features¶

Bindings for protocols::features namespace

class pyrosetta.rosetta.protocols.features.AtomAtomPairFeatures¶

Bases: 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.

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

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

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: 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: 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.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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: 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_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: 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: 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: 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.

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

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

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

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

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

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

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

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

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_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: 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.

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>

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: 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.

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

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

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

property value¶

class pyrosetta.rosetta.protocols.features.HBondFeatures¶

Bases: 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.

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

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

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

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

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

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

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

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

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

Calculates ddG of binding

add_chain_id(*args, **kwargs)¶

Overloaded function.

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

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.

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

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.

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

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_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.

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

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.

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

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.

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

Outputs details about the Mover, including current settings.

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

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

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

type(*args, **kwargs)¶

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

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: 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: 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.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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>

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(