check_relevant_residues(*args, **kwargs)

Overloaded function.

  1. check_relevant_residues(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, res1: int) -> bool

C++: protocols::features::FeaturesReporter::check_relevant_residues(const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long) const –> bool

  1. check_relevant_residues(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, res1: int, res2: int) -> bool

C++: protocols::features::FeaturesReporter::check_relevant_residues(const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, unsigned long) const –> bool

  1. check_relevant_residues(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, residues: pyrosetta.rosetta.utility.vector1_unsigned_long) -> bool

C++: protocols::features::FeaturesReporter::check_relevant_residues(const class utility::vector1<bool, class std::allocator<bool> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> bool

check_relevant_residues_range(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, res1: int, res2: int) bool

C++: protocols::features::FeaturesReporter::check_relevant_residues_range(const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, unsigned long) const –> bool

static class_name() str

C++: protocols::features::HBondFeatures::class_name() –> std::string

delete_record(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, : int, : pyrosetta.rosetta.utility.sql_database.session) None

C++: protocols::features::FeaturesReporter::delete_record(unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> void

features_reporter_dependencies(self: pyrosetta.rosetta.protocols.features.HBondFeatures) pyrosetta.rosetta.utility.vector1_std_string

return the set of features reporters that are required to also already be extracted by the time this one is used.

C++: protocols::features::HBondFeatures::features_reporter_dependencies() const –> class utility::vector1<std::string, class std::allocator<std::string > >

get_relevant_residues_mode(self: pyrosetta.rosetta.protocols.features.FeaturesReporter) pyrosetta.rosetta.protocols.features.RelevantResiduesMode.T

C++: protocols::features::FeaturesReporter::get_relevant_residues_mode() const –> enum protocols::features::RelevantResiduesMode::T

insert_hbond_dehydron_row(self: pyrosetta.rosetta.protocols.features.HBondFeatures, pose: pyrosetta.rosetta.core.pose.Pose, hbond: pyrosetta.rosetta.core.scoring.hbonds.HBond, struct_id: int, hbond_id: int, db_session: pyrosetta.rosetta.utility.sql_database.session) None

C++: protocols::features::HBondFeatures::insert_hbond_dehydron_row(const class core::pose::Pose &, const class core::scoring::hbonds::HBond &, unsigned long, unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> void

insert_hbond_geom_coords(self: pyrosetta.rosetta.protocols.features.HBondFeatures, pose: pyrosetta.rosetta.core.pose.Pose, hbond_options: pyrosetta.rosetta.core.scoring.hbonds.HBondOptions, hbond: pyrosetta.rosetta.core.scoring.hbonds.HBond, struct_id: int, hbond_id: int, db_session: pyrosetta.rosetta.utility.sql_database.session) None

C++: protocols::features::HBondFeatures::insert_hbond_geom_coords(const class core::pose::Pose &, const class core::scoring::hbonds::HBondOptions &, const class core::scoring::hbonds::HBond &, unsigned long, unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> void

insert_hbond_lennard_jones_row(self: pyrosetta.rosetta.protocols.features.HBondFeatures, pose: pyrosetta.rosetta.core.pose.Pose, hbond: pyrosetta.rosetta.core.scoring.hbonds.HBond, struct_id: int, hbond_id: int, db_session: pyrosetta.rosetta.utility.sql_database.session) None

C++: protocols::features::HBondFeatures::insert_hbond_lennard_jones_row(const class core::pose::Pose &, const class core::scoring::hbonds::HBond &, unsigned long, unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> void

insert_site_atoms_row(self: pyrosetta.rosetta.protocols.features.HBondFeatures, pose: pyrosetta.rosetta.core.pose.Pose, resNum: int, atmNum: int, struct_id: int, site_id: int, db_session: pyrosetta.rosetta.utility.sql_database.session) None

C++: protocols::features::HBondFeatures::insert_site_atoms_row(const class core::pose::Pose &, unsigned long, unsigned long, unsigned long, unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> void

insert_site_pdb_row(self: pyrosetta.rosetta.protocols.features.HBondFeatures, pose: pyrosetta.rosetta.core.pose.Pose, resNum: int, atmNum: int, heavy_atmNum: int, struct_id: int, site_id: int, db_session: pyrosetta.rosetta.utility.sql_database.session) None

C++: protocols::features::HBondFeatures::insert_site_pdb_row(const class core::pose::Pose &, unsigned long, unsigned long, unsigned long, unsigned long, unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> void

insert_site_row(self: pyrosetta.rosetta.protocols.features.HBondFeatures, pose: pyrosetta.rosetta.core.pose.Pose, struct_id: int, site_id: int, resNum: int, atmNum: int, is_donor: bool, db_session: pyrosetta.rosetta.utility.sql_database.session) None

C++: protocols::features::HBondFeatures::insert_site_row(const class core::pose::Pose &, unsigned long, unsigned long, unsigned long, unsigned long, bool, class std::shared_ptr<class utility::sql_database::session>) –> void

load_into_pose(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, : pyrosetta.rosetta.utility.sql_database.session, : int, : pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::features::FeaturesReporter::load_into_pose(class std::shared_ptr<class utility::sql_database::session>, unsigned long, class core::pose::Pose &) –> void

parse_my_tag(self: pyrosetta.rosetta.protocols.features.HBondFeatures, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None

C++: protocols::features::HBondFeatures::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::features::HBondFeatures::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

report_features(self: pyrosetta.rosetta.protocols.features.HBondFeatures, pose: pyrosetta.rosetta.core.pose.Pose, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, struct_id: int, db_session: pyrosetta.rosetta.utility.sql_database.session) int

collect all the feature data for the pose

C++: protocols::features::HBondFeatures::report_features(const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> unsigned long

schema(self: pyrosetta.rosetta.protocols.features.FeaturesReporter) str

return sql statements that sets up the appropriate tables to contain the features. This should be removed once everything has been moved to the schema generator

C++: protocols::features::FeaturesReporter::schema() const –> std::string

set_relevant_residues_mode(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, setting: pyrosetta.rosetta.protocols.features.RelevantResiduesMode.T) None

C++: protocols::features::FeaturesReporter::set_relevant_residues_mode(enum protocols::features::RelevantResiduesMode::T) –> void

type_name(self: pyrosetta.rosetta.protocols.features.HBondFeatures) str

C++: protocols::features::HBondFeatures::type_name() const –> std::string

write_schema_to_db(self: pyrosetta.rosetta.protocols.features.HBondFeatures, db_session: pyrosetta.rosetta.utility.sql_database.session) None

generate the table schemas and write them to the database

C++: protocols::features::HBondFeatures::write_schema_to_db(class std::shared_ptr<class utility::sql_database::session>) const –> void

class pyrosetta.rosetta.protocols.features.HBondFeaturesCreator

Bases: pyrosetta.rosetta.protocols.features.FeaturesReporterCreator

creator for the HBondFeatures class

assign(self: pyrosetta.rosetta.protocols.features.HBondFeaturesCreator, : pyrosetta.rosetta.protocols.features.HBondFeaturesCreator) pyrosetta.rosetta.protocols.features.HBondFeaturesCreator

C++: protocols::features::HBondFeaturesCreator::operator=(const class protocols::features::HBondFeaturesCreator &) –> class protocols::features::HBondFeaturesCreator &

create_features_reporter(self: pyrosetta.rosetta.protocols.features.HBondFeaturesCreator) pyrosetta.rosetta.protocols.features.FeaturesReporter

C++: protocols::features::HBondFeaturesCreator::create_features_reporter() const –> class std::shared_ptr<class protocols::features::FeaturesReporter>

provide_xml_schema(self: pyrosetta.rosetta.protocols.features.HBondFeaturesCreator, xsd: utility::tag::XMLSchemaDefinition) None

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

type_name(self: pyrosetta.rosetta.protocols.features.HBondFeaturesCreator) str

C++: protocols::features::HBondFeaturesCreator::type_name() const –> std::string

class pyrosetta.rosetta.protocols.features.HBondParameterFeatures

Bases: pyrosetta.rosetta.protocols.features.FeaturesReporter

assign(self: pyrosetta.rosetta.protocols.features.HBondParameterFeatures, : pyrosetta.rosetta.protocols.features.HBondParameterFeatures) pyrosetta.rosetta.protocols.features.HBondParameterFeatures

C++: protocols::features::HBondParameterFeatures::operator=(const class protocols::features::HBondParameterFeatures &) –> class protocols::features::HBondParameterFeatures &

check_relevant_residues(*args, **kwargs)

Overloaded function.

  1. check_relevant_residues(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, res1: int) -> bool

C++: protocols::features::FeaturesReporter::check_relevant_residues(const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long) const –> bool

  1. check_relevant_residues(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, res1: int, res2: int) -> bool

C++: protocols::features::FeaturesReporter::check_relevant_residues(const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, unsigned long) const –> bool

  1. check_relevant_residues(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, residues: pyrosetta.rosetta.utility.vector1_unsigned_long) -> bool

C++: protocols::features::FeaturesReporter::check_relevant_residues(const class utility::vector1<bool, class std::allocator<bool> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> bool

check_relevant_residues_range(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, res1: int, res2: int) bool

C++: protocols::features::FeaturesReporter::check_relevant_residues_range(const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, unsigned long) const –> bool

static class_name() str

C++: protocols::features::HBondParameterFeatures::class_name() –> std::string

delete_record(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, : int, : pyrosetta.rosetta.utility.sql_database.session) None

C++: protocols::features::FeaturesReporter::delete_record(unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> void

features_reporter_dependencies(self: pyrosetta.rosetta.protocols.features.HBondParameterFeatures) pyrosetta.rosetta.utility.vector1_std_string

return the set of features reporters that are required to also already be extracted by the time this one is used.

C++: protocols::features::HBondParameterFeatures::features_reporter_dependencies() const –> class utility::vector1<std::string, class std::allocator<std::string > >

get_relevant_residues_mode(self: pyrosetta.rosetta.protocols.features.FeaturesReporter) pyrosetta.rosetta.protocols.features.RelevantResiduesMode.T

C++: protocols::features::FeaturesReporter::get_relevant_residues_mode() const –> enum protocols::features::RelevantResiduesMode::T

load_into_pose(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, : pyrosetta.rosetta.utility.sql_database.session, : int, : pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::features::FeaturesReporter::load_into_pose(class std::shared_ptr<class utility::sql_database::session>, unsigned long, class core::pose::Pose &) –> void

parse_my_tag(self: pyrosetta.rosetta.protocols.features.HBondParameterFeatures, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None

C++: protocols::features::HBondParameterFeatures::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::features::HBondParameterFeatures::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

report_features(self: pyrosetta.rosetta.protocols.features.HBondParameterFeatures, pose: pyrosetta.rosetta.core.pose.Pose, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, struct_id: int, db_session: pyrosetta.rosetta.utility.sql_database.session) int

collect all the feature data for the pose

C++: protocols::features::HBondParameterFeatures::report_features(const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> unsigned long

schema(self: pyrosetta.rosetta.protocols.features.FeaturesReporter) str

return sql statements that sets up the appropriate tables to contain the features. This should be removed once everything has been moved to the schema generator

C++: protocols::features::FeaturesReporter::schema() const –> std::string

set_relevant_residues_mode(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, setting: pyrosetta.rosetta.protocols.features.RelevantResiduesMode.T) None

C++: protocols::features::FeaturesReporter::set_relevant_residues_mode(enum protocols::features::RelevantResiduesMode::T) –> void

type_name(self: pyrosetta.rosetta.protocols.features.HBondParameterFeatures) str

C++: protocols::features::HBondParameterFeatures::type_name() const –> std::string

write_schema_to_db(self: pyrosetta.rosetta.protocols.features.HBondParameterFeatures, db_session: pyrosetta.rosetta.utility.sql_database.session) None

generate the table schemas and write them to the database

C++: protocols::features::HBondParameterFeatures::write_schema_to_db(class std::shared_ptr<class utility::sql_database::session>) const –> void

class pyrosetta.rosetta.protocols.features.HBondParameterFeaturesCreator

Bases: pyrosetta.rosetta.protocols.features.FeaturesReporterCreator

creator for the HBondParameterFeatures class

assign(self: pyrosetta.rosetta.protocols.features.HBondParameterFeaturesCreator, : pyrosetta.rosetta.protocols.features.HBondParameterFeaturesCreator) pyrosetta.rosetta.protocols.features.HBondParameterFeaturesCreator

C++: protocols::features::HBondParameterFeaturesCreator::operator=(const class protocols::features::HBondParameterFeaturesCreator &) –> class protocols::features::HBondParameterFeaturesCreator &

create_features_reporter(self: pyrosetta.rosetta.protocols.features.HBondParameterFeaturesCreator) pyrosetta.rosetta.protocols.features.FeaturesReporter

C++: protocols::features::HBondParameterFeaturesCreator::create_features_reporter() const –> class std::shared_ptr<class protocols::features::FeaturesReporter>

provide_xml_schema(self: pyrosetta.rosetta.protocols.features.HBondParameterFeaturesCreator, xsd: utility::tag::XMLSchemaDefinition) None

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

type_name(self: pyrosetta.rosetta.protocols.features.HBondParameterFeaturesCreator) str

C++: protocols::features::HBondParameterFeaturesCreator::type_name() const –> std::string

class pyrosetta.rosetta.protocols.features.HelixCapFeatures

Bases: pyrosetta.rosetta.protocols.features.FeaturesReporter

assign(self: pyrosetta.rosetta.protocols.features.HelixCapFeatures, : pyrosetta.rosetta.protocols.features.HelixCapFeatures) pyrosetta.rosetta.protocols.features.HelixCapFeatures

C++: protocols::features::HelixCapFeatures::operator=(const class protocols::features::HelixCapFeatures &) –> class protocols::features::HelixCapFeatures &

check_relevant_residues(*args, **kwargs)

Overloaded function.

  1. check_relevant_residues(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, res1: int) -> bool

C++: protocols::features::FeaturesReporter::check_relevant_residues(const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long) const –> bool

  1. check_relevant_residues(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, res1: int, res2: int) -> bool

C++: protocols::features::FeaturesReporter::check_relevant_residues(const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, unsigned long) const –> bool

  1. check_relevant_residues(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, residues: pyrosetta.rosetta.utility.vector1_unsigned_long) -> bool

C++: protocols::features::FeaturesReporter::check_relevant_residues(const class utility::vector1<bool, class std::allocator<bool> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> bool

check_relevant_residues_range(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, res1: int, res2: int) bool

C++: protocols::features::FeaturesReporter::check_relevant_residues_range(const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, unsigned long) const –> bool

static class_name() str

C++: protocols::features::HelixCapFeatures::class_name() –> std::string

delete_record(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, : int, : pyrosetta.rosetta.utility.sql_database.session) None

C++: protocols::features::FeaturesReporter::delete_record(unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> void

features_reporter_dependencies(self: pyrosetta.rosetta.protocols.features.HelixCapFeatures) pyrosetta.rosetta.utility.vector1_std_string

return the set of features reporters that are required to also already be extracted by the time this one is used.

C++: protocols::features::HelixCapFeatures::features_reporter_dependencies() const –> class utility::vector1<std::string, class std::allocator<std::string > >

get_relevant_residues_mode(self: pyrosetta.rosetta.protocols.features.FeaturesReporter) pyrosetta.rosetta.protocols.features.RelevantResiduesMode.T

C++: protocols::features::FeaturesReporter::get_relevant_residues_mode() const –> enum protocols::features::RelevantResiduesMode::T

is_loop(self: pyrosetta.rosetta.protocols.features.HelixCapFeatures, dssp_code: str) bool

C++: protocols::features::HelixCapFeatures::is_loop(std::string) –> bool

load_into_pose(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, : pyrosetta.rosetta.utility.sql_database.session, : int, : pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::features::FeaturesReporter::load_into_pose(class std::shared_ptr<class utility::sql_database::session>, unsigned long, class core::pose::Pose &) –> void

parse_my_tag(self: pyrosetta.rosetta.protocols.features.HelixCapFeatures, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None

C++: protocols::features::HelixCapFeatures::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::features::HelixCapFeatures::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

report_features(self: pyrosetta.rosetta.protocols.features.HelixCapFeatures, pose: pyrosetta.rosetta.core.pose.Pose, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, struct_id: int, db_session: pyrosetta.rosetta.utility.sql_database.session) int

collect all the feature data for the pose

C++: protocols::features::HelixCapFeatures::report_features(const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> unsigned long

schema(self: pyrosetta.rosetta.protocols.features.FeaturesReporter) str

return sql statements that sets up the appropriate tables to contain the features. This should be removed once everything has been moved to the schema generator

C++: protocols::features::FeaturesReporter::schema() const –> std::string

set_relevant_residues_mode(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, setting: pyrosetta.rosetta.protocols.features.RelevantResiduesMode.T) None

C++: protocols::features::FeaturesReporter::set_relevant_residues_mode(enum protocols::features::RelevantResiduesMode::T) –> void

type_name(self: pyrosetta.rosetta.protocols.features.HelixCapFeatures) str

C++: protocols::features::HelixCapFeatures::type_name() const –> std::string

write_schema_to_db(self: pyrosetta.rosetta.protocols.features.HelixCapFeatures, db_session: pyrosetta.rosetta.utility.sql_database.session) None

generate the table schemas and write them to the database

C++: protocols::features::HelixCapFeatures::write_schema_to_db(class std::shared_ptr<class utility::sql_database::session>) const –> void

class pyrosetta.rosetta.protocols.features.HelixCapFeaturesCreator

Bases: pyrosetta.rosetta.protocols.features.FeaturesReporterCreator

creator for the HelixCapFeaturesCreator class

assign(self: pyrosetta.rosetta.protocols.features.HelixCapFeaturesCreator, : pyrosetta.rosetta.protocols.features.HelixCapFeaturesCreator) pyrosetta.rosetta.protocols.features.HelixCapFeaturesCreator

C++: protocols::features::HelixCapFeaturesCreator::operator=(const class protocols::features::HelixCapFeaturesCreator &) –> class protocols::features::HelixCapFeaturesCreator &

create_features_reporter(self: pyrosetta.rosetta.protocols.features.HelixCapFeaturesCreator) pyrosetta.rosetta.protocols.features.FeaturesReporter

C++: protocols::features::HelixCapFeaturesCreator::create_features_reporter() const –> class std::shared_ptr<class protocols::features::FeaturesReporter>

provide_xml_schema(self: pyrosetta.rosetta.protocols.features.HelixCapFeaturesCreator, xsd: utility::tag::XMLSchemaDefinition) None

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

type_name(self: pyrosetta.rosetta.protocols.features.HelixCapFeaturesCreator) str

C++: protocols::features::HelixCapFeaturesCreator::type_name() const –> std::string

class pyrosetta.rosetta.protocols.features.InterfaceDdGMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

Calculates ddG of binding

add_chain_id(*args, **kwargs)

Overloaded function.

  1. add_chain_id(self: pyrosetta.rosetta.protocols.features.InterfaceDdGMover, chain_id: int, pose: pyrosetta.rosetta.core.pose.Pose) -> None

appends chain_id

C++: protocols::features::InterfaceDdGMover::add_chain_id(unsigned long, const class core::pose::Pose &) –> void

  1. add_chain_id(self: pyrosetta.rosetta.protocols.features.InterfaceDdGMover, chain_id: int) -> None

C++: protocols::features::InterfaceDdGMover::add_chain_id(unsigned long) –> void

add_chain_name(*args, **kwargs)

Overloaded function.

  1. add_chain_name(self: pyrosetta.rosetta.protocols.features.InterfaceDdGMover, chain_name: str, pose: pyrosetta.rosetta.core.pose.Pose) -> None

converts chain_name to a chain_id, and then appends

C++: protocols::features::InterfaceDdGMover::add_chain_name(const std::string &, const class core::pose::Pose &) –> void

  1. add_chain_name(self: pyrosetta.rosetta.protocols.features.InterfaceDdGMover, chain_name: str) -> None

C++: protocols::features::InterfaceDdGMover::add_chain_name(const std::string &) –> void

add_jump_id(*args, **kwargs)

Overloaded function.

  1. add_jump_id(self: pyrosetta.rosetta.protocols.features.InterfaceDdGMover, jump: int, pose: pyrosetta.rosetta.core.pose.Pose) -> None

gets chain_id from jump id, and then appends

C++: protocols::features::InterfaceDdGMover::add_jump_id(unsigned long, const class core::pose::Pose &) –> void

  1. add_jump_id(self: pyrosetta.rosetta.protocols.features.InterfaceDdGMover, jump: int) -> None

C++: protocols::features::InterfaceDdGMover::add_jump_id(unsigned long) –> void

apply(self: pyrosetta.rosetta.protocols.features.InterfaceDdGMover, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::features::InterfaceDdGMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.features.InterfaceDdGMover, : pyrosetta.rosetta.protocols.features.InterfaceDdGMover) pyrosetta.rosetta.protocols.features.InterfaceDdGMover

C++: protocols::features::InterfaceDdGMover::operator=(const class protocols::features::InterfaceDdGMover &) –> class protocols::features::InterfaceDdGMover &

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.features.InterfaceDdGMover) pyrosetta.rosetta.protocols.moves.Mover

required in the context of the parser/scripting scheme

C++: protocols::features::InterfaceDdGMover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

const_pose_apply(self: pyrosetta.rosetta.protocols.features.InterfaceDdGMover, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::features::InterfaceDdGMover::const_pose_apply(const class core::pose::Pose &) –> 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.features.InterfaceDdGMover) pyrosetta.rosetta.protocols.moves.Mover

required in the context of the parser/scripting scheme

C++: protocols::features::InterfaceDdGMover::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_all_scores(self: pyrosetta.rosetta.protocols.features.InterfaceDdGMover) pyrosetta.rosetta.utility.vector1_std_pair_std_string_double_t

C++: protocols::features::InterfaceDdGMover::get_all_scores() const –> class utility::vector1<struct std::pair<std::string, double>, class std::allocator<struct std::pair<std::string, double> > >

get_bound_mut_pose(self: pyrosetta.rosetta.protocols.features.InterfaceDdGMover) pyrosetta.rosetta.core.pose.Pose

C++: protocols::features::InterfaceDdGMover::get_bound_mut_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_bound_wt_pose(self: pyrosetta.rosetta.protocols.features.InterfaceDdGMover) pyrosetta.rosetta.core.pose.Pose

C++: protocols::features::InterfaceDdGMover::get_bound_wt_pose() const –> class std::shared_ptr<const 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_movable_jumps(self: pyrosetta.rosetta.protocols.features.InterfaceDdGMover, pose: pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.std.set_unsigned_long_t

C++: protocols::features::InterfaceDdGMover::get_movable_jumps(const class core::pose::Pose &) const –> class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> >

get_name(self: pyrosetta.rosetta.protocols.features.InterfaceDdGMover) str

C++: protocols::features::InterfaceDdGMover::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_unbound_mut_pose(self: pyrosetta.rosetta.protocols.features.InterfaceDdGMover) pyrosetta.rosetta.core.pose.Pose

C++: protocols::features::InterfaceDdGMover::get_unbound_mut_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_unbound_wt_pose(self: pyrosetta.rosetta.protocols.features.InterfaceDdGMover) pyrosetta.rosetta.core.pose.Pose

C++: protocols::features::InterfaceDdGMover::get_unbound_wt_pose() const –> class std::shared_ptr<const class core::pose::Pose>

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::features::InterfaceDdGMover::mover_name() –> std::string

static name() str

C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.features.InterfaceDdGMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None

parse XML tag (to use this Mover in Rosetta Scripts)

C++: protocols::features::InterfaceDdGMover::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::features::InterfaceDdGMover::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_db_reporter(self: pyrosetta.rosetta.protocols.features.InterfaceDdGMover, db_reporter: protocols::features::ReportToDB) None

Clones db_reporter into all member variable database reporters, and sets batch names accordingly

C++: protocols::features::InterfaceDdGMover::set_db_reporter(class std::shared_ptr<class protocols::features::ReportToDB>) –> 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_mut_pose(*args, **kwargs)

Overloaded function.

  1. set_mut_pose(self: pyrosetta.rosetta.protocols.features.InterfaceDdGMover, pose: pyrosetta.rosetta.core.pose.Pose) -> None

Stores the mutant pose

C++: protocols::features::InterfaceDdGMover::set_mut_pose(const class core::pose::Pose &) –> void

  1. set_mut_pose(self: pyrosetta.rosetta.protocols.features.InterfaceDdGMover, pose: pyrosetta.rosetta.core.pose.Pose) -> None

Stores the mutant pose

C++: protocols::features::InterfaceDdGMover::set_mut_pose(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_scorefxn(self: pyrosetta.rosetta.protocols.features.InterfaceDdGMover, sfxn_in: pyrosetta.rosetta.core.scoring.ScoreFunction) None

Sets the scorefunction.

C++: protocols::features::InterfaceDdGMover::set_scorefxn(class std::shared_ptr<const 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

set_wt_pose(*args, **kwargs)

Overloaded function.

  1. set_wt_pose(self: pyrosetta.rosetta.protocols.features.InterfaceDdGMover, pose: pyrosetta.rosetta.core.pose.Pose) -> None

Stores the wildtype pose

C++: protocols::features::InterfaceDdGMover::set_wt_pose(const class core::pose::Pose &) –> void

  1. set_wt_pose(self: pyrosetta.rosetta.protocols.features.InterfaceDdGMover, pose: pyrosetta.rosetta.core.pose.Pose) -> None

Stores the wildtype pose

C++: protocols::features::InterfaceDdGMover::set_wt_pose(class std::shared_ptr<class core::pose::Pose>) –> 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 &

unbind(self: pyrosetta.rosetta.protocols.features.InterfaceDdGMover, pose: pyrosetta.rosetta.core.pose.Pose) None

“unbinds” a pose based on degrees of freedom previously defined

C++: protocols::features::InterfaceDdGMover::unbind(class core::pose::Pose &) const –> void

class pyrosetta.rosetta.protocols.features.InterfaceDdGMoverCreator

Bases: pyrosetta.rosetta.protocols.moves.MoverCreator

assign(self: pyrosetta.rosetta.protocols.features.InterfaceDdGMoverCreator, : pyrosetta.rosetta.protocols.features.InterfaceDdGMoverCreator) pyrosetta.rosetta.protocols.features.InterfaceDdGMoverCreator

C++: protocols::features::InterfaceDdGMoverCreator::operator=(const class protocols::features::InterfaceDdGMoverCreator &) –> class protocols::features::InterfaceDdGMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.features.InterfaceDdGMoverCreator) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::features::InterfaceDdGMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.features.InterfaceDdGMoverCreator) str

C++: protocols::features::InterfaceDdGMoverCreator::keyname() const –> std::string

static mover_name() str

C++: protocols::features::InterfaceDdGMoverCreator::mover_name() –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.features.InterfaceDdGMoverCreator, xsd: utility::tag::XMLSchemaDefinition) None

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

class pyrosetta.rosetta.protocols.features.InterfaceFeatures

Bases: pyrosetta.rosetta.protocols.features.FeaturesReporter

Analyzes interfaces and interface residues of a pose mainly using InterfaceAnalayzerMover. By default, will analyze every interface with and report any that have dSASA > cutoff. Interfaces to report can be set via code or RS.

Should work (but untested) with most ligands if loaded, rna chains, and dna chains.

Note that interfacial waters and ions are currently ignored, but separate features reporters may soon be in the works to accomplish this.

Most main functions are virtual so you can derive from this and have more-specific interface analysis, such as an AntibodyInterfaceFeature class.

assign(self: pyrosetta.rosetta.protocols.features.InterfaceFeatures, : pyrosetta.rosetta.protocols.features.InterfaceFeatures) pyrosetta.rosetta.protocols.features.InterfaceFeatures

C++: protocols::features::InterfaceFeatures::operator=(const class protocols::features::InterfaceFeatures &) –> class protocols::features::InterfaceFeatures &

check_relevant_residues(*args, **kwargs)

Overloaded function.

  1. check_relevant_residues(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, res1: int) -> bool

C++: protocols::features::FeaturesReporter::check_relevant_residues(const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long) const –> bool

  1. check_relevant_residues(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, res1: int, res2: int) -> bool

C++: protocols::features::FeaturesReporter::check_relevant_residues(const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, unsigned long) const –> bool

  1. check_relevant_residues(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, residues: pyrosetta.rosetta.utility.vector1_unsigned_long) -> bool

C++: protocols::features::FeaturesReporter::check_relevant_residues(const class utility::vector1<bool, class std::allocator<bool> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> bool

check_relevant_residues_range(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, res1: int, res2: int) bool

C++: protocols::features::FeaturesReporter::check_relevant_residues_range(const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, unsigned long) const –> bool

static class_name() str

C++: protocols::features::InterfaceFeatures::class_name() –> std::string

delete_record(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, : int, : pyrosetta.rosetta.utility.sql_database.session) None

C++: protocols::features::FeaturesReporter::delete_record(unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> void

features_reporter_dependencies(self: pyrosetta.rosetta.protocols.features.InterfaceFeatures) pyrosetta.rosetta.utility.vector1_std_string

return the set of features reporters that are required to also already be extracted by the time this one is used.

C++: protocols::features::InterfaceFeatures::features_reporter_dependencies() const –> class utility::vector1<std::string, class std::allocator<std::string > >

get_relevant_residues_mode(self: pyrosetta.rosetta.protocols.features.FeaturesReporter) pyrosetta.rosetta.protocols.features.RelevantResiduesMode.T

C++: protocols::features::FeaturesReporter::get_relevant_residues_mode() const –> enum protocols::features::RelevantResiduesMode::T

load_into_pose(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, : pyrosetta.rosetta.utility.sql_database.session, : int, : pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::features::FeaturesReporter::load_into_pose(class std::shared_ptr<class utility::sql_database::session>, unsigned long, class core::pose::Pose &) –> void

make_interface_combos(self: pyrosetta.rosetta.protocols.features.InterfaceFeatures, pose: pyrosetta.rosetta.core.pose.Pose, interfaces: pyrosetta.rosetta.utility.vector1_std_string) None

Gets all possible interface combinations of a given pose.

C++: protocols::features::InterfaceFeatures::make_interface_combos(const class core::pose::Pose &, class utility::vector1<std::string, class std::allocator<std::string > > &) –> void

parse_my_tag(self: pyrosetta.rosetta.protocols.features.InterfaceFeatures, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None

C++: protocols::features::InterfaceFeatures::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::features::InterfaceFeatures::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

report_all_interface_features(self: pyrosetta.rosetta.protocols.features.InterfaceFeatures, pose: pyrosetta.rosetta.core.pose.Pose, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, struct_id: int, db_session: pyrosetta.rosetta.utility.sql_database.session, interface: str, db_interface: str) None

Report all features. Called by report_features. Easy interface for subclassing specific interfaces.

interface is the interface analyzed, db_interface is the name that is actually inserted into the database Usually this is the same, but useful when dealing with different chain ids but same interface type. db_interface should have sides as well (L_H))

C++: protocols::features::InterfaceFeatures::report_all_interface_features(const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, class std::shared_ptr<class utility::sql_database::session>, const std::string &, const std::string &) –> void

report_features(self: pyrosetta.rosetta.protocols.features.InterfaceFeatures, pose: pyrosetta.rosetta.core.pose.Pose, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, struct_id: int, db_session: pyrosetta.rosetta.utility.sql_database.session) int

collect all the feature data for the pose

C++: protocols::features::InterfaceFeatures::report_features(const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> unsigned long

report_interface_features(self: pyrosetta.rosetta.protocols.features.InterfaceFeatures, pose: pyrosetta.rosetta.core.pose.Pose, struct_id: int, db_session: pyrosetta.rosetta.utility.sql_database.session, chains_side1: str, chains_side2: str) None

Add interfaces table data to table

C++: protocols::features::InterfaceFeatures::report_interface_features(const class core::pose::Pose &, unsigned long, class std::shared_ptr<class utility::sql_database::session>, const std::string &, const std::string &) const –> void

report_interface_residue_features(self: pyrosetta.rosetta.protocols.features.InterfaceFeatures, pose: pyrosetta.rosetta.core.pose.Pose, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, struct_id: int, db_session: pyrosetta.rosetta.utility.sql_database.session, chains_side1: str, chains_side2: str) None

Add interface_residues data to table

C++: protocols::features::InterfaceFeatures::report_interface_residue_features(const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, class std::shared_ptr<class utility::sql_database::session>, const std::string &, const std::string &) const –> void

report_interface_side_features(self: pyrosetta.rosetta.protocols.features.InterfaceFeatures, pose: pyrosetta.rosetta.core.pose.Pose, struct_id: int, db_session: pyrosetta.rosetta.utility.sql_database.session, chains_side1: str, chains_side2: str, region: pyrosetta.rosetta.protocols.analysis.InterfaceRegion, region_string: str) None

Add interface_sides table data to table

C++: protocols::features::InterfaceFeatures::report_interface_side_features(const class core::pose::Pose &, unsigned long, class std::shared_ptr<class utility::sql_database::session>, const std::string &, const std::string &, enum protocols::analysis::InterfaceRegion, const std::string &) const –> void

schema(self: pyrosetta.rosetta.protocols.features.FeaturesReporter) str

return sql statements that sets up the appropriate tables to contain the features. This should be removed once everything has been moved to the schema generator

C++: protocols::features::FeaturesReporter::schema() const –> std::string

set_compute_packstat(self: pyrosetta.rosetta.protocols.features.InterfaceFeatures, compute_packstat: bool) None

Compute the packstat score? Default true

C++: protocols::features::InterfaceFeatures::set_compute_packstat(const bool) –> void

set_dSASA_cutoff(self: pyrosetta.rosetta.protocols.features.InterfaceFeatures, dSASA_cutoff: float) None

Set the reporter to only include interfaces >dSASA_cutoff.

C++: protocols::features::InterfaceFeatures::set_dSASA_cutoff(double) –> void

set_defaults(self: pyrosetta.rosetta.protocols.features.InterfaceFeatures) None

C++: protocols::features::InterfaceFeatures::set_defaults() –> void

set_interface_chains(self: pyrosetta.rosetta.protocols.features.InterfaceFeatures, interfaces: pyrosetta.rosetta.utility.vector1_std_string) None

Set the fixed chain combinations that will be analyzed. Default is all of them.

Example: AB_C would analyze the interface between AB and C, keeping AB fixed while separating C. Note that here, you can also give A_C and a new pose would be created with only A and C so that this interface can be tested. Note also that multiple pose interfaces can be set.

C++: protocols::features::InterfaceFeatures::set_interface_chains(const class utility::vector1<std::string, class std::allocator<std::string > > &) –> void

set_pack_separated(self: pyrosetta.rosetta.protocols.features.InterfaceFeatures, pack_separated: bool) None

Pack the interface before separation? Default is false.

C++: protocols::features::InterfaceFeatures::set_pack_separated(const bool) –> void

set_pack_together(self: pyrosetta.rosetta.protocols.features.InterfaceFeatures, pack_together: bool) None

Pack the interface after separation? Default is true.

C++: protocols::features::InterfaceFeatures::set_pack_together(const bool) –> void

set_relevant_residues_mode(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, setting: pyrosetta.rosetta.protocols.features.RelevantResiduesMode.T) None

C++: protocols::features::FeaturesReporter::set_relevant_residues_mode(enum protocols::features::RelevantResiduesMode::T) –> void

set_scorefxn(self: pyrosetta.rosetta.protocols.features.InterfaceFeatures, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) None

C++: protocols::features::InterfaceFeatures::set_scorefxn(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void

type_name(self: pyrosetta.rosetta.protocols.features.InterfaceFeatures) str

C++: protocols::features::InterfaceFeatures::type_name() const –> std::string

write_interface_residues_schema_to_db(self: pyrosetta.rosetta.protocols.features.InterfaceFeatures, db_session: pyrosetta.rosetta.utility.sql_database.session) None

C++: protocols::features::InterfaceFeatures::write_interface_residues_schema_to_db(class std::shared_ptr<class utility::sql_database::session>) const –> void

write_interface_schema_to_db(self: pyrosetta.rosetta.protocols.features.InterfaceFeatures, db_session: pyrosetta.rosetta.utility.sql_database.session) None

C++: protocols::features::InterfaceFeatures::write_interface_schema_to_db(class std::shared_ptr<class utility::sql_database::session>) const –> void

write_interface_side_schema_to_db(self: pyrosetta.rosetta.protocols.features.InterfaceFeatures, db_session: pyrosetta.rosetta.utility.sql_database.session) None

C++: protocols::features::InterfaceFeatures::write_interface_side_schema_to_db(class std::shared_ptr<class utility::sql_database::session>) const –> void

write_schema_to_db(self: pyrosetta.rosetta.protocols.features.InterfaceFeatures, db_session: pyrosetta.rosetta.utility.sql_database.session) None

generate the table schemas and write them to the database

C++: protocols::features::InterfaceFeatures::write_schema_to_db(class std::shared_ptr<class utility::sql_database::session>) const –> void

class pyrosetta.rosetta.protocols.features.InterfaceFeaturesCreator

Bases: pyrosetta.rosetta.protocols.features.FeaturesReporterCreator

creator for the HBondParameterFeatures class

assign(self: pyrosetta.rosetta.protocols.features.InterfaceFeaturesCreator, : pyrosetta.rosetta.protocols.features.InterfaceFeaturesCreator) pyrosetta.rosetta.protocols.features.InterfaceFeaturesCreator

C++: protocols::features::InterfaceFeaturesCreator::operator=(const class protocols::features::InterfaceFeaturesCreator &) –> class protocols::features::InterfaceFeaturesCreator &

create_features_reporter(self: pyrosetta.rosetta.protocols.features.InterfaceFeaturesCreator) pyrosetta.rosetta.protocols.features.FeaturesReporter

C++: protocols::features::InterfaceFeaturesCreator::create_features_reporter() const –> class std::shared_ptr<class protocols::features::FeaturesReporter>

provide_xml_schema(self: pyrosetta.rosetta.protocols.features.InterfaceFeaturesCreator, xsd: utility::tag::XMLSchemaDefinition) None

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

type_name(self: pyrosetta.rosetta.protocols.features.InterfaceFeaturesCreator) str

C++: protocols::features::InterfaceFeaturesCreator::type_name() const –> std::string

class pyrosetta.rosetta.protocols.features.JobDataFeatures

Bases: pyrosetta.rosetta.protocols.features.FeaturesReporter

assign(self: pyrosetta.rosetta.protocols.features.JobDataFeatures, : pyrosetta.rosetta.protocols.features.JobDataFeatures) pyrosetta.rosetta.protocols.features.JobDataFeatures

C++: protocols::features::JobDataFeatures::operator=(const class protocols::features::JobDataFeatures &) –> class protocols::features::JobDataFeatures &

check_relevant_residues(*args, **kwargs)

Overloaded function.

  1. check_relevant_residues(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, res1: int) -> bool

C++: protocols::features::FeaturesReporter::check_relevant_residues(const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long) const –> bool

  1. check_relevant_residues(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, res1: int, res2: int) -> bool

C++: protocols::features::FeaturesReporter::check_relevant_residues(const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, unsigned long) const –> bool

  1. check_relevant_residues(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, residues: pyrosetta.rosetta.utility.vector1_unsigned_long) -> bool

C++: protocols::features::FeaturesReporter::check_relevant_residues(const class utility::vector1<bool, class std::allocator<bool> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> bool

check_relevant_residues_range(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, res1: int, res2: int) bool

C++: protocols::features::FeaturesReporter::check_relevant_residues_range(const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, unsigned long) const –> bool

static class_name() str

C++: protocols::features::JobDataFeatures::class_name() –> std::string

delete_record(self: pyrosetta.rosetta.protocols.features.JobDataFeatures, struct_id: int, db_session: pyrosetta.rosetta.utility.sql_database.session) None

C++: protocols::features::JobDataFeatures::delete_record(unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> void

features_reporter_dependencies(self: pyrosetta.rosetta.protocols.features.JobDataFeatures) pyrosetta.rosetta.utility.vector1_std_string

return the set of features reporters that are required to also already be extracted by the time this one is used.

C++: protocols::features::JobDataFeatures::features_reporter_dependencies() const –> class utility::vector1<std::string, class std::allocator<std::string > >

get_relevant_residues_mode(self: pyrosetta.rosetta.protocols.features.FeaturesReporter) pyrosetta.rosetta.protocols.features.RelevantResiduesMode.T

C++: protocols::features::FeaturesReporter::get_relevant_residues_mode() const –> enum protocols::features::RelevantResiduesMode::T

load_into_pose(self: pyrosetta.rosetta.protocols.features.JobDataFeatures, db_session: pyrosetta.rosetta.utility.sql_database.session, struct_id: int, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::features::JobDataFeatures::load_into_pose(class std::shared_ptr<class utility::sql_database::session>, unsigned long, class core::pose::Pose &) –> void

parse_my_tag(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None

C++: protocols::features::FeaturesReporter::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::features::JobDataFeatures::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

report_features(self: pyrosetta.rosetta.protocols.features.JobDataFeatures, pose: pyrosetta.rosetta.core.pose.Pose, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, struct_id: int, db_session: pyrosetta.rosetta.utility.sql_database.session) int

collect all the feature data for the pose

C++: protocols::features::JobDataFeatures::report_features(const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> unsigned long

schema(self: pyrosetta.rosetta.protocols.features.FeaturesReporter) str

return sql statements that sets up the appropriate tables to contain the features. This should be removed once everything has been moved to the schema generator

C++: protocols::features::FeaturesReporter::schema() const –> std::string

set_relevant_residues_mode(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, setting: pyrosetta.rosetta.protocols.features.RelevantResiduesMode.T) None

C++: protocols::features::FeaturesReporter::set_relevant_residues_mode(enum protocols::features::RelevantResiduesMode::T) –> void

type_name(self: pyrosetta.rosetta.protocols.features.JobDataFeatures) str

C++: protocols::features::JobDataFeatures::type_name() const –> std::string

write_schema_to_db(self: pyrosetta.rosetta.protocols.features.JobDataFeatures, db_session: pyrosetta.rosetta.utility.sql_database.session) None

generate the table schemas and write them to the database

C++: protocols::features::JobDataFeatures::write_schema_to_db(class std::shared_ptr<class utility::sql_database::session>) const –> void

class pyrosetta.rosetta.protocols.features.JobDataFeaturesCreator

Bases: pyrosetta.rosetta.protocols.features.FeaturesReporterCreator

creator for the JobDataFeatures class

assign(self: pyrosetta.rosetta.protocols.features.JobDataFeaturesCreator, : pyrosetta.rosetta.protocols.features.JobDataFeaturesCreator) pyrosetta.rosetta.protocols.features.JobDataFeaturesCreator

C++: protocols::features::JobDataFeaturesCreator::operator=(const class protocols::features::JobDataFeaturesCreator &) –> class protocols::features::JobDataFeaturesCreator &

create_features_reporter(self: pyrosetta.rosetta.protocols.features.JobDataFeaturesCreator) pyrosetta.rosetta.protocols.features.FeaturesReporter

C++: protocols::features::JobDataFeaturesCreator::create_features_reporter() const –> class std::shared_ptr<class protocols::features::FeaturesReporter>

provide_xml_schema(self: pyrosetta.rosetta.protocols.features.JobDataFeaturesCreator, xsd: utility::tag::XMLSchemaDefinition) None

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

type_name(self: pyrosetta.rosetta.protocols.features.JobDataFeaturesCreator) str

C++: protocols::features::JobDataFeaturesCreator::type_name() const –> std::string

class pyrosetta.rosetta.protocols.features.LoopAnchorFeatures

Bases: pyrosetta.rosetta.protocols.features.FeaturesReporter

assign(self: pyrosetta.rosetta.protocols.features.LoopAnchorFeatures, : pyrosetta.rosetta.protocols.features.LoopAnchorFeatures) pyrosetta.rosetta.protocols.features.LoopAnchorFeatures

C++: protocols::features::LoopAnchorFeatures::operator=(const class protocols::features::LoopAnchorFeatures &) –> class protocols::features::LoopAnchorFeatures &

check_relevant_residues(*args, **kwargs)

Overloaded function.

  1. check_relevant_residues(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, res1: int) -> bool

C++: protocols::features::FeaturesReporter::check_relevant_residues(const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long) const –> bool

  1. check_relevant_residues(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, res1: int, res2: int) -> bool

C++: protocols::features::FeaturesReporter::check_relevant_residues(const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, unsigned long) const –> bool

  1. check_relevant_residues(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, residues: pyrosetta.rosetta.utility.vector1_unsigned_long) -> bool

C++: protocols::features::FeaturesReporter::check_relevant_residues(const class utility::vector1<bool, class std::allocator<bool> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> bool

check_relevant_residues_range(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, res1: int, res2: int) bool

C++: protocols::features::FeaturesReporter::check_relevant_residues_range(const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, unsigned long) const –> bool

static class_name() str

C++: protocols::features::LoopAnchorFeatures::class_name() –> std::string

delete_record(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, : int, : pyrosetta.rosetta.utility.sql_database.session) None

C++: protocols::features::FeaturesReporter::delete_record(unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> void

features_reporter_dependencies(self: pyrosetta.rosetta.protocols.features.LoopAnchorFeatures) pyrosetta.rosetta.utility.vector1_std_string

return the set of features reporters that are required to also already be extracted by the time this one is used.

C++: protocols::features::LoopAnchorFeatures::features_reporter_dependencies() const –> class utility::vector1<std::string, class std::allocator<std::string > >

get_relevant_residues_mode(self: pyrosetta.rosetta.protocols.features.FeaturesReporter) pyrosetta.rosetta.protocols.features.RelevantResiduesMode.T

C++: protocols::features::FeaturesReporter::get_relevant_residues_mode() const –> enum protocols::features::RelevantResiduesMode::T

load_into_pose(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, : pyrosetta.rosetta.utility.sql_database.session, : int, : pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::features::FeaturesReporter::load_into_pose(class std::shared_ptr<class utility::sql_database::session>, unsigned long, class core::pose::Pose &) –> void

parse_my_tag(self: pyrosetta.rosetta.protocols.features.LoopAnchorFeatures, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None

C++: protocols::features::LoopAnchorFeatures::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::features::LoopAnchorFeatures::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

report_features(self: pyrosetta.rosetta.protocols.features.LoopAnchorFeatures, pose: pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.utility.vector1_bool, struct_id: int, db_session: pyrosetta.rosetta.utility.sql_database.session) int

collect all the feature data for the pose

C++: protocols::features::LoopAnchorFeatures::report_features(const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> unsigned long

schema(self: pyrosetta.rosetta.protocols.features.FeaturesReporter) str

return sql statements that sets up the appropriate tables to contain the features. This should be removed once everything has been moved to the schema generator

C++: protocols::features::FeaturesReporter::schema() const –> std::string

set_relevant_residues_mode(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, setting: pyrosetta.rosetta.protocols.features.RelevantResiduesMode.T) None

C++: protocols::features::FeaturesReporter::set_relevant_residues_mode(enum protocols::features::RelevantResiduesMode::T) –> void

set_use_relevant_residues_as_loop_length(self: pyrosetta.rosetta.protocols.features.LoopAnchorFeatures, use_relevant_residues_as_loop_length: bool) None

C++: protocols::features::LoopAnchorFeatures::set_use_relevant_residues_as_loop_length(const bool) –> void

set_use_single_residue_to_define_anchor_transfrom(self: pyrosetta.rosetta.protocols.features.LoopAnchorFeatures, use_single_residue_to_define_anchor_transfrom: bool) None

C++: protocols::features::LoopAnchorFeatures::set_use_single_residue_to_define_anchor_transfrom(const bool) –> void

type_name(self: pyrosetta.rosetta.protocols.features.LoopAnchorFeatures) str

C++: protocols::features::LoopAnchorFeatures::type_name() const –> std::string

write_schema_to_db(self: pyrosetta.rosetta.protocols.features.LoopAnchorFeatures, db_session: pyrosetta.rosetta.utility.sql_database.session) None

generate the table schemas and write them to the database

C++: protocols::features::LoopAnchorFeatures::write_schema_to_db(class std::shared_ptr<class utility::sql_database::session>) const –> void

class pyrosetta.rosetta.protocols.features.LoopAnchorFeaturesCreator

Bases: pyrosetta.rosetta.protocols.features.FeaturesReporterCreator

creator for the LoopAnchorFeatures class

assign(self: pyrosetta.rosetta.protocols.features.LoopAnchorFeaturesCreator, : pyrosetta.rosetta.protocols.features.LoopAnchorFeaturesCreator) pyrosetta.rosetta.protocols.features.LoopAnchorFeaturesCreator

C++: protocols::features::LoopAnchorFeaturesCreator::operator=(const class protocols::features::LoopAnchorFeaturesCreator &) –> class protocols::features::LoopAnchorFeaturesCreator &

create_features_reporter(self: pyrosetta.rosetta.protocols.features.LoopAnchorFeaturesCreator) pyrosetta.rosetta.protocols.features.FeaturesReporter

C++: protocols::features::LoopAnchorFeaturesCreator::create_features_reporter() const –> class std::shared_ptr<class protocols::features::FeaturesReporter>

provide_xml_schema(self: pyrosetta.rosetta.protocols.features.LoopAnchorFeaturesCreator, xsd: utility::tag::XMLSchemaDefinition) None

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

type_name(self: pyrosetta.rosetta.protocols.features.LoopAnchorFeaturesCreator) str

C++: protocols::features::LoopAnchorFeaturesCreator::type_name() const –> std::string

class pyrosetta.rosetta.protocols.features.MetricData

Bases: pybind11_builtins.pybind11_object

assign(self: pyrosetta.rosetta.protocols.features.MetricData, : pyrosetta.rosetta.protocols.features.MetricData) pyrosetta.rosetta.protocols.features.MetricData

C++: protocols::features::MetricData::operator=(const struct protocols::features::MetricData &) –> struct protocols::features::MetricData &

property data_type
property real_value
property string_value
class pyrosetta.rosetta.protocols.features.ModelFeatures

Bases: pyrosetta.rosetta.protocols.features.FeaturesReporter

assign(self: pyrosetta.rosetta.protocols.features.ModelFeatures, : pyrosetta.rosetta.protocols.features.ModelFeatures) pyrosetta.rosetta.protocols.features.ModelFeatures

C++: protocols::features::ModelFeatures::operator=(const class protocols::features::ModelFeatures &) –> class protocols::features::ModelFeatures &

check_relevant_residues(*args, **kwargs)

Overloaded function.

  1. check_relevant_residues(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, res1: int) -> bool

C++: protocols::features::FeaturesReporter::check_relevant_residues(const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long) const –> bool

  1. check_relevant_residues(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, res1: int, res2: int) -> bool

C++: protocols::features::FeaturesReporter::check_relevant_residues(const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, unsigned long) const –> bool

  1. check_relevant_residues(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, residues: pyrosetta.rosetta.utility.vector1_unsigned_long) -> bool

C++: protocols::features::FeaturesReporter::check_relevant_residues(const class utility::vector1<bool, class std::allocator<bool> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> bool

check_relevant_residues_range(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, res1: int, res2: int) bool

C++: protocols::features::FeaturesReporter::check_relevant_residues_range(const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, unsigned long) const –> bool

static class_name() str

C++: protocols::features::ModelFeatures::class_name() –> std::string

delete_record(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, : int, : pyrosetta.rosetta.utility.sql_database.session) None

C++: protocols::features::FeaturesReporter::delete_record(unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> void

features_reporter_dependencies(self: pyrosetta.rosetta.protocols.features.ModelFeatures) pyrosetta.rosetta.utility.vector1_std_string

return the set of features reporters that are required to also already be extracted by the time this one is used.

C++: protocols::features::ModelFeatures::features_reporter_dependencies() const –> class utility::vector1<std::string, class std::allocator<std::string > >

get_relevant_residues_mode(self: pyrosetta.rosetta.protocols.features.FeaturesReporter) pyrosetta.rosetta.protocols.features.RelevantResiduesMode.T

C++: protocols::features::FeaturesReporter::get_relevant_residues_mode() const –> enum protocols::features::RelevantResiduesMode::T

load_into_pose(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, : pyrosetta.rosetta.utility.sql_database.session, : int, : pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::features::FeaturesReporter::load_into_pose(class std::shared_ptr<class utility::sql_database::session>, unsigned long, class core::pose::Pose &) –> void

parse_my_tag(self: pyrosetta.rosetta.protocols.features.ModelFeatures, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None

C++: protocols::features::ModelFeatures::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::features::ModelFeatures::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

report_features(self: pyrosetta.rosetta.protocols.features.ModelFeatures, pose: pyrosetta.rosetta.core.pose.Pose, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, struct_id: int, db_session: pyrosetta.rosetta.utility.sql_database.session) int

collect all the feature data for the pose

C++: protocols::features::ModelFeatures::report_features(const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> unsigned long

schema(self: pyrosetta.rosetta.protocols.features.FeaturesReporter) str

return sql statements that sets up the appropriate tables to contain the features. This should be removed once everything has been moved to the schema generator

C++: protocols::features::FeaturesReporter::schema() const –> std::string

set_relevant_residues_mode(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, setting: pyrosetta.rosetta.protocols.features.RelevantResiduesMode.T) None

C++: protocols::features::FeaturesReporter::set_relevant_residues_mode(enum protocols::features::RelevantResiduesMode::T) –> void

trim_pose(self: pyrosetta.rosetta.protocols.features.ModelFeatures, pose: pyrosetta.rosetta.core.pose.Pose, resnums: pyrosetta.rosetta.std.set_unsigned_long_t) None

for testing purposes only

C++: protocols::features::ModelFeatures::trim_pose(class core::pose::Pose &, class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> >) const –> void

type_name(self: pyrosetta.rosetta.protocols.features.ModelFeatures) str

C++: protocols::features::ModelFeatures::type_name() const –> std::string

write_clique_to_db(self: pyrosetta.rosetta.protocols.features.ModelFeatures, clique: pyrosetta.rosetta.std.set_unsigned_long_t, struct_id: int, db_session: pyrosetta.rosetta.utility.sql_database.session) None

C++: protocols::features::ModelFeatures::write_clique_to_db(const class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> > &, unsigned long, class std::shared_ptr<class utility::sql_database::session>) const –> void

write_schema_to_db(self: pyrosetta.rosetta.protocols.features.ModelFeatures, db_session: pyrosetta.rosetta.utility.sql_database.session) None

generate the table schemas and write them to the database

C++: protocols::features::ModelFeatures::write_schema_to_db(class std::shared_ptr<class utility::sql_database::session>) const –> void

class pyrosetta.rosetta.protocols.features.ModelFeaturesCreator

Bases: pyrosetta.rosetta.protocols.features.FeaturesReporterCreator

creator for the ModelFeatures class

assign(self: pyrosetta.rosetta.protocols.features.ModelFeaturesCreator, : pyrosetta.rosetta.protocols.features.ModelFeaturesCreator) pyrosetta.rosetta.protocols.features.ModelFeaturesCreator

C++: protocols::features::ModelFeaturesCreator::operator=(const class protocols::features::ModelFeaturesCreator &) –> class protocols::features::ModelFeaturesCreator &

create_features_reporter(self: pyrosetta.rosetta.protocols.features.ModelFeaturesCreator) pyrosetta.rosetta.protocols.features.FeaturesReporter

C++: protocols::features::ModelFeaturesCreator::create_features_reporter() const –> class std::shared_ptr<class protocols::features::FeaturesReporter>

provide_xml_schema(self: pyrosetta.rosetta.protocols.features.ModelFeaturesCreator, xsd: utility::tag::XMLSchemaDefinition) None

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

type_name(self: pyrosetta.rosetta.protocols.features.ModelFeaturesCreator) str

C++: protocols::features::ModelFeaturesCreator::type_name() const –> std::string

class pyrosetta.rosetta.protocols.features.OrbitalsFeatures

Bases: pyrosetta.rosetta.protocols.features.FeaturesReporter

assign(self: pyrosetta.rosetta.protocols.features.OrbitalsFeatures, : pyrosetta.rosetta.protocols.features.OrbitalsFeatures) pyrosetta.rosetta.protocols.features.OrbitalsFeatures

C++: protocols::features::OrbitalsFeatures::operator=(const class protocols::features::OrbitalsFeatures &) –> class protocols::features::OrbitalsFeatures &

check_relevant_residues(*args, **kwargs)

Overloaded function.

  1. check_relevant_residues(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, res1: int) -> bool

C++: protocols::features::FeaturesReporter::check_relevant_residues(const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long) const –> bool

  1. check_relevant_residues(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, res1: int, res2: int) -> bool

C++: protocols::features::FeaturesReporter::check_relevant_residues(const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, unsigned long) const –> bool

  1. check_relevant_residues(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, residues: pyrosetta.rosetta.utility.vector1_unsigned_long) -> bool

C++: protocols::features::FeaturesReporter::check_relevant_residues(const class utility::vector1<bool, class std::allocator<bool> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> bool

check_relevant_residues_range(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, res1: int, res2: int) bool

C++: protocols::features::FeaturesReporter::check_relevant_residues_range(const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, unsigned long) const –> bool

static class_name() str

C++: protocols::features::OrbitalsFeatures::class_name() –> std::string

delete_record(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, : int, : pyrosetta.rosetta.utility.sql_database.session) None

C++: protocols::features::FeaturesReporter::delete_record(unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> void

features_reporter_dependencies(self: pyrosetta.rosetta.protocols.features.OrbitalsFeatures) pyrosetta.rosetta.utility.vector1_std_string

return the set of features reporters that are required to also already be extracted by the time this one is used.

C++: protocols::features::OrbitalsFeatures::features_reporter_dependencies() const –> class utility::vector1<std::string, class std::allocator<std::string > >

get_relevant_residues_mode(self: pyrosetta.rosetta.protocols.features.FeaturesReporter) pyrosetta.rosetta.protocols.features.RelevantResiduesMode.T

C++: protocols::features::FeaturesReporter::get_relevant_residues_mode() const –> enum protocols::features::RelevantResiduesMode::T

load_into_pose(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, : pyrosetta.rosetta.utility.sql_database.session, : int, : pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::features::FeaturesReporter::load_into_pose(class std::shared_ptr<class utility::sql_database::session>, unsigned long, class core::pose::Pose &) –> void

parse_my_tag(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None

C++: protocols::features::FeaturesReporter::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::features::OrbitalsFeatures::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

report_features(self: pyrosetta.rosetta.protocols.features.OrbitalsFeatures, pose: pyrosetta.rosetta.core.pose.Pose, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, struct_id: int, db_session: pyrosetta.rosetta.utility.sql_database.session) int

collect all the feature data for the pose

C++: protocols::features::OrbitalsFeatures::report_features(const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> unsigned long

report_haro_orbital_interactions(self: pyrosetta.rosetta.protocols.features.OrbitalsFeatures, pose: pyrosetta.rosetta.core.pose.Pose, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, struct_id: int, db_session: pyrosetta.rosetta.utility.sql_database.session) None

C++: protocols::features::OrbitalsFeatures::report_haro_orbital_interactions(const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, const unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> void

report_hpol_orbital_interactions(self: pyrosetta.rosetta.protocols.features.OrbitalsFeatures, pose: pyrosetta.rosetta.core.pose.Pose, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, struct_id: int, db_session: pyrosetta.rosetta.utility.sql_database.session) None

C++: protocols::features::OrbitalsFeatures::report_hpol_orbital_interactions(const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, const unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> void

schema(self: pyrosetta.rosetta.protocols.features.FeaturesReporter) str

return sql statements that sets up the appropriate tables to contain the features. This should be removed once everything has been moved to the schema generator

C++: protocols::features::FeaturesReporter::schema() const –> std::string

set_OrbH_features_data(self: pyrosetta.rosetta.protocols.features.OrbitalsFeatures, res1: pyrosetta.rosetta.core.conformation.Residue, res2: pyrosetta.rosetta.core.conformation.Residue, Aindex: int, Hindex: int, Orbindex: int, Orbxyz: pyrosetta.rosetta.numeric.xyzVector_double_t, resNum2: int, orbName1: str, htype2: str, res2name: str, orbNum1: int, hpolNum2: int, cosAOH: float, cosDHO: float, chiBDHO: float, chiBAOH: float, AOH_angle: float, DHO_angle: float, chiBAHD: float, cosAHD: float, OrbHdist: float) None

C++: protocols::features::OrbitalsFeatures::set_OrbH_features_data(class core::conformation::Residue &, class core::conformation::Residue &, const unsigned long, const unsigned long, const unsigned long, const class numeric::xyzVector<double> &, unsigned long &, std::string &, std::string &, std::string &, unsigned long &, unsigned long &, double &, double &, double &, double &, double &, double &, double &, double &, double &) –> void

set_OrbOrb_features_data(self: pyrosetta.rosetta.protocols.features.OrbitalsFeatures, res1: pyrosetta.rosetta.core.conformation.Residue, res2: pyrosetta.rosetta.core.conformation.Residue, Aindex: int, Dindex: int, Orbindex1: int, Orbindex2: int, Orbxyz1: pyrosetta.rosetta.numeric.xyzVector_double_t, Orbxyz2: pyrosetta.rosetta.numeric.xyzVector_double_t, resNum2: int, orbName1: str, res2name: str, OrbName2: str, orbNum1: int, OrbNum2: int, cosAOO: float, cosDOO: float, chiBAOO: float, chiBDOO: float, AOO_angle: float, DOO_angle: float, OrbHdist: float, cosAOD: float, AOD_angle: float, chiBAHD: float, cosAHD: float) None

C++: protocols::features::OrbitalsFeatures::set_OrbOrb_features_data(class core::conformation::Residue &, class core::conformation::Residue &, unsigned long, unsigned long, unsigned long, unsigned long, const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, unsigned long &, std::string &, std::string &, std::string &, unsigned long &, unsigned long &, double &, double &, double &, double &, double &, double &, double &, double &, double &, double &, double &) –> void

set_relevant_residues_mode(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, setting: pyrosetta.rosetta.protocols.features.RelevantResiduesMode.T) None

C++: protocols::features::FeaturesReporter::set_relevant_residues_mode(enum protocols::features::RelevantResiduesMode::T) –> void

type_name(self: pyrosetta.rosetta.protocols.features.OrbitalsFeatures) str

C++: protocols::features::OrbitalsFeatures::type_name() const –> std::string

write_schema_to_db(self: pyrosetta.rosetta.protocols.features.OrbitalsFeatures, db_session: pyrosetta.rosetta.utility.sql_database.session) None

generate the table schemas and write them to the database

C++: protocols::features::OrbitalsFeatures::write_schema_to_db(class std::shared_ptr<class utility::sql_database::session>) const –> void

class pyrosetta.rosetta.protocols.features.OrbitalsFeaturesCreator

Bases: pyrosetta.rosetta.protocols.features.FeaturesReporterCreator

creator for the OrbitalsFeatures class

assign(self: pyrosetta.rosetta.protocols.features.OrbitalsFeaturesCreator, : pyrosetta.rosetta.protocols.features.OrbitalsFeaturesCreator) pyrosetta.rosetta.protocols.features.OrbitalsFeaturesCreator

C++: protocols::features::OrbitalsFeaturesCreator::operator=(const class protocols::features::OrbitalsFeaturesCreator &) –> class protocols::features::OrbitalsFeaturesCreator &

create_features_reporter(self: pyrosetta.rosetta.protocols.features.OrbitalsFeaturesCreator) pyrosetta.rosetta.protocols.features.FeaturesReporter

C++: protocols::features::OrbitalsFeaturesCreator::create_features_reporter() const –> class std::shared_ptr<class protocols::features::FeaturesReporter>

provide_xml_schema(self: pyrosetta.rosetta.protocols.features.OrbitalsFeaturesCreator, xsd: utility::tag::XMLSchemaDefinition) None

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

type_name(self: pyrosetta.rosetta.protocols.features.OrbitalsFeaturesCreator) str

C++: protocols::features::OrbitalsFeaturesCreator::type_name() const –> std::string

class pyrosetta.rosetta.protocols.features.PairFeatures

Bases: pyrosetta.rosetta.protocols.features.FeaturesReporter

assign(self: pyrosetta.rosetta.protocols.features.PairFeatures, : pyrosetta.rosetta.protocols.features.PairFeatures) pyrosetta.rosetta.protocols.features.PairFeatures

C++: protocols::features::PairFeatures::operator=(const class protocols::features::PairFeatures &) –> class protocols::features::PairFeatures &

check_relevant_residues(*args, **kwargs)

Overloaded function.

  1. check_relevant_residues(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, res1: int) -> bool

C++: protocols::features::FeaturesReporter::check_relevant_residues(const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long) const –> bool

  1. check_relevant_residues(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, res1: int, res2: int) -> bool

C++: protocols::features::FeaturesReporter::check_relevant_residues(const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, unsigned long) const –> bool

  1. check_relevant_residues(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, residues: pyrosetta.rosetta.utility.vector1_unsigned_long) -> bool

C++: protocols::features::FeaturesReporter::check_relevant_residues(const class utility::vector1<bool, class std::allocator<bool> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> bool

check_relevant_residues_range(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, res1: int, res2: int) bool

C++: protocols::features::FeaturesReporter::check_relevant_residues_range(const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, unsigned long) const –> bool

static class_name() str

C++: protocols::features::PairFeatures::class_name() –> std::string

delete_record(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, : int, : pyrosetta.rosetta.utility.sql_database.session) None

C++: protocols::features::FeaturesReporter::delete_record(unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> void

features_reporter_dependencies(self: pyrosetta.rosetta.protocols.features.PairFeatures) pyrosetta.rosetta.utility.vector1_std_string

return the set of features reporters that are required to also already be extracted by the time this one is used.

C++: protocols::features::PairFeatures::features_reporter_dependencies() const –> class utility::vector1<std::string, class std::allocator<std::string > >

get_relevant_residues_mode(self: pyrosetta.rosetta.protocols.features.FeaturesReporter) pyrosetta.rosetta.protocols.features.RelevantResiduesMode.T

C++: protocols::features::FeaturesReporter::get_relevant_residues_mode() const –> enum protocols::features::RelevantResiduesMode::T

load_into_pose(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, : pyrosetta.rosetta.utility.sql_database.session, : int, : pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::features::FeaturesReporter::load_into_pose(class std::shared_ptr<class utility::sql_database::session>, unsigned long, class core::pose::Pose &) –> void

parse_my_tag(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None

C++: protocols::features::FeaturesReporter::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::features::PairFeatures::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

report_features(self: pyrosetta.rosetta.protocols.features.PairFeatures, pose: pyrosetta.rosetta.core.pose.Pose, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, struct_id: int, db_session: pyrosetta.rosetta.utility.sql_database.session) int

collect all the feature data for the pose

C++: protocols::features::PairFeatures::report_features(const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> unsigned long

report_residue_pairs(self: pyrosetta.rosetta.protocols.features.PairFeatures, pose: pyrosetta.rosetta.core.pose.Pose, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, struct_id: int, db_session: pyrosetta.rosetta.utility.sql_database.session) None

C++: protocols::features::PairFeatures::report_residue_pairs(const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, const unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> void

schema(self: pyrosetta.rosetta.protocols.features.FeaturesReporter) str

return sql statements that sets up the appropriate tables to contain the features. This should be removed once everything has been moved to the schema generator

C++: protocols::features::FeaturesReporter::schema() const –> std::string

set_relevant_residues_mode(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, setting: pyrosetta.rosetta.protocols.features.RelevantResiduesMode.T) None

C++: protocols::features::FeaturesReporter::set_relevant_residues_mode(enum protocols::features::RelevantResiduesMode::T) –> void

type_name(self: pyrosetta.rosetta.protocols.features.PairFeatures) str

C++: protocols::features::PairFeatures::type_name() const –> std::string

write_schema_to_db(self: pyrosetta.rosetta.protocols.features.PairFeatures, db_session: pyrosetta.rosetta.utility.sql_database.session) None

generate the table schemas and write them to the database

C++: protocols::features::PairFeatures::write_schema_to_db(class std::shared_ptr<class utility::sql_database::session>) const –> void

class pyrosetta.rosetta.protocols.features.PairFeaturesCreator

Bases: pyrosetta.rosetta.protocols.features.FeaturesReporterCreator

creator for the PairFeatures class

assign(self: pyrosetta.rosetta.protocols.features.PairFeaturesCreator, : pyrosetta.rosetta.protocols.features.PairFeaturesCreator) pyrosetta.rosetta.protocols.features.PairFeaturesCreator

C++: protocols::features::PairFeaturesCreator::operator=(const class protocols::features::PairFeaturesCreator &) –> class protocols::features::PairFeaturesCreator &

create_features_reporter(self: pyrosetta.rosetta.protocols.features.PairFeaturesCreator) pyrosetta.rosetta.protocols.features.FeaturesReporter

C++: protocols::features::PairFeaturesCreator::create_features_reporter() const –> class std::shared_ptr<class protocols::features::FeaturesReporter>

provide_xml_schema(self: pyrosetta.rosetta.protocols.features.PairFeaturesCreator, xsd: utility::tag::XMLSchemaDefinition) None

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

type_name(self: pyrosetta.rosetta.protocols.features.PairFeaturesCreator) str

C++: protocols::features::PairFeaturesCreator::type_name() const –> std::string

class pyrosetta.rosetta.protocols.features.PdbDataFeatures

Bases: pyrosetta.rosetta.protocols.features.FeaturesReporter

assign(self: pyrosetta.rosetta.protocols.features.PdbDataFeatures, : pyrosetta.rosetta.protocols.features.PdbDataFeatures) pyrosetta.rosetta.protocols.features.PdbDataFeatures

C++: protocols::features::PdbDataFeatures::operator=(const class protocols::features::PdbDataFeatures &) –> class protocols::features::PdbDataFeatures &

check_relevant_residues(*args, **kwargs)

Overloaded function.

  1. check_relevant_residues(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, res1: int) -> bool

C++: protocols::features::FeaturesReporter::check_relevant_residues(const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long) const –> bool

  1. check_relevant_residues(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, res1: int, res2: int) -> bool

C++: protocols::features::FeaturesReporter::check_relevant_residues(const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, unsigned long) const –> bool

  1. check_relevant_residues(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, residues: pyrosetta.rosetta.utility.vector1_unsigned_long) -> bool

C++: protocols::features::FeaturesReporter::check_relevant_residues(const class utility::vector1<bool, class std::allocator<bool> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> bool

check_relevant_residues_range(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, res1: int, res2: int) bool

C++: protocols::features::FeaturesReporter::check_relevant_residues_range(const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, unsigned long) const –> bool

static class_name() str

C++: protocols::features::PdbDataFeatures::class_name() –> std::string

delete_record(self: pyrosetta.rosetta.protocols.features.PdbDataFeatures, struct_id: int, db_session: pyrosetta.rosetta.utility.sql_database.session) None

C++: protocols::features::PdbDataFeatures::delete_record(unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> void

features_reporter_dependencies(self: pyrosetta.rosetta.protocols.features.PdbDataFeatures) pyrosetta.rosetta.utility.vector1_std_string

return the set of features reporters that are required to also already be extracted by the time this one is used.

C++: protocols::features::PdbDataFeatures::features_reporter_dependencies() const –> class utility::vector1<std::string, class std::allocator<std::string > >

get_relevant_residues_mode(self: pyrosetta.rosetta.protocols.features.FeaturesReporter) pyrosetta.rosetta.protocols.features.RelevantResiduesMode.T

C++: protocols::features::FeaturesReporter::get_relevant_residues_mode() const –> enum protocols::features::RelevantResiduesMode::T

load_into_pose(self: pyrosetta.rosetta.protocols.features.PdbDataFeatures, db_session: pyrosetta.rosetta.utility.sql_database.session, struct_id: int, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::features::PdbDataFeatures::load_into_pose(class std::shared_ptr<class utility::sql_database::session>, unsigned long, class core::pose::Pose &) –> void

parse_my_tag(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None

C++: protocols::features::FeaturesReporter::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::features::PdbDataFeatures::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

report_features(self: pyrosetta.rosetta.protocols.features.PdbDataFeatures, pose: pyrosetta.rosetta.core.pose.Pose, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, struct_id: int, db_session: pyrosetta.rosetta.utility.sql_database.session) int

collect all the feature data for the pose

C++: protocols::features::PdbDataFeatures::report_features(const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> unsigned long

schema(self: pyrosetta.rosetta.protocols.features.FeaturesReporter) str

return sql statements that sets up the appropriate tables to contain the features. This should be removed once everything has been moved to the schema generator

C++: protocols::features::FeaturesReporter::schema() const –> std::string

set_relevant_residues_mode(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, setting: pyrosetta.rosetta.protocols.features.RelevantResiduesMode.T) None

C++: protocols::features::FeaturesReporter::set_relevant_residues_mode(enum protocols::features::RelevantResiduesMode::T) –> void

type_name(self: pyrosetta.rosetta.protocols.features.PdbDataFeatures) str

C++: protocols::features::PdbDataFeatures::type_name() const –> std::string

write_schema_to_db(self: pyrosetta.rosetta.protocols.features.PdbDataFeatures, db_session: pyrosetta.rosetta.utility.sql_database.session) None

generate the table schemas and write them to the database

C++: protocols::features::PdbDataFeatures::write_schema_to_db(class std::shared_ptr<class utility::sql_database::session>) const –> void

class pyrosetta.rosetta.protocols.features.PdbDataFeaturesCreator

Bases: pyrosetta.rosetta.protocols.features.FeaturesReporterCreator

creator for the PdbDataFeatures class

assign(self: pyrosetta.rosetta.protocols.features.PdbDataFeaturesCreator, : pyrosetta.rosetta.protocols.features.PdbDataFeaturesCreator) pyrosetta.rosetta.protocols.features.PdbDataFeaturesCreator

C++: protocols::features::PdbDataFeaturesCreator::operator=(const class protocols::features::PdbDataFeaturesCreator &) –> class protocols::features::PdbDataFeaturesCreator &

create_features_reporter(self: pyrosetta.rosetta.protocols.features.PdbDataFeaturesCreator) pyrosetta.rosetta.protocols.features.FeaturesReporter

C++: protocols::features::PdbDataFeaturesCreator::create_features_reporter() const –> class std::shared_ptr<class protocols::features::FeaturesReporter>

provide_xml_schema(self: pyrosetta.rosetta.protocols.features.PdbDataFeaturesCreator, xsd: utility::tag::XMLSchemaDefinition) None

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

type_name(self: pyrosetta.rosetta.protocols.features.PdbDataFeaturesCreator) str

C++: protocols::features::PdbDataFeaturesCreator::type_name() const –> std::string

class pyrosetta.rosetta.protocols.features.PoseCommentsFeatures

Bases: pyrosetta.rosetta.protocols.features.FeaturesReporter

assign(self: pyrosetta.rosetta.protocols.features.PoseCommentsFeatures, : pyrosetta.rosetta.protocols.features.PoseCommentsFeatures) pyrosetta.rosetta.protocols.features.PoseCommentsFeatures

C++: protocols::features::PoseCommentsFeatures::operator=(const class protocols::features::PoseCommentsFeatures &) –> class protocols::features::PoseCommentsFeatures &

check_relevant_residues(*args, **kwargs)

Overloaded function.

  1. check_relevant_residues(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, res1: int) -> bool

C++: protocols::features::FeaturesReporter::check_relevant_residues(const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long) const –> bool

  1. check_relevant_residues(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, res1: int, res2: int) -> bool

C++: protocols::features::FeaturesReporter::check_relevant_residues(const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, unsigned long) const –> bool

  1. check_relevant_residues(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, residues: pyrosetta.rosetta.utility.vector1_unsigned_long) -> bool

C++: protocols::features::FeaturesReporter::check_relevant_residues(const class utility::vector1<bool, class std::allocator<bool> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> bool

check_relevant_residues_range(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, res1: int, res2: int) bool

C++: protocols::features::FeaturesReporter::check_relevant_residues_range(const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, unsigned long) const –> bool

static class_name() str

C++: protocols::features::PoseCommentsFeatures::class_name() –> std::string

delete_record(self: pyrosetta.rosetta.protocols.features.PoseCommentsFeatures, struct_id: int, db_session: pyrosetta.rosetta.utility.sql_database.session) None

C++: protocols::features::PoseCommentsFeatures::delete_record(unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> void

features_reporter_dependencies(self: pyrosetta.rosetta.protocols.features.PoseCommentsFeatures) pyrosetta.rosetta.utility.vector1_std_string

return the set of features reporters that are required to also already be extracted by the time this one is used.

C++: protocols::features::PoseCommentsFeatures::features_reporter_dependencies() const –> class utility::vector1<std::string, class std::allocator<std::string > >

get_relevant_residues_mode(self: pyrosetta.rosetta.protocols.features.FeaturesReporter) pyrosetta.rosetta.protocols.features.RelevantResiduesMode.T

C++: protocols::features::FeaturesReporter::get_relevant_residues_mode() const –> enum protocols::features::RelevantResiduesMode::T

load_into_pose(self: pyrosetta.rosetta.protocols.features.PoseCommentsFeatures, db_session: pyrosetta.rosetta.utility.sql_database.session, struct_id: int, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::features::PoseCommentsFeatures::load_into_pose(class std::shared_ptr<class utility::sql_database::session>, unsigned long, class core::pose::Pose &) –> void

parse_my_tag(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None

C++: protocols::features::FeaturesReporter::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::features::PoseCommentsFeatures::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

report_features(self: pyrosetta.rosetta.protocols.features.PoseCommentsFeatures, pose: pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.utility.vector1_bool, struct_id: int, db_session: pyrosetta.rosetta.utility.sql_database.session) int

collect all the feature data for the pose

C++: protocols::features::PoseCommentsFeatures::report_features(const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> unsigned long

schema(self: pyrosetta.rosetta.protocols.features.FeaturesReporter) str

return sql statements that sets up the appropriate tables to contain the features. This should be removed once everything has been moved to the schema generator

C++: protocols::features::FeaturesReporter::schema() const –> std::string

set_relevant_residues_mode(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, setting: pyrosetta.rosetta.protocols.features.RelevantResiduesMode.T) None

C++: protocols::features::FeaturesReporter::set_relevant_residues_mode(enum protocols::features::RelevantResiduesMode::T) –> void

type_name(self: pyrosetta.rosetta.protocols.features.PoseCommentsFeatures) str

C++: protocols::features::PoseCommentsFeatures::type_name() const –> std::string

write_schema_to_db(self: pyrosetta.rosetta.protocols.features.PoseCommentsFeatures, db_session: pyrosetta.rosetta.utility.sql_database.session) None

generate the table schemas and write them to the database

C++: protocols::features::PoseCommentsFeatures::write_schema_to_db(class std::shared_ptr<class utility::sql_database::session>) const –> void

class pyrosetta.rosetta.protocols.features.PoseCommentsFeaturesCreator

Bases: pyrosetta.rosetta.protocols.features.FeaturesReporterCreator

creator for the PoseCommentsFeatures class

assign(self: pyrosetta.rosetta.protocols.features.PoseCommentsFeaturesCreator, : pyrosetta.rosetta.protocols.features.PoseCommentsFeaturesCreator) pyrosetta.rosetta.protocols.features.PoseCommentsFeaturesCreator

C++: protocols::features::PoseCommentsFeaturesCreator::operator=(const class protocols::features::PoseCommentsFeaturesCreator &) –> class protocols::features::PoseCommentsFeaturesCreator &

create_features_reporter(self: pyrosetta.rosetta.protocols.features.PoseCommentsFeaturesCreator) pyrosetta.rosetta.protocols.features.FeaturesReporter

C++: protocols::features::PoseCommentsFeaturesCreator::create_features_reporter() const –> class std::shared_ptr<class protocols::features::FeaturesReporter>

provide_xml_schema(self: pyrosetta.rosetta.protocols.features.PoseCommentsFeaturesCreator, xsd: utility::tag::XMLSchemaDefinition) None

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

type_name(self: pyrosetta.rosetta.protocols.features.PoseCommentsFeaturesCreator) str

C++: protocols::features::PoseCommentsFeaturesCreator::type_name() const –> std::string

class pyrosetta.rosetta.protocols.features.PoseConformationFeatures

Bases: pyrosetta.rosetta.protocols.features.FeaturesReporter

assign(self: pyrosetta.rosetta.protocols.features.PoseConformationFeatures, : pyrosetta.rosetta.protocols.features.PoseConformationFeatures) pyrosetta.rosetta.protocols.features.PoseConformationFeatures

C++: protocols::features::PoseConformationFeatures::operator=(const class protocols::features::PoseConformationFeatures &) –> class protocols::features::PoseConformationFeatures &

check_relevant_residues(*args, **kwargs)

Overloaded function.

  1. check_relevant_residues(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, res1: int) -> bool

C++: protocols::features::FeaturesReporter::check_relevant_residues(const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long) const –> bool

  1. check_relevant_residues(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, res1: int, res2: int) -> bool

C++: protocols::features::FeaturesReporter::check_relevant_residues(const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, unsigned long) const –> bool

  1. check_relevant_residues(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, residues: pyrosetta.rosetta.utility.vector1_unsigned_long) -> bool

C++: protocols::features::FeaturesReporter::check_relevant_residues(const class utility::vector1<bool, class std::allocator<bool> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> bool

check_relevant_residues_range(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, res1: int, res2: int) bool

C++: protocols::features::FeaturesReporter::check_relevant_residues_range(const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, unsigned long) const –> bool

static class_name() str

C++: protocols::features::PoseConformationFeatures::class_name() –> std::string

delete_record(self: pyrosetta.rosetta.protocols.features.PoseConformationFeatures, struct_id: int, db_session: pyrosetta.rosetta.utility.sql_database.session) None

C++: protocols::features::PoseConformationFeatures::delete_record(unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> void

features_reporter_dependencies(self: pyrosetta.rosetta.protocols.features.PoseConformationFeatures) pyrosetta.rosetta.utility.vector1_std_string

return the set of features reporters that are required to also already be extracted by the time this one is used.

C++: protocols::features::PoseConformationFeatures::features_reporter_dependencies() const –> class utility::vector1<std::string, class std::allocator<std::string > >

get_relevant_residues_mode(self: pyrosetta.rosetta.protocols.features.FeaturesReporter) pyrosetta.rosetta.protocols.features.RelevantResiduesMode.T

C++: protocols::features::FeaturesReporter::get_relevant_residues_mode() const –> enum protocols::features::RelevantResiduesMode::T

load_into_pose(*args, **kwargs)

Overloaded function.

  1. load_into_pose(self: pyrosetta.rosetta.protocols.features.PoseConformationFeatures, : pyrosetta.rosetta.utility.sql_database.session, : int, : pyrosetta.rosetta.core.pose.Pose) -> None

  2. load_into_pose(self: pyrosetta.rosetta.protocols.features.PoseConformationFeatures, db_session: pyrosetta.rosetta.utility.sql_database.session, struct_id: int, pose: pyrosetta.rosetta.core.pose.Pose, ideal: bool) -> None

Load information from pose_conformations into pose

  • true if structure is ideal, false if not

C++: protocols::features::PoseConformationFeatures::load_into_pose(class std::shared_ptr<class utility::sql_database::session>, unsigned long, class core::pose::Pose &, bool &) –> void

parse_my_tag(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None

C++: protocols::features::FeaturesReporter::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::features::PoseConformationFeatures::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

report_features(self: pyrosetta.rosetta.protocols.features.PoseConformationFeatures, pose: pyrosetta.rosetta.core.pose.Pose, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, struct_id: int, db_session: pyrosetta.rosetta.utility.sql_database.session) int

collect all the feature data for the pose

C++: protocols::features::PoseConformationFeatures::report_features(const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> unsigned long

schema(self: pyrosetta.rosetta.protocols.features.FeaturesReporter) str

return sql statements that sets up the appropriate tables to contain the features. This should be removed once everything has been moved to the schema generator

C++: protocols::features::FeaturesReporter::schema() const –> std::string

set_relevant_residues_mode(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, setting: pyrosetta.rosetta.protocols.features.RelevantResiduesMode.T) None

C++: protocols::features::FeaturesReporter::set_relevant_residues_mode(enum protocols::features::RelevantResiduesMode::T) –> void

type_name(self: pyrosetta.rosetta.protocols.features.PoseConformationFeatures) str

C++: protocols::features::PoseConformationFeatures::type_name() const –> std::string

write_schema_to_db(self: pyrosetta.rosetta.protocols.features.PoseConformationFeatures, db_session: pyrosetta.rosetta.utility.sql_database.session) None

generate the table schemas and write them to the database

C++: protocols::features::PoseConformationFeatures::write_schema_to_db(class std::shared_ptr<class utility::sql_database::session>) const –> void

class pyrosetta.rosetta.protocols.features.PoseConformationFeaturesCreator

Bases: pyrosetta.rosetta.protocols.features.FeaturesReporterCreator

creator for the PoseConformationFeatures class

assign(self: pyrosetta.rosetta.protocols.features.PoseConformationFeaturesCreator, : pyrosetta.rosetta.protocols.features.PoseConformationFeaturesCreator) pyrosetta.rosetta.protocols.features.PoseConformationFeaturesCreator

C++: protocols::features::PoseConformationFeaturesCreator::operator=(const class protocols::features::PoseConformationFeaturesCreator &) –> class protocols::features::PoseConformationFeaturesCreator &

create_features_reporter(self: pyrosetta.rosetta.protocols.features.PoseConformationFeaturesCreator) pyrosetta.rosetta.protocols.features.FeaturesReporter

C++: protocols::features::PoseConformationFeaturesCreator::create_features_reporter() const –> class std::shared_ptr<class protocols::features::FeaturesReporter>

provide_xml_schema(self: pyrosetta.rosetta.protocols.features.PoseConformationFeaturesCreator, xsd: utility::tag::XMLSchemaDefinition) None

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

type_name(self: pyrosetta.rosetta.protocols.features.PoseConformationFeaturesCreator) str

C++: protocols::features::PoseConformationFeaturesCreator::type_name() const –> std::string

class pyrosetta.rosetta.protocols.features.ProteinBackboneAtomAtomPairFeatures

Bases: pyrosetta.rosetta.protocols.features.FeaturesReporter

assign(self: pyrosetta.rosetta.protocols.features.ProteinBackboneAtomAtomPairFeatures, : pyrosetta.rosetta.protocols.features.ProteinBackboneAtomAtomPairFeatures) pyrosetta.rosetta.protocols.features.ProteinBackboneAtomAtomPairFeatures

C++: protocols::features::ProteinBackboneAtomAtomPairFeatures::operator=(const class protocols::features::ProteinBackboneAtomAtomPairFeatures &) –> class protocols::features::ProteinBackboneAtomAtomPairFeatures &

check_relevant_residues(*args, **kwargs)

Overloaded function.

  1. check_relevant_residues(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, res1: int) -> bool

C++: protocols::features::FeaturesReporter::check_relevant_residues(const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long) const –> bool

  1. check_relevant_residues(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, res1: int, res2: int) -> bool

C++: protocols::features::FeaturesReporter::check_relevant_residues(const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, unsigned long) const –> bool

  1. check_relevant_residues(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, residues: pyrosetta.rosetta.utility.vector1_unsigned_long) -> bool

C++: protocols::features::FeaturesReporter::check_relevant_residues(const class utility::vector1<bool, class std::allocator<bool> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> bool

check_relevant_residues_range(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, res1: int, res2: int) bool

C++: protocols::features::FeaturesReporter::check_relevant_residues_range(const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, unsigned long) const –> bool

static class_name() str

C++: protocols::features::ProteinBackboneAtomAtomPairFeatures::class_name() –> std::string

delete_record(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, : int, : pyrosetta.rosetta.utility.sql_database.session) None

C++: protocols::features::FeaturesReporter::delete_record(unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> void

features_reporter_dependencies(self: pyrosetta.rosetta.protocols.features.ProteinBackboneAtomAtomPairFeatures) pyrosetta.rosetta.utility.vector1_std_string

return the set of features reporters that are required to also already be extracted by the time this one is used.

C++: protocols::features::ProteinBackboneAtomAtomPairFeatures::features_reporter_dependencies() const –> class utility::vector1<std::string, class std::allocator<std::string > >

get_relevant_residues_mode(self: pyrosetta.rosetta.protocols.features.FeaturesReporter) pyrosetta.rosetta.protocols.features.RelevantResiduesMode.T

C++: protocols::features::FeaturesReporter::get_relevant_residues_mode() const –> enum protocols::features::RelevantResiduesMode::T

load_into_pose(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, : pyrosetta.rosetta.utility.sql_database.session, : int, : pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::features::FeaturesReporter::load_into_pose(class std::shared_ptr<class utility::sql_database::session>, unsigned long, class core::pose::Pose &) –> void

parse_my_tag(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None

C++: protocols::features::FeaturesReporter::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::features::ProteinBackboneAtomAtomPairFeatures::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

report_features(self: pyrosetta.rosetta.protocols.features.ProteinBackboneAtomAtomPairFeatures, pose: pyrosetta.rosetta.core.pose.Pose, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, struct_id: int, db_session: pyrosetta.rosetta.utility.sql_database.session) int

collect all the feature data for the pose

C++: protocols::features::ProteinBackboneAtomAtomPairFeatures::report_features(const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> unsigned long

schema(self: pyrosetta.rosetta.protocols.features.FeaturesReporter) str

return sql statements that sets up the appropriate tables to contain the features. This should be removed once everything has been moved to the schema generator

C++: protocols::features::FeaturesReporter::schema() const –> std::string

set_relevant_residues_mode(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, setting: pyrosetta.rosetta.protocols.features.RelevantResiduesMode.T) None

C++: protocols::features::FeaturesReporter::set_relevant_residues_mode(enum protocols::features::RelevantResiduesMode::T) –> void

type_name(self: pyrosetta.rosetta.protocols.features.ProteinBackboneAtomAtomPairFeatures) str

C++: protocols::features::ProteinBackboneAtomAtomPairFeatures::type_name() const –> std::string

write_schema_to_db(self: pyrosetta.rosetta.protocols.features.ProteinBackboneAtomAtomPairFeatures, db_session: pyrosetta.rosetta.utility.sql_database.session) None

generate the table schemas and write them to the database

C++: protocols::features::ProteinBackboneAtomAtomPairFeatures::write_schema_to_db(class std::shared_ptr<class utility::sql_database::session>) const –> void

class pyrosetta.rosetta.protocols.features.ProteinBackboneAtomAtomPairFeaturesCreator

Bases: pyrosetta.rosetta.protocols.features.FeaturesReporterCreator

creator for the ProteinBackboneAtomAtomPairFeatures class

assign(self: pyrosetta.rosetta.protocols.features.ProteinBackboneAtomAtomPairFeaturesCreator, : pyrosetta.rosetta.protocols.features.ProteinBackboneAtomAtomPairFeaturesCreator) pyrosetta.rosetta.protocols.features.ProteinBackboneAtomAtomPairFeaturesCreator

C++: protocols::features::ProteinBackboneAtomAtomPairFeaturesCreator::operator=(const class protocols::features::ProteinBackboneAtomAtomPairFeaturesCreator &) –> class protocols::features::ProteinBackboneAtomAtomPairFeaturesCreator &

create_features_reporter(self: pyrosetta.rosetta.protocols.features.ProteinBackboneAtomAtomPairFeaturesCreator) pyrosetta.rosetta.protocols.features.FeaturesReporter

C++: protocols::features::ProteinBackboneAtomAtomPairFeaturesCreator::create_features_reporter() const –> class std::shared_ptr<class protocols::features::FeaturesReporter>

provide_xml_schema(self: pyrosetta.rosetta.protocols.features.ProteinBackboneAtomAtomPairFeaturesCreator, xsd: utility::tag::XMLSchemaDefinition) None

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

type_name(self: pyrosetta.rosetta.protocols.features.ProteinBackboneAtomAtomPairFeaturesCreator) str

C++: protocols::features::ProteinBackboneAtomAtomPairFeaturesCreator::type_name() const –> std::string

class pyrosetta.rosetta.protocols.features.ProteinBackboneTorsionAngleFeatures

Bases: pyrosetta.rosetta.protocols.features.FeaturesReporter

assign(self: pyrosetta.rosetta.protocols.features.ProteinBackboneTorsionAngleFeatures, : pyrosetta.rosetta.protocols.features.ProteinBackboneTorsionAngleFeatures) pyrosetta.rosetta.protocols.features.ProteinBackboneTorsionAngleFeatures

C++: protocols::features::ProteinBackboneTorsionAngleFeatures::operator=(const class protocols::features::ProteinBackboneTorsionAngleFeatures &) –> class protocols::features::ProteinBackboneTorsionAngleFeatures &

check_relevant_residues(*args, **kwargs)

Overloaded function.

  1. check_relevant_residues(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, res1: int) -> bool

C++: protocols::features::FeaturesReporter::check_relevant_residues(const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long) const –> bool

  1. check_relevant_residues(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, res1: int, res2: int) -> bool

C++: protocols::features::FeaturesReporter::check_relevant_residues(const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, unsigned long) const –> bool

  1. check_relevant_residues(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, residues: pyrosetta.rosetta.utility.vector1_unsigned_long) -> bool

C++: protocols::features::FeaturesReporter::check_relevant_residues(const class utility::vector1<bool, class std::allocator<bool> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> bool

check_relevant_residues_range(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, res1: int, res2: int) bool

C++: protocols::features::FeaturesReporter::check_relevant_residues_range(const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, unsigned long) const –> bool

static class_name() str

C++: protocols::features::ProteinBackboneTorsionAngleFeatures::class_name() –> std::string

delete_record(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, : int, : pyrosetta.rosetta.utility.sql_database.session) None

C++: protocols::features::FeaturesReporter::delete_record(unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> void

features_reporter_dependencies(self: pyrosetta.rosetta.protocols.features.ProteinBackboneTorsionAngleFeatures) pyrosetta.rosetta.utility.vector1_std_string

return the set of features reporters that are required to also already be extracted by the time this one is used.

C++: protocols::features::ProteinBackboneTorsionAngleFeatures::features_reporter_dependencies() const –> class utility::vector1<std::string, class std::allocator<std::string > >

get_relevant_residues_mode(self: pyrosetta.rosetta.protocols.features.FeaturesReporter) pyrosetta.rosetta.protocols.features.RelevantResiduesMode.T

C++: protocols::features::FeaturesReporter::get_relevant_residues_mode() const –> enum protocols::features::RelevantResiduesMode::T

load_into_pose(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, : pyrosetta.rosetta.utility.sql_database.session, : int, : pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::features::FeaturesReporter::load_into_pose(class std::shared_ptr<class utility::sql_database::session>, unsigned long, class core::pose::Pose &) –> void

parse_my_tag(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None

C++: protocols::features::FeaturesReporter::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::features::ProteinBackboneTorsionAngleFeatures::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

report_features(self: pyrosetta.rosetta.protocols.features.ProteinBackboneTorsionAngleFeatures, pose: pyrosetta.rosetta.core.pose.Pose, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, struct_id: int, db_session: pyrosetta.rosetta.utility.sql_database.session) int

collect all the feature data for the pose

C++: protocols::features::ProteinBackboneTorsionAngleFeatures::report_features(const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> unsigned long

schema(self: pyrosetta.rosetta.protocols.features.FeaturesReporter) str

return sql statements that sets up the appropriate tables to contain the features. This should be removed once everything has been moved to the schema generator

C++: protocols::features::FeaturesReporter::schema() const –> std::string

set_relevant_residues_mode(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, setting: pyrosetta.rosetta.protocols.features.RelevantResiduesMode.T) None

C++: protocols::features::FeaturesReporter::set_relevant_residues_mode(enum protocols::features::RelevantResiduesMode::T) –> void

type_name(self: pyrosetta.rosetta.protocols.features.ProteinBackboneTorsionAngleFeatures) str

C++: protocols::features::ProteinBackboneTorsionAngleFeatures::type_name() const –> std::string

write_schema_to_db(self: pyrosetta.rosetta.protocols.features.ProteinBackboneTorsionAngleFeatures, db_session: pyrosetta.rosetta.utility.sql_database.session) None

generate the table schemas and write them to the database

C++: protocols::features::ProteinBackboneTorsionAngleFeatures::write_schema_to_db(class std::shared_ptr<class utility::sql_database::session>) const –> void

class pyrosetta.rosetta.protocols.features.ProteinBackboneTorsionAngleFeaturesCreator

Bases: pyrosetta.rosetta.protocols.features.FeaturesReporterCreator

creator for the ProteinBackboneTorsionAngleFeatures class

assign(self: pyrosetta.rosetta.protocols.features.ProteinBackboneTorsionAngleFeaturesCreator, : pyrosetta.rosetta.protocols.features.ProteinBackboneTorsionAngleFeaturesCreator) pyrosetta.rosetta.protocols.features.ProteinBackboneTorsionAngleFeaturesCreator

C++: protocols::features::ProteinBackboneTorsionAngleFeaturesCreator::operator=(const class protocols::features::ProteinBackboneTorsionAngleFeaturesCreator &) –> class protocols::features::ProteinBackboneTorsionAngleFeaturesCreator &

create_features_reporter(self: pyrosetta.rosetta.protocols.features.ProteinBackboneTorsionAngleFeaturesCreator) pyrosetta.rosetta.protocols.features.FeaturesReporter

C++: protocols::features::ProteinBackboneTorsionAngleFeaturesCreator::create_features_reporter() const –> class std::shared_ptr<class protocols::features::FeaturesReporter>

provide_xml_schema(self: pyrosetta.rosetta.protocols.features.ProteinBackboneTorsionAngleFeaturesCreator, xsd: utility::tag::XMLSchemaDefinition) None

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

type_name(self: pyrosetta.rosetta.protocols.features.ProteinBackboneTorsionAngleFeaturesCreator) str

C++: protocols::features::ProteinBackboneTorsionAngleFeaturesCreator::type_name() const –> std::string

class pyrosetta.rosetta.protocols.features.ProteinBondGeometryFeatures

Bases: pyrosetta.rosetta.protocols.features.FeaturesReporter

assign(self: pyrosetta.rosetta.protocols.features.ProteinBondGeometryFeatures, : pyrosetta.rosetta.protocols.features.ProteinBondGeometryFeatures) pyrosetta.rosetta.protocols.features.ProteinBondGeometryFeatures

C++: protocols::features::ProteinBondGeometryFeatures::operator=(const class protocols::features::ProteinBondGeometryFeatures &) –> class protocols::features::ProteinBondGeometryFeatures &

check_relevant_residues(*args, **kwargs)

Overloaded function.

  1. check_relevant_residues(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, res1: int) -> bool

C++: protocols::features::FeaturesReporter::check_relevant_residues(const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long) const –> bool

  1. check_relevant_residues(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, res1: int, res2: int) -> bool

C++: protocols::features::FeaturesReporter::check_relevant_residues(const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, unsigned long) const –> bool

  1. check_relevant_residues(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, residues: pyrosetta.rosetta.utility.vector1_unsigned_long) -> bool

C++: protocols::features::FeaturesReporter::check_relevant_residues(const class utility::vector1<bool, class std::allocator<bool> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> bool

check_relevant_residues_range(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, res1: int, res2: int) bool

C++: protocols::features::FeaturesReporter::check_relevant_residues_range(const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, unsigned long) const –> bool

static class_name() str

C++: protocols::features::ProteinBondGeometryFeatures::class_name() –> std::string

delete_record(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, : int, : pyrosetta.rosetta.utility.sql_database.session) None

C++: protocols::features::FeaturesReporter::delete_record(unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> void

features_reporter_dependencies(self: pyrosetta.rosetta.protocols.features.ProteinBondGeometryFeatures) pyrosetta.rosetta.utility.vector1_std_string

return the set of features reporters that are required to also already be extracted by the time this one is used.

C++: protocols::features::ProteinBondGeometryFeatures::features_reporter_dependencies() const –> class utility::vector1<std::string, class std::allocator<std::string > >

get_relevant_residues_mode(self: pyrosetta.rosetta.protocols.features.FeaturesReporter) pyrosetta.rosetta.protocols.features.RelevantResiduesMode.T

C++: protocols::features::FeaturesReporter::get_relevant_residues_mode() const –> enum protocols::features::RelevantResiduesMode::T

load_into_pose(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, : pyrosetta.rosetta.utility.sql_database.session, : int, : pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::features::FeaturesReporter::load_into_pose(class std::shared_ptr<class utility::sql_database::session>, unsigned long, class core::pose::Pose &) –> void

parse_my_tag(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None

C++: protocols::features::FeaturesReporter::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::features::ProteinBondGeometryFeatures::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

report_features(self: pyrosetta.rosetta.protocols.features.ProteinBondGeometryFeatures, pose: pyrosetta.rosetta.core.pose.Pose, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, struct_id: int, db_session: pyrosetta.rosetta.utility.sql_database.session) int

collect all the feature data for the pose

C++: protocols::features::ProteinBondGeometryFeatures::report_features(const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> unsigned long

report_interres_angles(self: pyrosetta.rosetta.protocols.features.ProteinBondGeometryFeatures, pose: pyrosetta.rosetta.core.pose.Pose, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, struct_id: int, db_session: pyrosetta.rosetta.utility.sql_database.session) None

C++: protocols::features::ProteinBondGeometryFeatures::report_interres_angles(const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> void

report_interres_lengths(self: pyrosetta.rosetta.protocols.features.ProteinBondGeometryFeatures, pose: pyrosetta.rosetta.core.pose.Pose, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, struct_id: int, db_session: pyrosetta.rosetta.utility.sql_database.session) None

C++: protocols::features::ProteinBondGeometryFeatures::report_interres_lengths(const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> void

report_intrares_angles(self: pyrosetta.rosetta.protocols.features.ProteinBondGeometryFeatures, pose: pyrosetta.rosetta.core.pose.Pose, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, struct_id: int, db_session: pyrosetta.rosetta.utility.sql_database.session) None

C++: protocols::features::ProteinBondGeometryFeatures::report_intrares_angles(const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> void

report_intrares_lengths(self: pyrosetta.rosetta.protocols.features.ProteinBondGeometryFeatures, pose: pyrosetta.rosetta.core.pose.Pose, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, struct_id: int, db_session: pyrosetta.rosetta.utility.sql_database.session) None

C++: protocols::features::ProteinBondGeometryFeatures::report_intrares_lengths(const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> void

report_intrares_torsions(self: pyrosetta.rosetta.protocols.features.ProteinBondGeometryFeatures, pose: pyrosetta.rosetta.core.pose.Pose, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, struct_id: int, db_session: pyrosetta.rosetta.utility.sql_database.session) None

C++: protocols::features::ProteinBondGeometryFeatures::report_intrares_torsions(const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> void

schema(self: pyrosetta.rosetta.protocols.features.FeaturesReporter) str

return sql statements that sets up the appropriate tables to contain the features. This should be removed once everything has been moved to the schema generator

C++: protocols::features::FeaturesReporter::schema() const –> std::string

set_relevant_residues_mode(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, setting: pyrosetta.rosetta.protocols.features.RelevantResiduesMode.T) None

C++: protocols::features::FeaturesReporter::set_relevant_residues_mode(enum protocols::features::RelevantResiduesMode::T) –> void

type_name(self: pyrosetta.rosetta.protocols.features.ProteinBondGeometryFeatures) str

C++: protocols::features::ProteinBondGeometryFeatures::type_name() const –> std::string

write_schema_to_db(self: pyrosetta.rosetta.protocols.features.ProteinBondGeometryFeatures, db_session: pyrosetta.rosetta.utility.sql_database.session) None

generate the table schemas and write them to the database

C++: protocols::features::ProteinBondGeometryFeatures::write_schema_to_db(class std::shared_ptr<class utility::sql_database::session>) const –> void

class pyrosetta.rosetta.protocols.features.ProteinBondGeometryFeaturesCreator

Bases: pyrosetta.rosetta.protocols.features.FeaturesReporterCreator

creator for the ProteinBondGeometryFeatures class

assign(self: pyrosetta.rosetta.protocols.features.ProteinBondGeometryFeaturesCreator, : pyrosetta.rosetta.protocols.features.ProteinBondGeometryFeaturesCreator) pyrosetta.rosetta.protocols.features.ProteinBondGeometryFeaturesCreator

C++: protocols::features::ProteinBondGeometryFeaturesCreator::operator=(const class protocols::features::ProteinBondGeometryFeaturesCreator &) –> class protocols::features::ProteinBondGeometryFeaturesCreator &

create_features_reporter(self: pyrosetta.rosetta.protocols.features.ProteinBondGeometryFeaturesCreator) pyrosetta.rosetta.protocols.features.FeaturesReporter

C++: protocols::features::ProteinBondGeometryFeaturesCreator::create_features_reporter() const –> class std::shared_ptr<class protocols::features::FeaturesReporter>

provide_xml_schema(self: pyrosetta.rosetta.protocols.features.ProteinBondGeometryFeaturesCreator, xsd: utility::tag::XMLSchemaDefinition) None

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

type_name(self: pyrosetta.rosetta.protocols.features.ProteinBondGeometryFeaturesCreator) str

C++: protocols::features::ProteinBondGeometryFeaturesCreator::type_name() const –> std::string

class pyrosetta.rosetta.protocols.features.ProteinRMSDFeatures

Bases: pyrosetta.rosetta.protocols.features.FeaturesReporter

assign(self: pyrosetta.rosetta.protocols.features.ProteinRMSDFeatures, : pyrosetta.rosetta.protocols.features.ProteinRMSDFeatures) pyrosetta.rosetta.protocols.features.ProteinRMSDFeatures

C++: protocols::features::ProteinRMSDFeatures::operator=(const class protocols::features::ProteinRMSDFeatures &) –> class protocols::features::ProteinRMSDFeatures &

check_relevant_residues(*args, **kwargs)

Overloaded function.

  1. check_relevant_residues(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, res1: int) -> bool

C++: protocols::features::FeaturesReporter::check_relevant_residues(const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long) const –> bool

  1. check_relevant_residues(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, res1: int, res2: int) -> bool

C++: protocols::features::FeaturesReporter::check_relevant_residues(const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, unsigned long) const –> bool

  1. check_relevant_residues(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, residues: pyrosetta.rosetta.utility.vector1_unsigned_long) -> bool

C++: protocols::features::FeaturesReporter::check_relevant_residues(const class utility::vector1<bool, class std::allocator<bool> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> bool

check_relevant_residues_range(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, res1: int, res2: int) bool

C++: protocols::features::FeaturesReporter::check_relevant_residues_range(const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, unsigned long) const –> bool

static class_name() str

C++: protocols::features::ProteinRMSDFeatures::class_name() –> std::string

delete_record(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, : int, : pyrosetta.rosetta.utility.sql_database.session) None

C++: protocols::features::FeaturesReporter::delete_record(unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> void

features_reporter_dependencies(self: pyrosetta.rosetta.protocols.features.ProteinRMSDFeatures) pyrosetta.rosetta.utility.vector1_std_string

return the set of features reporters that are required to also already be extracted by the time this one is used.

C++: protocols::features::ProteinRMSDFeatures::features_reporter_dependencies() const –> class utility::vector1<std::string, class std::allocator<std::string > >

get_relevant_residues_mode(self: pyrosetta.rosetta.protocols.features.FeaturesReporter) pyrosetta.rosetta.protocols.features.RelevantResiduesMode.T

C++: protocols::features::FeaturesReporter::get_relevant_residues_mode() const –> enum protocols::features::RelevantResiduesMode::T

load_into_pose(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, : pyrosetta.rosetta.utility.sql_database.session, : int, : pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::features::FeaturesReporter::load_into_pose(class std::shared_ptr<class utility::sql_database::session>, unsigned long, class core::pose::Pose &) –> void

parse_my_tag(self: pyrosetta.rosetta.protocols.features.ProteinRMSDFeatures, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None

C++: protocols::features::ProteinRMSDFeatures::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::features::ProteinRMSDFeatures::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

reference_pose(*args, **kwargs)

Overloaded function.

  1. reference_pose(self: pyrosetta.rosetta.protocols.features.ProteinRMSDFeatures) -> pyrosetta.rosetta.core.pose.Pose

C++: protocols::features::ProteinRMSDFeatures::reference_pose() const –> class std::shared_ptr<const class core::pose::Pose>

  1. reference_pose(self: pyrosetta.rosetta.protocols.features.ProteinRMSDFeatures, : pyrosetta.rosetta.core.pose.Pose) -> None

C++: protocols::features::ProteinRMSDFeatures::reference_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

report_features(self: pyrosetta.rosetta.protocols.features.ProteinRMSDFeatures, pose: pyrosetta.rosetta.core.pose.Pose, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, struct_id: int, db_session: pyrosetta.rosetta.utility.sql_database.session) int

collect all the feature data for the pose

C++: protocols::features::ProteinRMSDFeatures::report_features(const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> unsigned long

schema(self: pyrosetta.rosetta.protocols.features.FeaturesReporter) str

return sql statements that sets up the appropriate tables to contain the features. This should be removed once everything has been moved to the schema generator

C++: protocols::features::FeaturesReporter::schema() const –> std::string

set_relevant_residues_mode(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, setting: pyrosetta.rosetta.protocols.features.RelevantResiduesMode.T) None

C++: protocols::features::FeaturesReporter::set_relevant_residues_mode(enum protocols::features::RelevantResiduesMode::T) –> void

type_name(self: pyrosetta.rosetta.protocols.features.ProteinRMSDFeatures) str

C++: protocols::features::ProteinRMSDFeatures::type_name() const –> std::string

write_schema_to_db(self: pyrosetta.rosetta.protocols.features.ProteinRMSDFeatures, db_session: pyrosetta.rosetta.utility.sql_database.session) None

generate the table schemas and write them to the database

C++: protocols::features::ProteinRMSDFeatures::write_schema_to_db(class std::shared_ptr<class utility::sql_database::session>) const –> void

class pyrosetta.rosetta.protocols.features.ProteinRMSDFeaturesCreator

Bases: pyrosetta.rosetta.protocols.features.FeaturesReporterCreator

creator for the ProteinRMSDFeatures class

assign(self: pyrosetta.rosetta.protocols.features.ProteinRMSDFeaturesCreator, : pyrosetta.rosetta.protocols.features.ProteinRMSDFeaturesCreator) pyrosetta.rosetta.protocols.features.ProteinRMSDFeaturesCreator

C++: protocols::features::ProteinRMSDFeaturesCreator::operator=(const class protocols::features::ProteinRMSDFeaturesCreator &) –> class protocols::features::ProteinRMSDFeaturesCreator &

create_features_reporter(self: pyrosetta.rosetta.protocols.features.ProteinRMSDFeaturesCreator) pyrosetta.rosetta.protocols.features.FeaturesReporter

C++: protocols::features::ProteinRMSDFeaturesCreator::create_features_reporter() const –> class std::shared_ptr<class protocols::features::FeaturesReporter>

provide_xml_schema(self: pyrosetta.rosetta.protocols.features.ProteinRMSDFeaturesCreator, xsd: utility::tag::XMLSchemaDefinition) None

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

type_name(self: pyrosetta.rosetta.protocols.features.ProteinRMSDFeaturesCreator) str

C++: protocols::features::ProteinRMSDFeaturesCreator::type_name() const –> std::string

class pyrosetta.rosetta.protocols.features.ProteinRMSDNoSuperpositionFeatures

Bases: pyrosetta.rosetta.protocols.features.FeaturesReporter

assign(self: pyrosetta.rosetta.protocols.features.ProteinRMSDNoSuperpositionFeatures, : pyrosetta.rosetta.protocols.features.ProteinRMSDNoSuperpositionFeatures) pyrosetta.rosetta.protocols.features.ProteinRMSDNoSuperpositionFeatures

C++: protocols::features::ProteinRMSDNoSuperpositionFeatures::operator=(const class protocols::features::ProteinRMSDNoSuperpositionFeatures &) –> class protocols::features::ProteinRMSDNoSuperpositionFeatures &

check_relevant_residues(*args, **kwargs)

Overloaded function.

  1. check_relevant_residues(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, res1: int) -> bool

C++: protocols::features::FeaturesReporter::check_relevant_residues(const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long) const –> bool

  1. check_relevant_residues(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, res1: int, res2: int) -> bool

C++: protocols::features::FeaturesReporter::check_relevant_residues(const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, unsigned long) const –> bool

  1. check_relevant_residues(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, residues: pyrosetta.rosetta.utility.vector1_unsigned_long) -> bool

C++: protocols::features::FeaturesReporter::check_relevant_residues(const class utility::vector1<bool, class std::allocator<bool> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> bool

check_relevant_residues_range(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, res1: int, res2: int) bool

C++: protocols::features::FeaturesReporter::check_relevant_residues_range(const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, unsigned long) const –> bool

static class_name() str

C++: protocols::features::ProteinRMSDNoSuperpositionFeatures::class_name() –> std::string

delete_record(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, : int, : pyrosetta.rosetta.utility.sql_database.session) None

C++: protocols::features::FeaturesReporter::delete_record(unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> void

features_reporter_dependencies(self: pyrosetta.rosetta.protocols.features.ProteinRMSDNoSuperpositionFeatures) pyrosetta.rosetta.utility.vector1_std_string

return the set of features reporters that are required to also already be extracted by the time this one is used.

C++: protocols::features::ProteinRMSDNoSuperpositionFeatures::features_reporter_dependencies() const –> class utility::vector1<std::string, class std::allocator<std::string > >

get_relevant_residues_mode(self: pyrosetta.rosetta.protocols.features.FeaturesReporter) pyrosetta.rosetta.protocols.features.RelevantResiduesMode.T

C++: protocols::features::FeaturesReporter::get_relevant_residues_mode() const –> enum protocols::features::RelevantResiduesMode::T

load_into_pose(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, : pyrosetta.rosetta.utility.sql_database.session, : int, : pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::features::FeaturesReporter::load_into_pose(class std::shared_ptr<class utility::sql_database::session>, unsigned long, class core::pose::Pose &) –> void

parse_my_tag(self: pyrosetta.rosetta.protocols.features.ProteinRMSDNoSuperpositionFeatures, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None

C++: protocols::features::ProteinRMSDNoSuperpositionFeatures::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::features::ProteinRMSDNoSuperpositionFeatures::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

reference_pose(*args, **kwargs)

Overloaded function.

  1. reference_pose(self: pyrosetta.rosetta.protocols.features.ProteinRMSDNoSuperpositionFeatures) -> pyrosetta.rosetta.core.pose.Pose

C++: protocols::features::ProteinRMSDNoSuperpositionFeatures::reference_pose() const –> class std::shared_ptr<const class core::pose::Pose>

  1. reference_pose(self: pyrosetta.rosetta.protocols.features.ProteinRMSDNoSuperpositionFeatures, : pyrosetta.rosetta.core.pose.Pose) -> None

C++: protocols::features::ProteinRMSDNoSuperpositionFeatures::reference_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

report_features(self: pyrosetta.rosetta.protocols.features.ProteinRMSDNoSuperpositionFeatures, pose: pyrosetta.rosetta.core.pose.Pose, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, struct_id: int, db_session: pyrosetta.rosetta.utility.sql_database.session) int

collect all the feature data for the pose

C++: protocols::features::ProteinRMSDNoSuperpositionFeatures::report_features(const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> unsigned long

schema(self: pyrosetta.rosetta.protocols.features.FeaturesReporter) str

return sql statements that sets up the appropriate tables to contain the features. This should be removed once everything has been moved to the schema generator

C++: protocols::features::FeaturesReporter::schema() const –> std::string

set_relevant_residues_mode(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, setting: pyrosetta.rosetta.protocols.features.RelevantResiduesMode.T) None

C++: protocols::features::FeaturesReporter::set_relevant_residues_mode(enum protocols::features::RelevantResiduesMode::T) –> void

type_name(self: pyrosetta.rosetta.protocols.features.ProteinRMSDNoSuperpositionFeatures) str

C++: protocols::features::ProteinRMSDNoSuperpositionFeatures::type_name() const –> std::string

write_schema_to_db(self: pyrosetta.rosetta.protocols.features.ProteinRMSDNoSuperpositionFeatures, db_session: pyrosetta.rosetta.utility.sql_database.session) None

generate the table schemas and write them to the database

C++: protocols::features::ProteinRMSDNoSuperpositionFeatures::write_schema_to_db(class std::shared_ptr<class utility::sql_database::session>) const –> void

class pyrosetta.rosetta.protocols.features.ProteinRMSDNoSuperpositionFeaturesCreator

Bases: pyrosetta.rosetta.protocols.features.FeaturesReporterCreator

creator for the ProteinRMSDNoSuperpositionFeatures class

assign(self: pyrosetta.rosetta.protocols.features.ProteinRMSDNoSuperpositionFeaturesCreator, : pyrosetta.rosetta.protocols.features.ProteinRMSDNoSuperpositionFeaturesCreator) pyrosetta.rosetta.protocols.features.ProteinRMSDNoSuperpositionFeaturesCreator

C++: protocols::features::ProteinRMSDNoSuperpositionFeaturesCreator::operator=(const class protocols::features::ProteinRMSDNoSuperpositionFeaturesCreator &) –> class protocols::features::ProteinRMSDNoSuperpositionFeaturesCreator &

create_features_reporter(self: pyrosetta.rosetta.protocols.features.ProteinRMSDNoSuperpositionFeaturesCreator) pyrosetta.rosetta.protocols.features.FeaturesReporter

C++: protocols::features::ProteinRMSDNoSuperpositionFeaturesCreator::create_features_reporter() const –> class std::shared_ptr<class protocols::features::FeaturesReporter>

provide_xml_schema(self: pyrosetta.rosetta.protocols.features.ProteinRMSDNoSuperpositionFeaturesCreator, xsd: utility::tag::XMLSchemaDefinition) None

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

type_name(self: pyrosetta.rosetta.protocols.features.ProteinRMSDNoSuperpositionFeaturesCreator) str

C++: protocols::features::ProteinRMSDNoSuperpositionFeaturesCreator::type_name() const –> std::string

class pyrosetta.rosetta.protocols.features.ProteinResidueConformationFeatures

Bases: pyrosetta.rosetta.protocols.features.FeaturesReporter

assign(self: pyrosetta.rosetta.protocols.features.ProteinResidueConformationFeatures, : pyrosetta.rosetta.protocols.features.ProteinResidueConformationFeatures) pyrosetta.rosetta.protocols.features.ProteinResidueConformationFeatures

C++: protocols::features::ProteinResidueConformationFeatures::operator=(const class protocols::features::ProteinResidueConformationFeatures &) –> class protocols::features::ProteinResidueConformationFeatures &

check_relevant_residues(*args, **kwargs)

Overloaded function.

  1. check_relevant_residues(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, res1: int) -> bool

C++: protocols::features::FeaturesReporter::check_relevant_residues(const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long) const –> bool

  1. check_relevant_residues(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, res1: int, res2: int) -> bool

C++: protocols::features::FeaturesReporter::check_relevant_residues(const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, unsigned long) const –> bool

  1. check_relevant_residues(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, residues: pyrosetta.rosetta.utility.vector1_unsigned_long) -> bool

C++: protocols::features::FeaturesReporter::check_relevant_residues(const class utility::vector1<bool, class std::allocator<bool> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> bool

check_relevant_residues_range(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, res1: int, res2: int) bool

C++: protocols::features::FeaturesReporter::check_relevant_residues_range(const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, unsigned long) const –> bool

static class_name() str

C++: protocols::features::ProteinResidueConformationFeatures::class_name() –> std::string

delete_record(self: pyrosetta.rosetta.protocols.features.ProteinResidueConformationFeatures, struct_id: int, db_session: pyrosetta.rosetta.utility.sql_database.session) None

C++: protocols::features::ProteinResidueConformationFeatures::delete_record(unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> void

features_reporter_dependencies(self: pyrosetta.rosetta.protocols.features.ProteinResidueConformationFeatures) pyrosetta.rosetta.utility.vector1_std_string

return the set of features reporters that are required to also already be extracted by the time this one is used.

C++: protocols::features::ProteinResidueConformationFeatures::features_reporter_dependencies() const –> class utility::vector1<std::string, class std::allocator<std::string > >

get_relevant_residues_mode(self: pyrosetta.rosetta.protocols.features.FeaturesReporter) pyrosetta.rosetta.protocols.features.RelevantResiduesMode.T

C++: protocols::features::FeaturesReporter::get_relevant_residues_mode() const –> enum protocols::features::RelevantResiduesMode::T

load_conformation(self: pyrosetta.rosetta.protocols.features.ProteinResidueConformationFeatures, db_session: pyrosetta.rosetta.utility.sql_database.session, struct_id: int, pose: pyrosetta.rosetta.core.pose.Pose, ideal: bool) None
  • Is the input structure ideal? If so, load backbone torsions into pose

C++: protocols::features::ProteinResidueConformationFeatures::load_conformation(class std::shared_ptr<class utility::sql_database::session>, unsigned long, class core::pose::Pose &, bool) –> void

load_into_pose(*args, **kwargs)

Overloaded function.

  1. load_into_pose(self: pyrosetta.rosetta.protocols.features.ProteinResidueConformationFeatures, : pyrosetta.rosetta.utility.sql_database.session, : int, : pyrosetta.rosetta.core.pose.Pose) -> None

  2. load_into_pose(self: pyrosetta.rosetta.protocols.features.ProteinResidueConformationFeatures, db_session: pyrosetta.rosetta.utility.sql_database.session, struct_id: int, pose: pyrosetta.rosetta.core.pose.Pose, ideal: bool) -> None

  • Is the input structure ideal?

C++: protocols::features::ProteinResidueConformationFeatures::load_into_pose(class std::shared_ptr<class utility::sql_database::session>, unsigned long, class core::pose::Pose &, bool) –> void

parse_my_tag(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None

C++: protocols::features::FeaturesReporter::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::features::ProteinResidueConformationFeatures::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

report_features(self: pyrosetta.rosetta.protocols.features.ProteinResidueConformationFeatures, pose: pyrosetta.rosetta.core.pose.Pose, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, struct_id: int, db_session: pyrosetta.rosetta.utility.sql_database.session) int

collect all the feature data for the pose

C++: protocols::features::ProteinResidueConformationFeatures::report_features(const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> unsigned long

schema(self: pyrosetta.rosetta.protocols.features.FeaturesReporter) str

return sql statements that sets up the appropriate tables to contain the features. This should be removed once everything has been moved to the schema generator

C++: protocols::features::FeaturesReporter::schema() const –> std::string

set_relevant_residues_mode(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, setting: pyrosetta.rosetta.protocols.features.RelevantResiduesMode.T) None

C++: protocols::features::FeaturesReporter::set_relevant_residues_mode(enum protocols::features::RelevantResiduesMode::T) –> void

type_name(self: pyrosetta.rosetta.protocols.features.ProteinResidueConformationFeatures) str

C++: protocols::features::ProteinResidueConformationFeatures::type_name() const –> std::string

write_schema_to_db(self: pyrosetta.rosetta.protocols.features.ProteinResidueConformationFeatures, db_session: pyrosetta.rosetta.utility.sql_database.session) None

generate the table schemas and write them to the database

C++: protocols::features::ProteinResidueConformationFeatures::write_schema_to_db(class std::shared_ptr<class utility::sql_database::session>) const –> void

class pyrosetta.rosetta.protocols.features.ProteinResidueConformationFeaturesCreator

Bases: pyrosetta.rosetta.protocols.features.FeaturesReporterCreator

creator for the ProteinResidueConformationFeatures class

assign(self: pyrosetta.rosetta.protocols.features.ProteinResidueConformationFeaturesCreator, : pyrosetta.rosetta.protocols.features.ProteinResidueConformationFeaturesCreator) pyrosetta.rosetta.protocols.features.ProteinResidueConformationFeaturesCreator

C++: protocols::features::ProteinResidueConformationFeaturesCreator::operator=(const class protocols::features::ProteinResidueConformationFeaturesCreator &) –> class protocols::features::ProteinResidueConformationFeaturesCreator &

create_features_reporter(self: pyrosetta.rosetta.protocols.features.ProteinResidueConformationFeaturesCreator) pyrosetta.rosetta.protocols.features.FeaturesReporter

C++: protocols::features::ProteinResidueConformationFeaturesCreator::create_features_reporter() const –> class std::shared_ptr<class protocols::features::FeaturesReporter>

provide_xml_schema(self: pyrosetta.rosetta.protocols.features.ProteinResidueConformationFeaturesCreator, xsd: utility::tag::XMLSchemaDefinition) None

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

type_name(self: pyrosetta.rosetta.protocols.features.ProteinResidueConformationFeaturesCreator) str

C++: protocols::features::ProteinResidueConformationFeaturesCreator::type_name() const –> std::string

class pyrosetta.rosetta.protocols.features.ProteinSilentReport

Bases: pyrosetta.rosetta.protocols.features.Report

apply(*args, **kwargs)

Overloaded function.

  1. apply(self: pyrosetta.rosetta.protocols.features.ProteinSilentReport, pose: pyrosetta.rosetta.core.pose.Pose, db_sesion: pyrosetta.rosetta.utility.sql_database.session) -> None

C++: protocols::features::ProteinSilentReport::apply(const class core::pose::Pose &, class std::shared_ptr<class utility::sql_database::session>) –> void

  1. apply(self: pyrosetta.rosetta.protocols.features.ProteinSilentReport, pose: pyrosetta.rosetta.core.pose.Pose, db_sesion: pyrosetta.rosetta.utility.sql_database.session, tag: str) -> None

C++: protocols::features::ProteinSilentReport::apply(const class core::pose::Pose &, class std::shared_ptr<class utility::sql_database::session>, const std::string &) –> void

assign(self: pyrosetta.rosetta.protocols.features.ProteinSilentReport, : pyrosetta.rosetta.protocols.features.ProteinSilentReport) pyrosetta.rosetta.protocols.features.ProteinSilentReport

C++: protocols::features::ProteinSilentReport::operator=(const class protocols::features::ProteinSilentReport &) –> class protocols::features::ProteinSilentReport &

delete_pose(self: pyrosetta.rosetta.protocols.features.ProteinSilentReport, db_session: pyrosetta.rosetta.utility.sql_database.session, struct_id: int) None

C++: protocols::features::ProteinSilentReport::delete_pose(class std::shared_ptr<class utility::sql_database::session>, const unsigned long &) –> void

delete_pose_from_tag(self: pyrosetta.rosetta.protocols.features.ProteinSilentReport, db_session: pyrosetta.rosetta.utility.sql_database.session, tag: str) None

C++: protocols::features::ProteinSilentReport::delete_pose_from_tag(class std::shared_ptr<class utility::sql_database::session>, const std::string &) –> void

get_batch_id(self: pyrosetta.rosetta.protocols.features.ProteinSilentReport) int

C++: protocols::features::ProteinSilentReport::get_batch_id() const –> unsigned long

get_protocol_id(self: pyrosetta.rosetta.protocols.features.ProteinSilentReport) int

C++: protocols::features::ProteinSilentReport::get_protocol_id() const –> unsigned long

initialize(self: pyrosetta.rosetta.protocols.features.ProteinSilentReport, db_session: pyrosetta.rosetta.utility.sql_database.session) None

C++: protocols::features::ProteinSilentReport::initialize(class std::shared_ptr<class utility::sql_database::session>) –> void

is_initialized(self: pyrosetta.rosetta.protocols.features.ProteinSilentReport) bool

C++: protocols::features::ProteinSilentReport::is_initialized() const –> bool

load_pose(*args, **kwargs)

Overloaded function.

  1. load_pose(se