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
C++: protocols::features::FeaturesReporter::check_relevant_residues(const class utility::vector1<bool, class std::allocator<bool> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> bool
- check_relevant_residues_range(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, res1: int, res2: int) bool ¶
C++: protocols::features::FeaturesReporter::check_relevant_residues_range(const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, unsigned long) const –> bool
- static class_name() str ¶
C++: protocols::features::AtomInResidueAtomInResiduePairFeatures::class_name() –> std::string
- delete_record(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, : int, : pyrosetta.rosetta.utility.sql_database.session) None ¶
C++: protocols::features::FeaturesReporter::delete_record(unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> void
- features_reporter_dependencies(self: pyrosetta.rosetta.protocols.features.AtomInResidueAtomInResiduePairFeatures) pyrosetta.rosetta.utility.vector1_std_string ¶
return the set of features reporters that are required to also already be extracted by the time this one is used.
C++: protocols::features::AtomInResidueAtomInResiduePairFeatures::features_reporter_dependencies() const –> class utility::vector1<std::string, class std::allocator<std::string > >
- get_relevant_residues_mode(self: pyrosetta.rosetta.protocols.features.FeaturesReporter) pyrosetta.rosetta.protocols.features.RelevantResiduesMode.T ¶
C++: protocols::features::FeaturesReporter::get_relevant_residues_mode() const –> enum protocols::features::RelevantResiduesMode::T
- load_into_pose(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, : pyrosetta.rosetta.utility.sql_database.session, : int, : pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::features::FeaturesReporter::load_into_pose(class std::shared_ptr<class utility::sql_database::session>, unsigned long, class core::pose::Pose &) –> void
- parse_my_tag(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None ¶
C++: protocols::features::FeaturesReporter::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None ¶
C++: protocols::features::AtomInResidueAtomInResiduePairFeatures::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void
- report_atom_pairs(self: pyrosetta.rosetta.protocols.features.AtomInResidueAtomInResiduePairFeatures, pose: pyrosetta.rosetta.core.pose.Pose, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, struct_id: int, db_session: pyrosetta.rosetta.utility.sql_database.session) None ¶
Similar to radial density distributions defined in Lu H, Skolnick J. A distance-dependent atomic knowledge-based potential for improved protein structure selection. Proteins. 2001;44(3):223-32. Available at: http://www.ncbi.nlm.nih.gov/pubmed/11455595.
C++: protocols::features::AtomInResidueAtomInResiduePairFeatures::report_atom_pairs(const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> void
- report_features(self: pyrosetta.rosetta.protocols.features.AtomInResidueAtomInResiduePairFeatures, pose: pyrosetta.rosetta.core.pose.Pose, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, struct_id: int, db_session: pyrosetta.rosetta.utility.sql_database.session) int ¶
collect all the feature data for the pose
C++: protocols::features::AtomInResidueAtomInResiduePairFeatures::report_features(const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> unsigned long
- schema(self: pyrosetta.rosetta.protocols.features.FeaturesReporter) str ¶
return sql statements that sets up the appropriate tables to contain the features. This should be removed once everything has been moved to the schema generator
C++: protocols::features::FeaturesReporter::schema() const –> std::string
- set_relevant_residues_mode(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, setting: pyrosetta.rosetta.protocols.features.RelevantResiduesMode.T) None ¶
C++: protocols::features::FeaturesReporter::set_relevant_residues_mode(enum protocols::features::RelevantResiduesMode::T) –> void
- type_name(self: pyrosetta.rosetta.protocols.features.AtomInResidueAtomInResiduePairFeatures) str ¶
C++: protocols::features::AtomInResidueAtomInResiduePairFeatures::type_name() const –> std::string
- write_schema_to_db(self: pyrosetta.rosetta.protocols.features.AtomInResidueAtomInResiduePairFeatures, db_session: pyrosetta.rosetta.utility.sql_database.session) None ¶
generate the table schemas and write them to the database
C++: protocols::features::AtomInResidueAtomInResiduePairFeatures::write_schema_to_db(class std::shared_ptr<class utility::sql_database::session>) const –> void
- class pyrosetta.rosetta.protocols.features.AtomInResidueAtomInResiduePairFeaturesCreator¶
Bases:
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
C++: protocols::features::FeaturesReporter::check_relevant_residues(const class utility::vector1<bool, class std::allocator<bool> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> bool
- check_relevant_residues_range(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, res1: int, res2: int) bool ¶
C++: protocols::features::FeaturesReporter::check_relevant_residues_range(const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, unsigned long) const –> bool
- static class_name() str ¶
C++: protocols::features::AtomTypesFeatures::class_name() –> std::string
- delete_record(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, : int, : pyrosetta.rosetta.utility.sql_database.session) None ¶
C++: protocols::features::FeaturesReporter::delete_record(unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> void
- features_reporter_dependencies(self: pyrosetta.rosetta.protocols.features.AtomTypesFeatures) pyrosetta.rosetta.utility.vector1_std_string ¶
return the set of features reporters that are required to also already be extracted by the time this one is used.
C++: protocols::features::AtomTypesFeatures::features_reporter_dependencies() const –> class utility::vector1<std::string, class std::allocator<std::string > >
- get_relevant_residues_mode(self: pyrosetta.rosetta.protocols.features.FeaturesReporter) pyrosetta.rosetta.protocols.features.RelevantResiduesMode.T ¶
C++: protocols::features::FeaturesReporter::get_relevant_residues_mode() const –> enum protocols::features::RelevantResiduesMode::T
- load_into_pose(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, : pyrosetta.rosetta.utility.sql_database.session, : int, : pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::features::FeaturesReporter::load_into_pose(class std::shared_ptr<class utility::sql_database::session>, unsigned long, class core::pose::Pose &) –> void
- parse_my_tag(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None ¶
C++: protocols::features::FeaturesReporter::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None ¶
C++: protocols::features::AtomTypesFeatures::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void
- report_features(self: pyrosetta.rosetta.protocols.features.AtomTypesFeatures, pose: pyrosetta.rosetta.core.pose.Pose, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, struct_id: int, db_session: pyrosetta.rosetta.utility.sql_database.session) int ¶
collect all the feature data for the pose
C++: protocols::features::AtomTypesFeatures::report_features(const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> unsigned long
- schema(self: pyrosetta.rosetta.protocols.features.FeaturesReporter) str ¶
return sql statements that sets up the appropriate tables to contain the features. This should be removed once everything has been moved to the schema generator
C++: protocols::features::FeaturesReporter::schema() const –> std::string
- set_relevant_residues_mode(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, setting: pyrosetta.rosetta.protocols.features.RelevantResiduesMode.T) None ¶
C++: protocols::features::FeaturesReporter::set_relevant_residues_mode(enum protocols::features::RelevantResiduesMode::T) –> void
- type_name(self: pyrosetta.rosetta.protocols.features.AtomTypesFeatures) str ¶
C++: protocols::features::AtomTypesFeatures::type_name() const –> std::string
- write_schema_to_db(self: pyrosetta.rosetta.protocols.features.AtomTypesFeatures, db_session: pyrosetta.rosetta.utility.sql_database.session) None ¶
generate the table schemas and write them to the database
C++: protocols::features::AtomTypesFeatures::write_schema_to_db(class std::shared_ptr<class utility::sql_database::session>) const –> void
- class pyrosetta.rosetta.protocols.features.AtomTypesFeaturesCreator¶
Bases:
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
C++: protocols::features::FeaturesReporter::check_relevant_residues(const class utility::vector1<bool, class std::allocator<bool> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> bool
- check_relevant_residues_range(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, res1: int, res2: int) bool ¶
C++: protocols::features::FeaturesReporter::check_relevant_residues_range(const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, unsigned long) const –> bool
- static class_name() str ¶
C++: protocols::features::BetaTurnDetectionFeatures::class_name() –> std::string
- delete_record(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, : int, : pyrosetta.rosetta.utility.sql_database.session) None ¶
C++: protocols::features::FeaturesReporter::delete_record(unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> void
- features_reporter_dependencies(self: pyrosetta.rosetta.protocols.features.BetaTurnDetectionFeatures) pyrosetta.rosetta.utility.vector1_std_string ¶
return the set of features reporters that are required to also already be extracted by the time this one is used.
C++: protocols::features::BetaTurnDetectionFeatures::features_reporter_dependencies() const –> class utility::vector1<std::string, class std::allocator<std::string > >
- get_relevant_residues_mode(self: pyrosetta.rosetta.protocols.features.FeaturesReporter) pyrosetta.rosetta.protocols.features.RelevantResiduesMode.T ¶
C++: protocols::features::FeaturesReporter::get_relevant_residues_mode() const –> enum protocols::features::RelevantResiduesMode::T
- load_into_pose(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, : pyrosetta.rosetta.utility.sql_database.session, : int, : pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::features::FeaturesReporter::load_into_pose(class std::shared_ptr<class utility::sql_database::session>, unsigned long, class core::pose::Pose &) –> void
- parse_my_tag(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None ¶
C++: protocols::features::FeaturesReporter::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None ¶
C++: protocols::features::BetaTurnDetectionFeatures::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void
- report_features(self: pyrosetta.rosetta.protocols.features.BetaTurnDetectionFeatures, pose: pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.utility.vector1_bool, struct_id: int, db_session: pyrosetta.rosetta.utility.sql_database.session) int ¶
collect all the feature data for the pose
C++: protocols::features::BetaTurnDetectionFeatures::report_features(const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> unsigned long
- schema(self: pyrosetta.rosetta.protocols.features.FeaturesReporter) str ¶
return sql statements that sets up the appropriate tables to contain the features. This should be removed once everything has been moved to the schema generator
C++: protocols::features::FeaturesReporter::schema() const –> std::string
- set_relevant_residues_mode(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, setting: pyrosetta.rosetta.protocols.features.RelevantResiduesMode.T) None ¶
C++: protocols::features::FeaturesReporter::set_relevant_residues_mode(enum protocols::features::RelevantResiduesMode::T) –> void
- type_name(self: pyrosetta.rosetta.protocols.features.BetaTurnDetectionFeatures) str ¶
C++: protocols::features::BetaTurnDetectionFeatures::type_name() const –> std::string
- write_schema_to_db(self: pyrosetta.rosetta.protocols.features.BetaTurnDetectionFeatures, db_session: pyrosetta.rosetta.utility.sql_database.session) None ¶
generate the table schemas and write them to the database
C++: protocols::features::BetaTurnDetectionFeatures::write_schema_to_db(class std::shared_ptr<class utility::sql_database::session>) const –> void
- class pyrosetta.rosetta.protocols.features.BetaTurnDetectionFeaturesCreator¶
Bases:
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
C++: protocols::features::FeaturesReporter::check_relevant_residues(const class utility::vector1<bool, class std::allocator<bool> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> bool
- check_relevant_residues_range(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, res1: int, res2: int) bool ¶
C++: protocols::features::FeaturesReporter::check_relevant_residues_range(const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, unsigned long) const –> bool
- static class_name() str ¶
C++: protocols::features::ChargeChargeFeatures::class_name() –> std::string
- delete_record(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, : int, : pyrosetta.rosetta.utility.sql_database.session) None ¶
C++: protocols::features::FeaturesReporter::delete_record(unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> void
- distance_cutoff(*args, **kwargs)¶
Overloaded function.
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
C++: protocols::features::FeaturesReporter::check_relevant_residues(const class utility::vector1<bool, class std::allocator<bool> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> bool
- check_relevant_residues_range(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, res1: int, res2: int) bool ¶
C++: protocols::features::FeaturesReporter::check_relevant_residues_range(const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, unsigned long) const –> bool
- static class_name() str ¶
C++: protocols::features::DdGFeatures::class_name() –> std::string
- delete_record(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, : int, : pyrosetta.rosetta.utility.sql_database.session) None ¶
C++: protocols::features::FeaturesReporter::delete_record(unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> void
- features_reporter_dependencies(self: pyrosetta.rosetta.protocols.features.DdGFeatures) pyrosetta.rosetta.utility.vector1_std_string ¶
return the set of features reporters that are required to also already be extracted by the time this one is used.
C++: protocols::features::DdGFeatures::features_reporter_dependencies() const –> class utility::vector1<std::string, class std::allocator<std::string > >
- get_relevant_residues_mode(self: pyrosetta.rosetta.protocols.features.FeaturesReporter) pyrosetta.rosetta.protocols.features.RelevantResiduesMode.T ¶
C++: protocols::features::FeaturesReporter::get_relevant_residues_mode() const –> enum protocols::features::RelevantResiduesMode::T
- load_into_pose(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, : pyrosetta.rosetta.utility.sql_database.session, : int, : pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::features::FeaturesReporter::load_into_pose(class std::shared_ptr<class utility::sql_database::session>, unsigned long, class core::pose::Pose &) –> void
- parse_my_tag(self: pyrosetta.rosetta.protocols.features.DdGFeatures, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None ¶
C++: protocols::features::DdGFeatures::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None ¶
C++: protocols::features::DdGFeatures::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void
- report_features(self: pyrosetta.rosetta.protocols.features.DdGFeatures, pose: pyrosetta.rosetta.core.pose.Pose, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, struct_id: int, db_session: pyrosetta.rosetta.utility.sql_database.session) int ¶
collect all the feature data for the pose
C++: protocols::features::DdGFeatures::report_features(const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> unsigned long
- schema(self: pyrosetta.rosetta.protocols.features.FeaturesReporter) str ¶
return sql statements that sets up the appropriate tables to contain the features. This should be removed once everything has been moved to the schema generator
C++: protocols::features::FeaturesReporter::schema() const –> std::string
- set_relevant_residues_mode(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, setting: pyrosetta.rosetta.protocols.features.RelevantResiduesMode.T) None ¶
C++: protocols::features::FeaturesReporter::set_relevant_residues_mode(enum protocols::features::RelevantResiduesMode::T) –> void
- type_name(self: pyrosetta.rosetta.protocols.features.DdGFeatures) str ¶
C++: protocols::features::DdGFeatures::type_name() const –> std::string
- write_ddG_table_schema(self: pyrosetta.rosetta.protocols.features.DdGFeatures, db_session: pyrosetta.rosetta.utility.sql_database.session) None ¶
C++: protocols::features::DdGFeatures::write_ddG_table_schema(class std::shared_ptr<class utility::sql_database::session>) const –> void
- write_schema_to_db(self: pyrosetta.rosetta.protocols.features.DdGFeatures, db_session: pyrosetta.rosetta.utility.sql_database.session) None ¶
generate the table schemas and write them to the database
C++: protocols::features::DdGFeatures::write_schema_to_db(class std::shared_ptr<class utility::sql_database::session>) const –> void
- class pyrosetta.rosetta.protocols.features.DdGFeaturesCreator¶
Bases:
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
C++: protocols::features::FeaturesReporter::check_relevant_residues(const class utility::vector1<bool, class std::allocator<bool> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> bool
- check_relevant_residues_range(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, res1: int, res2: int) bool ¶
C++: protocols::features::FeaturesReporter::check_relevant_residues_range(const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, unsigned long) const –> bool
- delete_record(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, : int, : pyrosetta.rosetta.utility.sql_database.session) None ¶
C++: protocols::features::FeaturesReporter::delete_record(unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> void
- features_reporter_dependencies(self: pyrosetta.rosetta.protocols.features.FeaturesReporter) pyrosetta.rosetta.utility.vector1_std_string ¶
return the set of features reporters that are required to also already be extracted by the time this one is used.
C++: protocols::features::FeaturesReporter::features_reporter_dependencies() const –> class utility::vector1<std::string, class std::allocator<std::string > >
- get_relevant_residues_mode(self: pyrosetta.rosetta.protocols.features.FeaturesReporter) pyrosetta.rosetta.protocols.features.RelevantResiduesMode.T ¶
C++: protocols::features::FeaturesReporter::get_relevant_residues_mode() const –> enum protocols::features::RelevantResiduesMode::T
- load_into_pose(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, : pyrosetta.rosetta.utility.sql_database.session, : int, : pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::features::FeaturesReporter::load_into_pose(class std::shared_ptr<class utility::sql_database::session>, unsigned long, class core::pose::Pose &) –> void
- parse_my_tag(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None ¶
C++: protocols::features::FeaturesReporter::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- report_features(*args, **kwargs)¶
Overloaded function.
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
C++: protocols::features::FeaturesReporter::check_relevant_residues(const class utility::vector1<bool, class std::allocator<bool> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> bool
- check_relevant_residues_range(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, res1: int, res2: int) bool ¶
C++: protocols::features::FeaturesReporter::check_relevant_residues_range(const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, unsigned long) const –> bool
- static class_name() str ¶
C++: protocols::features::GeometricSolvationFeatures::class_name() –> std::string
- delete_record(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, : int, : pyrosetta.rosetta.utility.sql_database.session) None ¶
C++: protocols::features::FeaturesReporter::delete_record(unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> void
- features_reporter_dependencies(self: pyrosetta.rosetta.protocols.features.GeometricSolvationFeatures) pyrosetta.rosetta.utility.vector1_std_string ¶
return the set of features reporters that are required to also already be extracted by the time this one is used.
C++: protocols::features::GeometricSolvationFeatures::features_reporter_dependencies() const –> class utility::vector1<std::string, class std::allocator<std::string > >
- get_relevant_residues_mode(self: pyrosetta.rosetta.protocols.features.FeaturesReporter) pyrosetta.rosetta.protocols.features.RelevantResiduesMode.T ¶
C++: protocols::features::FeaturesReporter::get_relevant_residues_mode() const –> enum protocols::features::RelevantResiduesMode::T
- load_into_pose(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, : pyrosetta.rosetta.utility.sql_database.session, : int, : pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::features::FeaturesReporter::load_into_pose(class std::shared_ptr<class utility::sql_database::session>, unsigned long, class core::pose::Pose &) –> void
- parse_my_tag(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None ¶
C++: protocols::features::FeaturesReporter::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None ¶
C++: protocols::features::GeometricSolvationFeatures::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void
- report_features(self: pyrosetta.rosetta.protocols.features.GeometricSolvationFeatures, pose: pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.utility.vector1_bool, struct_id: int, db_session: pyrosetta.rosetta.utility.sql_database.session) int ¶
collect all the feature data for the pose
C++: protocols::features::GeometricSolvationFeatures::report_features(const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> unsigned long
- schema(self: pyrosetta.rosetta.protocols.features.FeaturesReporter) str ¶
return sql statements that sets up the appropriate tables to contain the features. This should be removed once everything has been moved to the schema generator
C++: protocols::features::FeaturesReporter::schema() const –> std::string
- set_relevant_residues_mode(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, setting: pyrosetta.rosetta.protocols.features.RelevantResiduesMode.T) None ¶
C++: protocols::features::FeaturesReporter::set_relevant_residues_mode(enum protocols::features::RelevantResiduesMode::T) –> void
- type_name(self: pyrosetta.rosetta.protocols.features.GeometricSolvationFeatures) str ¶
C++: protocols::features::GeometricSolvationFeatures::type_name() const –> std::string
- write_schema_to_db(self: pyrosetta.rosetta.protocols.features.GeometricSolvationFeatures, db_session: pyrosetta.rosetta.utility.sql_database.session) None ¶
generate the table schemas and write them to the database
C++: protocols::features::GeometricSolvationFeatures::write_schema_to_db(class std::shared_ptr<class utility::sql_database::session>) const –> void
- class pyrosetta.rosetta.protocols.features.GeometricSolvationFeaturesCreator¶
Bases:
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
C++: protocols::features::FeaturesReporter::check_relevant_residues(const class utility::vector1<bool, class std::allocator<bool> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> bool
- check_relevant_residues_range(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, res1: int, res2: int) bool ¶
C++: protocols::features::FeaturesReporter::check_relevant_residues_range(const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, unsigned long) const –> bool
- static class_name() str ¶
C++: protocols::features::HBondFeatures::class_name() –> std::string
- delete_record(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, : int, : pyrosetta.rosetta.utility.sql_database.session) None ¶
C++: protocols::features::FeaturesReporter::delete_record(unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> void
- features_reporter_dependencies(self: pyrosetta.rosetta.protocols.features.HBondFeatures) pyrosetta.rosetta.utility.vector1_std_string ¶
return the set of features reporters that are required to also already be extracted by the time this one is used.
C++: protocols::features::HBondFeatures::features_reporter_dependencies() const –> class utility::vector1<std::string, class std::allocator<std::string > >
- get_relevant_residues_mode(self: pyrosetta.rosetta.protocols.features.FeaturesReporter) pyrosetta.rosetta.protocols.features.RelevantResiduesMode.T ¶
C++: protocols::features::FeaturesReporter::get_relevant_residues_mode() const –> enum protocols::features::RelevantResiduesMode::T
- insert_hbond_dehydron_row(self: pyrosetta.rosetta.protocols.features.HBondFeatures, pose: pyrosetta.rosetta.core.pose.Pose, hbond: pyrosetta.rosetta.core.scoring.hbonds.HBond, struct_id: int, hbond_id: int, db_session: pyrosetta.rosetta.utility.sql_database.session) None ¶
C++: protocols::features::HBondFeatures::insert_hbond_dehydron_row(const class core::pose::Pose &, const class core::scoring::hbonds::HBond &, unsigned long, unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> void
- insert_hbond_geom_coords(self: pyrosetta.rosetta.protocols.features.HBondFeatures, pose: pyrosetta.rosetta.core.pose.Pose, hbond_options: pyrosetta.rosetta.core.scoring.hbonds.HBondOptions, hbond: pyrosetta.rosetta.core.scoring.hbonds.HBond, struct_id: int, hbond_id: int, db_session: pyrosetta.rosetta.utility.sql_database.session) None ¶
C++: protocols::features::HBondFeatures::insert_hbond_geom_coords(const class core::pose::Pose &, const class core::scoring::hbonds::HBondOptions &, const class core::scoring::hbonds::HBond &, unsigned long, unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> void
- insert_hbond_lennard_jones_row(self: pyrosetta.rosetta.protocols.features.HBondFeatures, pose: pyrosetta.rosetta.core.pose.Pose, hbond: pyrosetta.rosetta.core.scoring.hbonds.HBond, struct_id: int, hbond_id: int, db_session: pyrosetta.rosetta.utility.sql_database.session) None ¶
C++: protocols::features::HBondFeatures::insert_hbond_lennard_jones_row(const class core::pose::Pose &, const class core::scoring::hbonds::HBond &, unsigned long, unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> void
- insert_site_atoms_row(self: pyrosetta.rosetta.protocols.features.HBondFeatures, pose: pyrosetta.rosetta.core.pose.Pose, resNum: int, atmNum: int, struct_id: int, site_id: int, db_session: pyrosetta.rosetta.utility.sql_database.session) None ¶
C++: protocols::features::HBondFeatures::insert_site_atoms_row(const class core::pose::Pose &, unsigned long, unsigned long, unsigned long, unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> void
- insert_site_pdb_row(self: pyrosetta.rosetta.protocols.features.HBondFeatures, pose: pyrosetta.rosetta.core.pose.Pose, resNum: int, atmNum: int, heavy_atmNum: int, struct_id: int, site_id: int, db_session: pyrosetta.rosetta.utility.sql_database.session) None ¶
C++: protocols::features::HBondFeatures::insert_site_pdb_row(const class core::pose::Pose &, unsigned long, unsigned long, unsigned long, unsigned long, unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> void
- insert_site_row(self: pyrosetta.rosetta.protocols.features.HBondFeatures, pose: pyrosetta.rosetta.core.pose.Pose, struct_id: int, site_id: int, resNum: int, atmNum: int, is_donor: bool, db_session: pyrosetta.rosetta.utility.sql_database.session) None ¶
C++: protocols::features::HBondFeatures::insert_site_row(const class core::pose::Pose &, unsigned long, unsigned long, unsigned long, unsigned long, bool, class std::shared_ptr<class utility::sql_database::session>) –> void
- load_into_pose(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, : pyrosetta.rosetta.utility.sql_database.session, : int, : pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::features::FeaturesReporter::load_into_pose(class std::shared_ptr<class utility::sql_database::session>, unsigned long, class core::pose::Pose &) –> void
- parse_my_tag(self: pyrosetta.rosetta.protocols.features.HBondFeatures, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None ¶
C++: protocols::features::HBondFeatures::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None ¶
C++: protocols::features::HBondFeatures::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void
- report_features(self: pyrosetta.rosetta.protocols.features.HBondFeatures, pose: pyrosetta.rosetta.core.pose.Pose, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, struct_id: int, db_session: pyrosetta.rosetta.utility.sql_database.session) int ¶
collect all the feature data for the pose
C++: protocols::features::HBondFeatures::report_features(const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> unsigned long
- schema(self: pyrosetta.rosetta.protocols.features.FeaturesReporter) str ¶
return sql statements that sets up the appropriate tables to contain the features. This should be removed once everything has been moved to the schema generator
C++: protocols::features::FeaturesReporter::schema() const –> std::string
- set_relevant_residues_mode(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, setting: pyrosetta.rosetta.protocols.features.RelevantResiduesMode.T) None ¶
C++: protocols::features::FeaturesReporter::set_relevant_residues_mode(enum protocols::features::RelevantResiduesMode::T) –> void
- type_name(self: pyrosetta.rosetta.protocols.features.HBondFeatures) str ¶
C++: protocols::features::HBondFeatures::type_name() const –> std::string
- write_schema_to_db(self: pyrosetta.rosetta.protocols.features.HBondFeatures, db_session: pyrosetta.rosetta.utility.sql_database.session) None ¶
generate the table schemas and write them to the database
C++: protocols::features::HBondFeatures::write_schema_to_db(class std::shared_ptr<class utility::sql_database::session>) const –> void
- class pyrosetta.rosetta.protocols.features.HBondFeaturesCreator¶
Bases:
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
C++: protocols::features::FeaturesReporter::check_relevant_residues(const class utility::vector1<bool, class std::allocator<bool> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> bool
- check_relevant_residues_range(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, res1: int, res2: int) bool ¶
C++: protocols::features::FeaturesReporter::check_relevant_residues_range(const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, unsigned long) const –> bool
- static class_name() str ¶
C++: protocols::features::HBondParameterFeatures::class_name() –> std::string
- delete_record(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, : int, : pyrosetta.rosetta.utility.sql_database.session) None ¶
C++: protocols::features::FeaturesReporter::delete_record(unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> void
- features_reporter_dependencies(self: pyrosetta.rosetta.protocols.features.HBondParameterFeatures) pyrosetta.rosetta.utility.vector1_std_string ¶
return the set of features reporters that are required to also already be extracted by the time this one is used.
C++: protocols::features::HBondParameterFeatures::features_reporter_dependencies() const –> class utility::vector1<std::string, class std::allocator<std::string > >
- get_relevant_residues_mode(self: pyrosetta.rosetta.protocols.features.FeaturesReporter) pyrosetta.rosetta.protocols.features.RelevantResiduesMode.T ¶
C++: protocols::features::FeaturesReporter::get_relevant_residues_mode() const –> enum protocols::features::RelevantResiduesMode::T
- load_into_pose(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, : pyrosetta.rosetta.utility.sql_database.session, : int, : pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::features::FeaturesReporter::load_into_pose(class std::shared_ptr<class utility::sql_database::session>, unsigned long, class core::pose::Pose &) –> void
- parse_my_tag(self: pyrosetta.rosetta.protocols.features.HBondParameterFeatures, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None ¶
C++: protocols::features::HBondParameterFeatures::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None ¶
C++: protocols::features::HBondParameterFeatures::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void
- report_features(self: pyrosetta.rosetta.protocols.features.HBondParameterFeatures, pose: pyrosetta.rosetta.core.pose.Pose, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, struct_id: int, db_session: pyrosetta.rosetta.utility.sql_database.session) int ¶
collect all the feature data for the pose
C++: protocols::features::HBondParameterFeatures::report_features(const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> unsigned long
- schema(self: pyrosetta.rosetta.protocols.features.FeaturesReporter) str ¶
return sql statements that sets up the appropriate tables to contain the features. This should be removed once everything has been moved to the schema generator
C++: protocols::features::FeaturesReporter::schema() const –> std::string
- set_relevant_residues_mode(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, setting: pyrosetta.rosetta.protocols.features.RelevantResiduesMode.T) None ¶
C++: protocols::features::FeaturesReporter::set_relevant_residues_mode(enum protocols::features::RelevantResiduesMode::T) –> void
- type_name(self: pyrosetta.rosetta.protocols.features.HBondParameterFeatures) str ¶
C++: protocols::features::HBondParameterFeatures::type_name() const –> std::string
- write_schema_to_db(self: pyrosetta.rosetta.protocols.features.HBondParameterFeatures, db_session: pyrosetta.rosetta.utility.sql_database.session) None ¶
generate the table schemas and write them to the database
C++: protocols::features::HBondParameterFeatures::write_schema_to_db(class std::shared_ptr<class utility::sql_database::session>) const –> void
- class pyrosetta.rosetta.protocols.features.HBondParameterFeaturesCreator¶
Bases:
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
C++: protocols::features::FeaturesReporter::check_relevant_residues(const class utility::vector1<bool, class std::allocator<bool> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> bool
- check_relevant_residues_range(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, res1: int, res2: int) bool ¶
C++: protocols::features::FeaturesReporter::check_relevant_residues_range(const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, unsigned long) const –> bool
- static class_name() str ¶
C++: protocols::features::HelixCapFeatures::class_name() –> std::string
- delete_record(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, : int, : pyrosetta.rosetta.utility.sql_database.session) None ¶
C++: protocols::features::FeaturesReporter::delete_record(unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> void
- features_reporter_dependencies(self: pyrosetta.rosetta.protocols.features.HelixCapFeatures) pyrosetta.rosetta.utility.vector1_std_string ¶
return the set of features reporters that are required to also already be extracted by the time this one is used.
C++: protocols::features::HelixCapFeatures::features_reporter_dependencies() const –> class utility::vector1<std::string, class std::allocator<std::string > >
- get_relevant_residues_mode(self: pyrosetta.rosetta.protocols.features.FeaturesReporter) pyrosetta.rosetta.protocols.features.RelevantResiduesMode.T ¶
C++: protocols::features::FeaturesReporter::get_relevant_residues_mode() const –> enum protocols::features::RelevantResiduesMode::T
- is_loop(self: pyrosetta.rosetta.protocols.features.HelixCapFeatures, dssp_code: str) bool ¶
C++: protocols::features::HelixCapFeatures::is_loop(std::string) –> bool
- load_into_pose(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, : pyrosetta.rosetta.utility.sql_database.session, : int, : pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::features::FeaturesReporter::load_into_pose(class std::shared_ptr<class utility::sql_database::session>, unsigned long, class core::pose::Pose &) –> void
- parse_my_tag(self: pyrosetta.rosetta.protocols.features.HelixCapFeatures, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None ¶
C++: protocols::features::HelixCapFeatures::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None ¶
C++: protocols::features::HelixCapFeatures::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void
- report_features(self: pyrosetta.rosetta.protocols.features.HelixCapFeatures, pose: pyrosetta.rosetta.core.pose.Pose, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, struct_id: int, db_session: pyrosetta.rosetta.utility.sql_database.session) int ¶
collect all the feature data for the pose
C++: protocols::features::HelixCapFeatures::report_features(const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> unsigned long
- schema(self: pyrosetta.rosetta.protocols.features.FeaturesReporter) str ¶
return sql statements that sets up the appropriate tables to contain the features. This should be removed once everything has been moved to the schema generator
C++: protocols::features::FeaturesReporter::schema() const –> std::string
- set_relevant_residues_mode(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, setting: pyrosetta.rosetta.protocols.features.RelevantResiduesMode.T) None ¶
C++: protocols::features::FeaturesReporter::set_relevant_residues_mode(enum protocols::features::RelevantResiduesMode::T) –> void
- type_name(self: pyrosetta.rosetta.protocols.features.HelixCapFeatures) str ¶
C++: protocols::features::HelixCapFeatures::type_name() const –> std::string
- write_schema_to_db(self: pyrosetta.rosetta.protocols.features.HelixCapFeatures, db_session: pyrosetta.rosetta.utility.sql_database.session) None ¶
generate the table schemas and write them to the database
C++: protocols::features::HelixCapFeatures::write_schema_to_db(class std::shared_ptr<class utility::sql_database::session>) const –> void
- class pyrosetta.rosetta.protocols.features.HelixCapFeaturesCreator¶
Bases:
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
- 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
C++: protocols::features::FeaturesReporter::check_relevant_residues(const class utility::vector1<bool, class std::allocator<bool> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> bool
- check_relevant_residues_range(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, res1: int, res2: int) bool ¶
C++: protocols::features::FeaturesReporter::check_relevant_residues_range(const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, unsigned long) const –> bool
- static class_name() str ¶
C++: protocols::features::InterfaceFeatures::class_name() –> std::string
- delete_record(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, : int, : pyrosetta.rosetta.utility.sql_database.session) None ¶
C++: protocols::features::FeaturesReporter::delete_record(unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> void
- features_reporter_dependencies(self: pyrosetta.rosetta.protocols.features.InterfaceFeatures) pyrosetta.rosetta.utility.vector1_std_string ¶
return the set of features reporters that are required to also already be extracted by the time this one is used.
C++: protocols::features::InterfaceFeatures::features_reporter_dependencies() const –> class utility::vector1<std::string, class std::allocator<std::string > >
- get_relevant_residues_mode(self: pyrosetta.rosetta.protocols.features.FeaturesReporter) pyrosetta.rosetta.protocols.features.RelevantResiduesMode.T ¶
C++: protocols::features::FeaturesReporter::get_relevant_residues_mode() const –> enum protocols::features::RelevantResiduesMode::T
- load_into_pose(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, : pyrosetta.rosetta.utility.sql_database.session, : int, : pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::features::FeaturesReporter::load_into_pose(class std::shared_ptr<class utility::sql_database::session>, unsigned long, class core::pose::Pose &) –> void
- make_interface_combos(self: pyrosetta.rosetta.protocols.features.InterfaceFeatures, pose: pyrosetta.rosetta.core.pose.Pose, interfaces: pyrosetta.rosetta.utility.vector1_std_string) None ¶
Gets all possible interface combinations of a given pose.
C++: protocols::features::InterfaceFeatures::make_interface_combos(const class core::pose::Pose &, class utility::vector1<std::string, class std::allocator<std::string > > &) –> void
- parse_my_tag(self: pyrosetta.rosetta.protocols.features.InterfaceFeatures, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None ¶
C++: protocols::features::InterfaceFeatures::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None ¶
C++: protocols::features::InterfaceFeatures::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void
- report_all_interface_features(self: pyrosetta.rosetta.protocols.features.InterfaceFeatures, pose: pyrosetta.rosetta.core.pose.Pose, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, struct_id: int, db_session: pyrosetta.rosetta.utility.sql_database.session, interface: str, db_interface: str) None ¶
Report all features. Called by report_features. Easy interface for subclassing specific interfaces.
interface is the interface analyzed, db_interface is the name that is actually inserted into the database Usually this is the same, but useful when dealing with different chain ids but same interface type. db_interface should have sides as well (L_H))
C++: protocols::features::InterfaceFeatures::report_all_interface_features(const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, class std::shared_ptr<class utility::sql_database::session>, const std::string &, const std::string &) –> void
- report_features(self: pyrosetta.rosetta.protocols.features.InterfaceFeatures, pose: pyrosetta.rosetta.core.pose.Pose, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, struct_id: int, db_session: pyrosetta.rosetta.utility.sql_database.session) int ¶
collect all the feature data for the pose
C++: protocols::features::InterfaceFeatures::report_features(const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> unsigned long
- report_interface_features(self: pyrosetta.rosetta.protocols.features.InterfaceFeatures, pose: pyrosetta.rosetta.core.pose.Pose, struct_id: int, db_session: pyrosetta.rosetta.utility.sql_database.session, chains_side1: str, chains_side2: str) None ¶
Add interfaces table data to table
C++: protocols::features::InterfaceFeatures::report_interface_features(const class core::pose::Pose &, unsigned long, class std::shared_ptr<class utility::sql_database::session>, const std::string &, const std::string &) const –> void
- report_interface_residue_features(self: pyrosetta.rosetta.protocols.features.InterfaceFeatures, pose: pyrosetta.rosetta.core.pose.Pose, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, struct_id: int, db_session: pyrosetta.rosetta.utility.sql_database.session, chains_side1: str, chains_side2: str) None ¶
Add interface_residues data to table
C++: protocols::features::InterfaceFeatures::report_interface_residue_features(const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, class std::shared_ptr<class utility::sql_database::session>, const std::string &, const std::string &) const –> void
- report_interface_side_features(self: pyrosetta.rosetta.protocols.features.InterfaceFeatures, pose: pyrosetta.rosetta.core.pose.Pose, struct_id: int, db_session: pyrosetta.rosetta.utility.sql_database.session, chains_side1: str, chains_side2: str, region: pyrosetta.rosetta.protocols.analysis.InterfaceRegion, region_string: str) None ¶
Add interface_sides table data to table
C++: protocols::features::InterfaceFeatures::report_interface_side_features(const class core::pose::Pose &, unsigned long, class std::shared_ptr<class utility::sql_database::session>, const std::string &, const std::string &, enum protocols::analysis::InterfaceRegion, const std::string &) const –> void
- schema(self: pyrosetta.rosetta.protocols.features.FeaturesReporter) str ¶
return sql statements that sets up the appropriate tables to contain the features. This should be removed once everything has been moved to the schema generator
C++: protocols::features::FeaturesReporter::schema() const –> std::string
- set_compute_packstat(self: pyrosetta.rosetta.protocols.features.InterfaceFeatures, compute_packstat: bool) None ¶
Compute the packstat score? Default true
C++: protocols::features::InterfaceFeatures::set_compute_packstat(const bool) –> void
- set_dSASA_cutoff(self: pyrosetta.rosetta.protocols.features.InterfaceFeatures, dSASA_cutoff: float) None ¶
Set the reporter to only include interfaces >dSASA_cutoff.
C++: protocols::features::InterfaceFeatures::set_dSASA_cutoff(double) –> void
- set_defaults(self: pyrosetta.rosetta.protocols.features.InterfaceFeatures) None ¶
C++: protocols::features::InterfaceFeatures::set_defaults() –> void
- set_interface_chains(self: pyrosetta.rosetta.protocols.features.InterfaceFeatures, interfaces: pyrosetta.rosetta.utility.vector1_std_string) None ¶
Set the fixed chain combinations that will be analyzed. Default is all of them.
Example: AB_C would analyze the interface between AB and C, keeping AB fixed while separating C. Note that here, you can also give A_C and a new pose would be created with only A and C so that this interface can be tested. Note also that multiple pose interfaces can be set.
C++: protocols::features::InterfaceFeatures::set_interface_chains(const class utility::vector1<std::string, class std::allocator<std::string > > &) –> void
- set_pack_separated(self: pyrosetta.rosetta.protocols.features.InterfaceFeatures, pack_separated: bool) None ¶
Pack the interface before separation? Default is false.
C++: protocols::features::InterfaceFeatures::set_pack_separated(const bool) –> void
- set_pack_together(self: pyrosetta.rosetta.protocols.features.InterfaceFeatures, pack_together: bool) None ¶
Pack the interface after separation? Default is true.
C++: protocols::features::InterfaceFeatures::set_pack_together(const bool) –> void
- set_relevant_residues_mode(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, setting: pyrosetta.rosetta.protocols.features.RelevantResiduesMode.T) None ¶
C++: protocols::features::FeaturesReporter::set_relevant_residues_mode(enum protocols::features::RelevantResiduesMode::T) –> void
- set_scorefxn(self: pyrosetta.rosetta.protocols.features.InterfaceFeatures, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) None ¶
C++: protocols::features::InterfaceFeatures::set_scorefxn(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void
- type_name(self: pyrosetta.rosetta.protocols.features.InterfaceFeatures) str ¶
C++: protocols::features::InterfaceFeatures::type_name() const –> std::string
- write_interface_residues_schema_to_db(self: pyrosetta.rosetta.protocols.features.InterfaceFeatures, db_session: pyrosetta.rosetta.utility.sql_database.session) None ¶
C++: protocols::features::InterfaceFeatures::write_interface_residues_schema_to_db(class std::shared_ptr<class utility::sql_database::session>) const –> void
- write_interface_schema_to_db(self: pyrosetta.rosetta.protocols.features.InterfaceFeatures, db_session: pyrosetta.rosetta.utility.sql_database.session) None ¶
C++: protocols::features::InterfaceFeatures::write_interface_schema_to_db(class std::shared_ptr<class utility::sql_database::session>) const –> void
- write_interface_side_schema_to_db(self: pyrosetta.rosetta.protocols.features.InterfaceFeatures, db_session: pyrosetta.rosetta.utility.sql_database.session) None ¶
C++: protocols::features::InterfaceFeatures::write_interface_side_schema_to_db(class std::shared_ptr<class utility::sql_database::session>) const –> void
- write_schema_to_db(self: pyrosetta.rosetta.protocols.features.InterfaceFeatures, db_session: pyrosetta.rosetta.utility.sql_database.session) None ¶
generate the table schemas and write them to the database
C++: protocols::features::InterfaceFeatures::write_schema_to_db(class std::shared_ptr<class utility::sql_database::session>) const –> void
- class pyrosetta.rosetta.protocols.features.InterfaceFeaturesCreator¶
Bases:
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
C++: protocols::features::FeaturesReporter::check_relevant_residues(const class utility::vector1<bool, class std::allocator<bool> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> bool
- check_relevant_residues_range(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, res1: int, res2: int) bool ¶
C++: protocols::features::FeaturesReporter::check_relevant_residues_range(const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, unsigned long) const –> bool
- static class_name() str ¶
C++: protocols::features::JobDataFeatures::class_name() –> std::string
- delete_record(self: pyrosetta.rosetta.protocols.features.JobDataFeatures, struct_id: int, db_session: pyrosetta.rosetta.utility.sql_database.session) None ¶
C++: protocols::features::JobDataFeatures::delete_record(unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> void
- features_reporter_dependencies(self: pyrosetta.rosetta.protocols.features.JobDataFeatures) pyrosetta.rosetta.utility.vector1_std_string ¶
return the set of features reporters that are required to also already be extracted by the time this one is used.
C++: protocols::features::JobDataFeatures::features_reporter_dependencies() const –> class utility::vector1<std::string, class std::allocator<std::string > >
- get_relevant_residues_mode(self: pyrosetta.rosetta.protocols.features.FeaturesReporter) pyrosetta.rosetta.protocols.features.RelevantResiduesMode.T ¶
C++: protocols::features::FeaturesReporter::get_relevant_residues_mode() const –> enum protocols::features::RelevantResiduesMode::T
- load_into_pose(self: pyrosetta.rosetta.protocols.features.JobDataFeatures, db_session: pyrosetta.rosetta.utility.sql_database.session, struct_id: int, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::features::JobDataFeatures::load_into_pose(class std::shared_ptr<class utility::sql_database::session>, unsigned long, class core::pose::Pose &) –> void
- parse_my_tag(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None ¶
C++: protocols::features::FeaturesReporter::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None ¶
C++: protocols::features::JobDataFeatures::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void
- report_features(self: pyrosetta.rosetta.protocols.features.JobDataFeatures, pose: pyrosetta.rosetta.core.pose.Pose, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, struct_id: int, db_session: pyrosetta.rosetta.utility.sql_database.session) int ¶
collect all the feature data for the pose
C++: protocols::features::JobDataFeatures::report_features(const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> unsigned long
- schema(self: pyrosetta.rosetta.protocols.features.FeaturesReporter) str ¶
return sql statements that sets up the appropriate tables to contain the features. This should be removed once everything has been moved to the schema generator
C++: protocols::features::FeaturesReporter::schema() const –> std::string
- set_relevant_residues_mode(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, setting: pyrosetta.rosetta.protocols.features.RelevantResiduesMode.T) None ¶
C++: protocols::features::FeaturesReporter::set_relevant_residues_mode(enum protocols::features::RelevantResiduesMode::T) –> void
- type_name(self: pyrosetta.rosetta.protocols.features.JobDataFeatures) str ¶
C++: protocols::features::JobDataFeatures::type_name() const –> std::string
- write_schema_to_db(self: pyrosetta.rosetta.protocols.features.JobDataFeatures, db_session: pyrosetta.rosetta.utility.sql_database.session) None ¶
generate the table schemas and write them to the database
C++: protocols::features::JobDataFeatures::write_schema_to_db(class std::shared_ptr<class utility::sql_database::session>) const –> void
- class pyrosetta.rosetta.protocols.features.JobDataFeaturesCreator¶
Bases:
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
C++: protocols::features::FeaturesReporter::check_relevant_residues(const class utility::vector1<bool, class std::allocator<bool> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> bool
- check_relevant_residues_range(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, res1: int, res2: int) bool ¶
C++: protocols::features::FeaturesReporter::check_relevant_residues_range(const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, unsigned long) const –> bool
- static class_name() str ¶
C++: protocols::features::LoopAnchorFeatures::class_name() –> std::string
- delete_record(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, : int, : pyrosetta.rosetta.utility.sql_database.session) None ¶
C++: protocols::features::FeaturesReporter::delete_record(unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> void
- features_reporter_dependencies(self: pyrosetta.rosetta.protocols.features.LoopAnchorFeatures) pyrosetta.rosetta.utility.vector1_std_string ¶
return the set of features reporters that are required to also already be extracted by the time this one is used.
C++: protocols::features::LoopAnchorFeatures::features_reporter_dependencies() const –> class utility::vector1<std::string, class std::allocator<std::string > >
- get_relevant_residues_mode(self: pyrosetta.rosetta.protocols.features.FeaturesReporter) pyrosetta.rosetta.protocols.features.RelevantResiduesMode.T ¶
C++: protocols::features::FeaturesReporter::get_relevant_residues_mode() const –> enum protocols::features::RelevantResiduesMode::T
- load_into_pose(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, : pyrosetta.rosetta.utility.sql_database.session, : int, : pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::features::FeaturesReporter::load_into_pose(class std::shared_ptr<class utility::sql_database::session>, unsigned long, class core::pose::Pose &) –> void
- parse_my_tag(self: pyrosetta.rosetta.protocols.features.LoopAnchorFeatures, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None ¶
C++: protocols::features::LoopAnchorFeatures::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None ¶
C++: protocols::features::LoopAnchorFeatures::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void
- report_features(self: pyrosetta.rosetta.protocols.features.LoopAnchorFeatures, pose: pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.utility.vector1_bool, struct_id: int, db_session: pyrosetta.rosetta.utility.sql_database.session) int ¶
collect all the feature data for the pose
C++: protocols::features::LoopAnchorFeatures::report_features(const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> unsigned long
- schema(self: pyrosetta.rosetta.protocols.features.FeaturesReporter) str ¶
return sql statements that sets up the appropriate tables to contain the features. This should be removed once everything has been moved to the schema generator
C++: protocols::features::FeaturesReporter::schema() const –> std::string
- set_relevant_residues_mode(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, setting: pyrosetta.rosetta.protocols.features.RelevantResiduesMode.T) None ¶
C++: protocols::features::FeaturesReporter::set_relevant_residues_mode(enum protocols::features::RelevantResiduesMode::T) –> void
- set_use_relevant_residues_as_loop_length(self: pyrosetta.rosetta.protocols.features.LoopAnchorFeatures, use_relevant_residues_as_loop_length: bool) None ¶
C++: protocols::features::LoopAnchorFeatures::set_use_relevant_residues_as_loop_length(const bool) –> void
- set_use_single_residue_to_define_anchor_transfrom(self: pyrosetta.rosetta.protocols.features.LoopAnchorFeatures, use_single_residue_to_define_anchor_transfrom: bool) None ¶
C++: protocols::features::LoopAnchorFeatures::set_use_single_residue_to_define_anchor_transfrom(const bool) –> void
- type_name(self: pyrosetta.rosetta.protocols.features.LoopAnchorFeatures) str ¶
C++: protocols::features::LoopAnchorFeatures::type_name() const –> std::string
- write_schema_to_db(self: pyrosetta.rosetta.protocols.features.LoopAnchorFeatures, db_session: pyrosetta.rosetta.utility.sql_database.session) None ¶
generate the table schemas and write them to the database
C++: protocols::features::LoopAnchorFeatures::write_schema_to_db(class std::shared_ptr<class utility::sql_database::session>) const –> void
- class pyrosetta.rosetta.protocols.features.LoopAnchorFeaturesCreator¶
Bases:
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
C++: protocols::features::FeaturesReporter::check_relevant_residues(const class utility::vector1<bool, class std::allocator<bool> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> bool
- check_relevant_residues_range(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, res1: int, res2: int) bool ¶
C++: protocols::features::FeaturesReporter::check_relevant_residues_range(const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, unsigned long) const –> bool
- static class_name() str ¶
C++: protocols::features::ModelFeatures::class_name() –> std::string
- delete_record(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, : int, : pyrosetta.rosetta.utility.sql_database.session) None ¶
C++: protocols::features::FeaturesReporter::delete_record(unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> void
- features_reporter_dependencies(self: pyrosetta.rosetta.protocols.features.ModelFeatures) pyrosetta.rosetta.utility.vector1_std_string ¶
return the set of features reporters that are required to also already be extracted by the time this one is used.
C++: protocols::features::ModelFeatures::features_reporter_dependencies() const –> class utility::vector1<std::string, class std::allocator<std::string > >
- get_relevant_residues_mode(self: pyrosetta.rosetta.protocols.features.FeaturesReporter) pyrosetta.rosetta.protocols.features.RelevantResiduesMode.T ¶
C++: protocols::features::FeaturesReporter::get_relevant_residues_mode() const –> enum protocols::features::RelevantResiduesMode::T
- load_into_pose(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, : pyrosetta.rosetta.utility.sql_database.session, : int, : pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::features::FeaturesReporter::load_into_pose(class std::shared_ptr<class utility::sql_database::session>, unsigned long, class core::pose::Pose &) –> void
- parse_my_tag(self: pyrosetta.rosetta.protocols.features.ModelFeatures, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None ¶
C++: protocols::features::ModelFeatures::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None ¶
C++: protocols::features::ModelFeatures::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void
- report_features(self: pyrosetta.rosetta.protocols.features.ModelFeatures, pose: pyrosetta.rosetta.core.pose.Pose, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, struct_id: int, db_session: pyrosetta.rosetta.utility.sql_database.session) int ¶
collect all the feature data for the pose
C++: protocols::features::ModelFeatures::report_features(const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> unsigned long
- schema(self: pyrosetta.rosetta.protocols.features.FeaturesReporter) str ¶
return sql statements that sets up the appropriate tables to contain the features. This should be removed once everything has been moved to the schema generator
C++: protocols::features::FeaturesReporter::schema() const –> std::string
- set_relevant_residues_mode(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, setting: pyrosetta.rosetta.protocols.features.RelevantResiduesMode.T) None ¶
C++: protocols::features::FeaturesReporter::set_relevant_residues_mode(enum protocols::features::RelevantResiduesMode::T) –> void
- trim_pose(self: pyrosetta.rosetta.protocols.features.ModelFeatures, pose: pyrosetta.rosetta.core.pose.Pose, resnums: pyrosetta.rosetta.std.set_unsigned_long_t) None ¶
for testing purposes only
C++: protocols::features::ModelFeatures::trim_pose(class core::pose::Pose &, class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> >) const –> void
- type_name(self: pyrosetta.rosetta.protocols.features.ModelFeatures) str ¶
C++: protocols::features::ModelFeatures::type_name() const –> std::string
- write_clique_to_db(self: pyrosetta.rosetta.protocols.features.ModelFeatures, clique: pyrosetta.rosetta.std.set_unsigned_long_t, struct_id: int, db_session: pyrosetta.rosetta.utility.sql_database.session) None ¶
C++: protocols::features::ModelFeatures::write_clique_to_db(const class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> > &, unsigned long, class std::shared_ptr<class utility::sql_database::session>) const –> void
- write_schema_to_db(self: pyrosetta.rosetta.protocols.features.ModelFeatures, db_session: pyrosetta.rosetta.utility.sql_database.session) None ¶
generate the table schemas and write them to the database
C++: protocols::features::ModelFeatures::write_schema_to_db(class std::shared_ptr<class utility::sql_database::session>) const –> void
- class pyrosetta.rosetta.protocols.features.ModelFeaturesCreator¶
Bases:
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
C++: protocols::features::FeaturesReporter::check_relevant_residues(const class utility::vector1<bool, class std::allocator<bool> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> bool
- check_relevant_residues_range(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, res1: int, res2: int) bool ¶
C++: protocols::features::FeaturesReporter::check_relevant_residues_range(const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, unsigned long) const –> bool
- static class_name() str ¶
C++: protocols::features::OrbitalsFeatures::class_name() –> std::string
- delete_record(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, : int, : pyrosetta.rosetta.utility.sql_database.session) None ¶
C++: protocols::features::FeaturesReporter::delete_record(unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> void
- features_reporter_dependencies(self: pyrosetta.rosetta.protocols.features.OrbitalsFeatures) pyrosetta.rosetta.utility.vector1_std_string ¶
return the set of features reporters that are required to also already be extracted by the time this one is used.
C++: protocols::features::OrbitalsFeatures::features_reporter_dependencies() const –> class utility::vector1<std::string, class std::allocator<std::string > >
- get_relevant_residues_mode(self: pyrosetta.rosetta.protocols.features.FeaturesReporter) pyrosetta.rosetta.protocols.features.RelevantResiduesMode.T ¶
C++: protocols::features::FeaturesReporter::get_relevant_residues_mode() const –> enum protocols::features::RelevantResiduesMode::T
- load_into_pose(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, : pyrosetta.rosetta.utility.sql_database.session, : int, : pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::features::FeaturesReporter::load_into_pose(class std::shared_ptr<class utility::sql_database::session>, unsigned long, class core::pose::Pose &) –> void
- parse_my_tag(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None ¶
C++: protocols::features::FeaturesReporter::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None ¶
C++: protocols::features::OrbitalsFeatures::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void
- report_features(self: pyrosetta.rosetta.protocols.features.OrbitalsFeatures, pose: pyrosetta.rosetta.core.pose.Pose, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, struct_id: int, db_session: pyrosetta.rosetta.utility.sql_database.session) int ¶
collect all the feature data for the pose
C++: protocols::features::OrbitalsFeatures::report_features(const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> unsigned long
- report_haro_orbital_interactions(self: pyrosetta.rosetta.protocols.features.OrbitalsFeatures, pose: pyrosetta.rosetta.core.pose.Pose, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, struct_id: int, db_session: pyrosetta.rosetta.utility.sql_database.session) None ¶
C++: protocols::features::OrbitalsFeatures::report_haro_orbital_interactions(const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, const unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> void
- report_hpol_orbital_interactions(self: pyrosetta.rosetta.protocols.features.OrbitalsFeatures, pose: pyrosetta.rosetta.core.pose.Pose, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, struct_id: int, db_session: pyrosetta.rosetta.utility.sql_database.session) None ¶
C++: protocols::features::OrbitalsFeatures::report_hpol_orbital_interactions(const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, const unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> void
- schema(self: pyrosetta.rosetta.protocols.features.FeaturesReporter) str ¶
return sql statements that sets up the appropriate tables to contain the features. This should be removed once everything has been moved to the schema generator
C++: protocols::features::FeaturesReporter::schema() const –> std::string
- set_OrbH_features_data(self: pyrosetta.rosetta.protocols.features.OrbitalsFeatures, res1: pyrosetta.rosetta.core.conformation.Residue, res2: pyrosetta.rosetta.core.conformation.Residue, Aindex: int, Hindex: int, Orbindex: int, Orbxyz: pyrosetta.rosetta.numeric.xyzVector_double_t, resNum2: int, orbName1: str, htype2: str, res2name: str, orbNum1: int, hpolNum2: int, cosAOH: float, cosDHO: float, chiBDHO: float, chiBAOH: float, AOH_angle: float, DHO_angle: float, chiBAHD: float, cosAHD: float, OrbHdist: float) None ¶
C++: protocols::features::OrbitalsFeatures::set_OrbH_features_data(class core::conformation::Residue &, class core::conformation::Residue &, const unsigned long, const unsigned long, const unsigned long, const class numeric::xyzVector<double> &, unsigned long &, std::string &, std::string &, std::string &, unsigned long &, unsigned long &, double &, double &, double &, double &, double &, double &, double &, double &, double &) –> void
- set_OrbOrb_features_data(self: pyrosetta.rosetta.protocols.features.OrbitalsFeatures, res1: pyrosetta.rosetta.core.conformation.Residue, res2: pyrosetta.rosetta.core.conformation.Residue, Aindex: int, Dindex: int, Orbindex1: int, Orbindex2: int, Orbxyz1: pyrosetta.rosetta.numeric.xyzVector_double_t, Orbxyz2: pyrosetta.rosetta.numeric.xyzVector_double_t, resNum2: int, orbName1: str, res2name: str, OrbName2: str, orbNum1: int, OrbNum2: int, cosAOO: float, cosDOO: float, chiBAOO: float, chiBDOO: float, AOO_angle: float, DOO_angle: float, OrbHdist: float, cosAOD: float, AOD_angle: float, chiBAHD: float, cosAHD: float) None ¶
C++: protocols::features::OrbitalsFeatures::set_OrbOrb_features_data(class core::conformation::Residue &, class core::conformation::Residue &, unsigned long, unsigned long, unsigned long, unsigned long, const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, unsigned long &, std::string &, std::string &, std::string &, unsigned long &, unsigned long &, double &, double &, double &, double &, double &, double &, double &, double &, double &, double &, double &) –> void
- set_relevant_residues_mode(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, setting: pyrosetta.rosetta.protocols.features.RelevantResiduesMode.T) None ¶
C++: protocols::features::FeaturesReporter::set_relevant_residues_mode(enum protocols::features::RelevantResiduesMode::T) –> void
- type_name(self: pyrosetta.rosetta.protocols.features.OrbitalsFeatures) str ¶
C++: protocols::features::OrbitalsFeatures::type_name() const –> std::string
- write_schema_to_db(self: pyrosetta.rosetta.protocols.features.OrbitalsFeatures, db_session: pyrosetta.rosetta.utility.sql_database.session) None ¶
generate the table schemas and write them to the database
C++: protocols::features::OrbitalsFeatures::write_schema_to_db(class std::shared_ptr<class utility::sql_database::session>) const –> void
- class pyrosetta.rosetta.protocols.features.OrbitalsFeaturesCreator¶
Bases:
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
C++: protocols::features::FeaturesReporter::check_relevant_residues(const class utility::vector1<bool, class std::allocator<bool> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> bool
- check_relevant_residues_range(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, res1: int, res2: int) bool ¶
C++: protocols::features::FeaturesReporter::check_relevant_residues_range(const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, unsigned long) const –> bool
- static class_name() str ¶
C++: protocols::features::PairFeatures::class_name() –> std::string
- delete_record(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, : int, : pyrosetta.rosetta.utility.sql_database.session) None ¶
C++: protocols::features::FeaturesReporter::delete_record(unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> void
- features_reporter_dependencies(self: pyrosetta.rosetta.protocols.features.PairFeatures) pyrosetta.rosetta.utility.vector1_std_string ¶
return the set of features reporters that are required to also already be extracted by the time this one is used.
C++: protocols::features::PairFeatures::features_reporter_dependencies() const –> class utility::vector1<std::string, class std::allocator<std::string > >
- get_relevant_residues_mode(self: pyrosetta.rosetta.protocols.features.FeaturesReporter) pyrosetta.rosetta.protocols.features.RelevantResiduesMode.T ¶
C++: protocols::features::FeaturesReporter::get_relevant_residues_mode() const –> enum protocols::features::RelevantResiduesMode::T
- load_into_pose(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, : pyrosetta.rosetta.utility.sql_database.session, : int, : pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::features::FeaturesReporter::load_into_pose(class std::shared_ptr<class utility::sql_database::session>, unsigned long, class core::pose::Pose &) –> void
- parse_my_tag(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None ¶
C++: protocols::features::FeaturesReporter::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None ¶
C++: protocols::features::PairFeatures::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void
- report_features(self: pyrosetta.rosetta.protocols.features.PairFeatures, pose: pyrosetta.rosetta.core.pose.Pose, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, struct_id: int, db_session: pyrosetta.rosetta.utility.sql_database.session) int ¶
collect all the feature data for the pose
C++: protocols::features::PairFeatures::report_features(const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> unsigned long
- report_residue_pairs(self: pyrosetta.rosetta.protocols.features.PairFeatures, pose: pyrosetta.rosetta.core.pose.Pose, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, struct_id: int, db_session: pyrosetta.rosetta.utility.sql_database.session) None ¶
C++: protocols::features::PairFeatures::report_residue_pairs(const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, const unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> void
- schema(self: pyrosetta.rosetta.protocols.features.FeaturesReporter) str ¶
return sql statements that sets up the appropriate tables to contain the features. This should be removed once everything has been moved to the schema generator
C++: protocols::features::FeaturesReporter::schema() const –> std::string
- set_relevant_residues_mode(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, setting: pyrosetta.rosetta.protocols.features.RelevantResiduesMode.T) None ¶
C++: protocols::features::FeaturesReporter::set_relevant_residues_mode(enum protocols::features::RelevantResiduesMode::T) –> void
- type_name(self: pyrosetta.rosetta.protocols.features.PairFeatures) str ¶
C++: protocols::features::PairFeatures::type_name() const –> std::string
- write_schema_to_db(self: pyrosetta.rosetta.protocols.features.PairFeatures, db_session: pyrosetta.rosetta.utility.sql_database.session) None ¶
generate the table schemas and write them to the database
C++: protocols::features::PairFeatures::write_schema_to_db(class std::shared_ptr<class utility::sql_database::session>) const –> void
- class pyrosetta.rosetta.protocols.features.PairFeaturesCreator¶
Bases:
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
C++: protocols::features::FeaturesReporter::check_relevant_residues(const class utility::vector1<bool, class std::allocator<bool> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> bool
- check_relevant_residues_range(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, res1: int, res2: int) bool ¶
C++: protocols::features::FeaturesReporter::check_relevant_residues_range(const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, unsigned long) const –> bool
- static class_name() str ¶
C++: protocols::features::PdbDataFeatures::class_name() –> std::string
- delete_record(self: pyrosetta.rosetta.protocols.features.PdbDataFeatures, struct_id: int, db_session: pyrosetta.rosetta.utility.sql_database.session) None ¶
C++: protocols::features::PdbDataFeatures::delete_record(unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> void
- features_reporter_dependencies(self: pyrosetta.rosetta.protocols.features.PdbDataFeatures) pyrosetta.rosetta.utility.vector1_std_string ¶
return the set of features reporters that are required to also already be extracted by the time this one is used.
C++: protocols::features::PdbDataFeatures::features_reporter_dependencies() const –> class utility::vector1<std::string, class std::allocator<std::string > >
- get_relevant_residues_mode(self: pyrosetta.rosetta.protocols.features.FeaturesReporter) pyrosetta.rosetta.protocols.features.RelevantResiduesMode.T ¶
C++: protocols::features::FeaturesReporter::get_relevant_residues_mode() const –> enum protocols::features::RelevantResiduesMode::T
- load_into_pose(self: pyrosetta.rosetta.protocols.features.PdbDataFeatures, db_session: pyrosetta.rosetta.utility.sql_database.session, struct_id: int, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::features::PdbDataFeatures::load_into_pose(class std::shared_ptr<class utility::sql_database::session>, unsigned long, class core::pose::Pose &) –> void
- parse_my_tag(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None ¶
C++: protocols::features::FeaturesReporter::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None ¶
C++: protocols::features::PdbDataFeatures::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void
- report_features(self: pyrosetta.rosetta.protocols.features.PdbDataFeatures, pose: pyrosetta.rosetta.core.pose.Pose, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, struct_id: int, db_session: pyrosetta.rosetta.utility.sql_database.session) int ¶
collect all the feature data for the pose
C++: protocols::features::PdbDataFeatures::report_features(const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> unsigned long
- schema(self: pyrosetta.rosetta.protocols.features.FeaturesReporter) str ¶
return sql statements that sets up the appropriate tables to contain the features. This should be removed once everything has been moved to the schema generator
C++: protocols::features::FeaturesReporter::schema() const –> std::string
- set_relevant_residues_mode(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, setting: pyrosetta.rosetta.protocols.features.RelevantResiduesMode.T) None ¶
C++: protocols::features::FeaturesReporter::set_relevant_residues_mode(enum protocols::features::RelevantResiduesMode::T) –> void
- type_name(self: pyrosetta.rosetta.protocols.features.PdbDataFeatures) str ¶
C++: protocols::features::PdbDataFeatures::type_name() const –> std::string
- write_schema_to_db(self: pyrosetta.rosetta.protocols.features.PdbDataFeatures, db_session: pyrosetta.rosetta.utility.sql_database.session) None ¶
generate the table schemas and write them to the database
C++: protocols::features::PdbDataFeatures::write_schema_to_db(class std::shared_ptr<class utility::sql_database::session>) const –> void
- class pyrosetta.rosetta.protocols.features.PdbDataFeaturesCreator¶
Bases:
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
C++: protocols::features::FeaturesReporter::check_relevant_residues(const class utility::vector1<bool, class std::allocator<bool> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> bool
- check_relevant_residues_range(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, res1: int, res2: int) bool ¶
C++: protocols::features::FeaturesReporter::check_relevant_residues_range(const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, unsigned long) const –> bool
- static class_name() str ¶
C++: protocols::features::PoseCommentsFeatures::class_name() –> std::string
- delete_record(self: pyrosetta.rosetta.protocols.features.PoseCommentsFeatures, struct_id: int, db_session: pyrosetta.rosetta.utility.sql_database.session) None ¶
C++: protocols::features::PoseCommentsFeatures::delete_record(unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> void
- features_reporter_dependencies(self: pyrosetta.rosetta.protocols.features.PoseCommentsFeatures) pyrosetta.rosetta.utility.vector1_std_string ¶
return the set of features reporters that are required to also already be extracted by the time this one is used.
C++: protocols::features::PoseCommentsFeatures::features_reporter_dependencies() const –> class utility::vector1<std::string, class std::allocator<std::string > >
- get_relevant_residues_mode(self: pyrosetta.rosetta.protocols.features.FeaturesReporter) pyrosetta.rosetta.protocols.features.RelevantResiduesMode.T ¶
C++: protocols::features::FeaturesReporter::get_relevant_residues_mode() const –> enum protocols::features::RelevantResiduesMode::T
- load_into_pose(self: pyrosetta.rosetta.protocols.features.PoseCommentsFeatures, db_session: pyrosetta.rosetta.utility.sql_database.session, struct_id: int, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::features::PoseCommentsFeatures::load_into_pose(class std::shared_ptr<class utility::sql_database::session>, unsigned long, class core::pose::Pose &) –> void
- parse_my_tag(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None ¶
C++: protocols::features::FeaturesReporter::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None ¶
C++: protocols::features::PoseCommentsFeatures::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void
- report_features(self: pyrosetta.rosetta.protocols.features.PoseCommentsFeatures, pose: pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.utility.vector1_bool, struct_id: int, db_session: pyrosetta.rosetta.utility.sql_database.session) int ¶
collect all the feature data for the pose
C++: protocols::features::PoseCommentsFeatures::report_features(const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> unsigned long
- schema(self: pyrosetta.rosetta.protocols.features.FeaturesReporter) str ¶
return sql statements that sets up the appropriate tables to contain the features. This should be removed once everything has been moved to the schema generator
C++: protocols::features::FeaturesReporter::schema() const –> std::string
- set_relevant_residues_mode(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, setting: pyrosetta.rosetta.protocols.features.RelevantResiduesMode.T) None ¶
C++: protocols::features::FeaturesReporter::set_relevant_residues_mode(enum protocols::features::RelevantResiduesMode::T) –> void
- type_name(self: pyrosetta.rosetta.protocols.features.PoseCommentsFeatures) str ¶
C++: protocols::features::PoseCommentsFeatures::type_name() const –> std::string
- write_schema_to_db(self: pyrosetta.rosetta.protocols.features.PoseCommentsFeatures, db_session: pyrosetta.rosetta.utility.sql_database.session) None ¶
generate the table schemas and write them to the database
C++: protocols::features::PoseCommentsFeatures::write_schema_to_db(class std::shared_ptr<class utility::sql_database::session>) const –> void
- class pyrosetta.rosetta.protocols.features.PoseCommentsFeaturesCreator¶
Bases:
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
C++: protocols::features::FeaturesReporter::check_relevant_residues(const class utility::vector1<bool, class std::allocator<bool> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> bool
- check_relevant_residues_range(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, res1: int, res2: int) bool ¶
C++: protocols::features::FeaturesReporter::check_relevant_residues_range(const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, unsigned long) const –> bool
- static class_name() str ¶
C++: protocols::features::PoseConformationFeatures::class_name() –> std::string
- delete_record(self: pyrosetta.rosetta.protocols.features.PoseConformationFeatures, struct_id: int, db_session: pyrosetta.rosetta.utility.sql_database.session) None ¶
C++: protocols::features::PoseConformationFeatures::delete_record(unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> void
- features_reporter_dependencies(self: pyrosetta.rosetta.protocols.features.PoseConformationFeatures) pyrosetta.rosetta.utility.vector1_std_string ¶
return the set of features reporters that are required to also already be extracted by the time this one is used.
C++: protocols::features::PoseConformationFeatures::features_reporter_dependencies() const –> class utility::vector1<std::string, class std::allocator<std::string > >
- get_relevant_residues_mode(self: pyrosetta.rosetta.protocols.features.FeaturesReporter) pyrosetta.rosetta.protocols.features.RelevantResiduesMode.T ¶
C++: protocols::features::FeaturesReporter::get_relevant_residues_mode() const –> enum protocols::features::RelevantResiduesMode::T
- load_into_pose(*args, **kwargs)¶
Overloaded function.
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
C++: protocols::features::FeaturesReporter::check_relevant_residues(const class utility::vector1<bool, class std::allocator<bool> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> bool
- check_relevant_residues_range(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, res1: int, res2: int) bool ¶
C++: protocols::features::FeaturesReporter::check_relevant_residues_range(const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, unsigned long) const –> bool
- static class_name() str ¶
C++: protocols::features::ProteinBackboneAtomAtomPairFeatures::class_name() –> std::string
- delete_record(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, : int, : pyrosetta.rosetta.utility.sql_database.session) None ¶
C++: protocols::features::FeaturesReporter::delete_record(unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> void
- features_reporter_dependencies(self: pyrosetta.rosetta.protocols.features.ProteinBackboneAtomAtomPairFeatures) pyrosetta.rosetta.utility.vector1_std_string ¶
return the set of features reporters that are required to also already be extracted by the time this one is used.
C++: protocols::features::ProteinBackboneAtomAtomPairFeatures::features_reporter_dependencies() const –> class utility::vector1<std::string, class std::allocator<std::string > >
- get_relevant_residues_mode(self: pyrosetta.rosetta.protocols.features.FeaturesReporter) pyrosetta.rosetta.protocols.features.RelevantResiduesMode.T ¶
C++: protocols::features::FeaturesReporter::get_relevant_residues_mode() const –> enum protocols::features::RelevantResiduesMode::T
- load_into_pose(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, : pyrosetta.rosetta.utility.sql_database.session, : int, : pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::features::FeaturesReporter::load_into_pose(class std::shared_ptr<class utility::sql_database::session>, unsigned long, class core::pose::Pose &) –> void
- parse_my_tag(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None ¶
C++: protocols::features::FeaturesReporter::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None ¶
C++: protocols::features::ProteinBackboneAtomAtomPairFeatures::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void
- report_features(self: pyrosetta.rosetta.protocols.features.ProteinBackboneAtomAtomPairFeatures, pose: pyrosetta.rosetta.core.pose.Pose, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, struct_id: int, db_session: pyrosetta.rosetta.utility.sql_database.session) int ¶
collect all the feature data for the pose
C++: protocols::features::ProteinBackboneAtomAtomPairFeatures::report_features(const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> unsigned long
- schema(self: pyrosetta.rosetta.protocols.features.FeaturesReporter) str ¶
return sql statements that sets up the appropriate tables to contain the features. This should be removed once everything has been moved to the schema generator
C++: protocols::features::FeaturesReporter::schema() const –> std::string
- set_relevant_residues_mode(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, setting: pyrosetta.rosetta.protocols.features.RelevantResiduesMode.T) None ¶
C++: protocols::features::FeaturesReporter::set_relevant_residues_mode(enum protocols::features::RelevantResiduesMode::T) –> void
- type_name(self: pyrosetta.rosetta.protocols.features.ProteinBackboneAtomAtomPairFeatures) str ¶
C++: protocols::features::ProteinBackboneAtomAtomPairFeatures::type_name() const –> std::string
- write_schema_to_db(self: pyrosetta.rosetta.protocols.features.ProteinBackboneAtomAtomPairFeatures, db_session: pyrosetta.rosetta.utility.sql_database.session) None ¶
generate the table schemas and write them to the database
C++: protocols::features::ProteinBackboneAtomAtomPairFeatures::write_schema_to_db(class std::shared_ptr<class utility::sql_database::session>) const –> void
- class pyrosetta.rosetta.protocols.features.ProteinBackboneAtomAtomPairFeaturesCreator¶
Bases:
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
C++: protocols::features::FeaturesReporter::check_relevant_residues(const class utility::vector1<bool, class std::allocator<bool> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> bool
- check_relevant_residues_range(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, res1: int, res2: int) bool ¶
C++: protocols::features::FeaturesReporter::check_relevant_residues_range(const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, unsigned long) const –> bool
- static class_name() str ¶
C++: protocols::features::ProteinBackboneTorsionAngleFeatures::class_name() –> std::string
- delete_record(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, : int, : pyrosetta.rosetta.utility.sql_database.session) None ¶
C++: protocols::features::FeaturesReporter::delete_record(unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> void
- features_reporter_dependencies(self: pyrosetta.rosetta.protocols.features.ProteinBackboneTorsionAngleFeatures) pyrosetta.rosetta.utility.vector1_std_string ¶
return the set of features reporters that are required to also already be extracted by the time this one is used.
C++: protocols::features::ProteinBackboneTorsionAngleFeatures::features_reporter_dependencies() const –> class utility::vector1<std::string, class std::allocator<std::string > >
- get_relevant_residues_mode(self: pyrosetta.rosetta.protocols.features.FeaturesReporter) pyrosetta.rosetta.protocols.features.RelevantResiduesMode.T ¶
C++: protocols::features::FeaturesReporter::get_relevant_residues_mode() const –> enum protocols::features::RelevantResiduesMode::T
- load_into_pose(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, : pyrosetta.rosetta.utility.sql_database.session, : int, : pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::features::FeaturesReporter::load_into_pose(class std::shared_ptr<class utility::sql_database::session>, unsigned long, class core::pose::Pose &) –> void
- parse_my_tag(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None ¶
C++: protocols::features::FeaturesReporter::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None ¶
C++: protocols::features::ProteinBackboneTorsionAngleFeatures::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void
- report_features(self: pyrosetta.rosetta.protocols.features.ProteinBackboneTorsionAngleFeatures, pose: pyrosetta.rosetta.core.pose.Pose, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, struct_id: int, db_session: pyrosetta.rosetta.utility.sql_database.session) int ¶
collect all the feature data for the pose
C++: protocols::features::ProteinBackboneTorsionAngleFeatures::report_features(const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> unsigned long
- schema(self: pyrosetta.rosetta.protocols.features.FeaturesReporter) str ¶
return sql statements that sets up the appropriate tables to contain the features. This should be removed once everything has been moved to the schema generator
C++: protocols::features::FeaturesReporter::schema() const –> std::string
- set_relevant_residues_mode(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, setting: pyrosetta.rosetta.protocols.features.RelevantResiduesMode.T) None ¶
C++: protocols::features::FeaturesReporter::set_relevant_residues_mode(enum protocols::features::RelevantResiduesMode::T) –> void
- type_name(self: pyrosetta.rosetta.protocols.features.ProteinBackboneTorsionAngleFeatures) str ¶
C++: protocols::features::ProteinBackboneTorsionAngleFeatures::type_name() const –> std::string
- write_schema_to_db(self: pyrosetta.rosetta.protocols.features.ProteinBackboneTorsionAngleFeatures, db_session: pyrosetta.rosetta.utility.sql_database.session) None ¶
generate the table schemas and write them to the database
C++: protocols::features::ProteinBackboneTorsionAngleFeatures::write_schema_to_db(class std::shared_ptr<class utility::sql_database::session>) const –> void
- class pyrosetta.rosetta.protocols.features.ProteinBackboneTorsionAngleFeaturesCreator¶
Bases:
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
C++: protocols::features::FeaturesReporter::check_relevant_residues(const class utility::vector1<bool, class std::allocator<bool> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> bool
- check_relevant_residues_range(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, res1: int, res2: int) bool ¶
C++: protocols::features::FeaturesReporter::check_relevant_residues_range(const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, unsigned long) const –> bool
- static class_name() str ¶
C++: protocols::features::ProteinBondGeometryFeatures::class_name() –> std::string
- delete_record(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, : int, : pyrosetta.rosetta.utility.sql_database.session) None ¶
C++: protocols::features::FeaturesReporter::delete_record(unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> void
- features_reporter_dependencies(self: pyrosetta.rosetta.protocols.features.ProteinBondGeometryFeatures) pyrosetta.rosetta.utility.vector1_std_string ¶
return the set of features reporters that are required to also already be extracted by the time this one is used.
C++: protocols::features::ProteinBondGeometryFeatures::features_reporter_dependencies() const –> class utility::vector1<std::string, class std::allocator<std::string > >
- get_relevant_residues_mode(self: pyrosetta.rosetta.protocols.features.FeaturesReporter) pyrosetta.rosetta.protocols.features.RelevantResiduesMode.T ¶
C++: protocols::features::FeaturesReporter::get_relevant_residues_mode() const –> enum protocols::features::RelevantResiduesMode::T
- load_into_pose(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, : pyrosetta.rosetta.utility.sql_database.session, : int, : pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::features::FeaturesReporter::load_into_pose(class std::shared_ptr<class utility::sql_database::session>, unsigned long, class core::pose::Pose &) –> void
- parse_my_tag(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None ¶
C++: protocols::features::FeaturesReporter::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None ¶
C++: protocols::features::ProteinBondGeometryFeatures::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void
- report_features(self: pyrosetta.rosetta.protocols.features.ProteinBondGeometryFeatures, pose: pyrosetta.rosetta.core.pose.Pose, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, struct_id: int, db_session: pyrosetta.rosetta.utility.sql_database.session) int ¶
collect all the feature data for the pose
C++: protocols::features::ProteinBondGeometryFeatures::report_features(const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> unsigned long
- report_interres_angles(self: pyrosetta.rosetta.protocols.features.ProteinBondGeometryFeatures, pose: pyrosetta.rosetta.core.pose.Pose, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, struct_id: int, db_session: pyrosetta.rosetta.utility.sql_database.session) None ¶
C++: protocols::features::ProteinBondGeometryFeatures::report_interres_angles(const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> void
- report_interres_lengths(self: pyrosetta.rosetta.protocols.features.ProteinBondGeometryFeatures, pose: pyrosetta.rosetta.core.pose.Pose, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, struct_id: int, db_session: pyrosetta.rosetta.utility.sql_database.session) None ¶
C++: protocols::features::ProteinBondGeometryFeatures::report_interres_lengths(const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> void
- report_intrares_angles(self: pyrosetta.rosetta.protocols.features.ProteinBondGeometryFeatures, pose: pyrosetta.rosetta.core.pose.Pose, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, struct_id: int, db_session: pyrosetta.rosetta.utility.sql_database.session) None ¶
C++: protocols::features::ProteinBondGeometryFeatures::report_intrares_angles(const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> void
- report_intrares_lengths(self: pyrosetta.rosetta.protocols.features.ProteinBondGeometryFeatures, pose: pyrosetta.rosetta.core.pose.Pose, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, struct_id: int, db_session: pyrosetta.rosetta.utility.sql_database.session) None ¶
C++: protocols::features::ProteinBondGeometryFeatures::report_intrares_lengths(const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> void
- report_intrares_torsions(self: pyrosetta.rosetta.protocols.features.ProteinBondGeometryFeatures, pose: pyrosetta.rosetta.core.pose.Pose, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, struct_id: int, db_session: pyrosetta.rosetta.utility.sql_database.session) None ¶
C++: protocols::features::ProteinBondGeometryFeatures::report_intrares_torsions(const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> void
- schema(self: pyrosetta.rosetta.protocols.features.FeaturesReporter) str ¶
return sql statements that sets up the appropriate tables to contain the features. This should be removed once everything has been moved to the schema generator
C++: protocols::features::FeaturesReporter::schema() const –> std::string
- set_relevant_residues_mode(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, setting: pyrosetta.rosetta.protocols.features.RelevantResiduesMode.T) None ¶
C++: protocols::features::FeaturesReporter::set_relevant_residues_mode(enum protocols::features::RelevantResiduesMode::T) –> void
- type_name(self: pyrosetta.rosetta.protocols.features.ProteinBondGeometryFeatures) str ¶
C++: protocols::features::ProteinBondGeometryFeatures::type_name() const –> std::string
- write_schema_to_db(self: pyrosetta.rosetta.protocols.features.ProteinBondGeometryFeatures, db_session: pyrosetta.rosetta.utility.sql_database.session) None ¶
generate the table schemas and write them to the database
C++: protocols::features::ProteinBondGeometryFeatures::write_schema_to_db(class std::shared_ptr<class utility::sql_database::session>) const –> void
- class pyrosetta.rosetta.protocols.features.ProteinBondGeometryFeaturesCreator¶
Bases:
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
C++: protocols::features::FeaturesReporter::check_relevant_residues(const class utility::vector1<bool, class std::allocator<bool> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> bool
- check_relevant_residues_range(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, relevant_residues: pyrosetta.rosetta.utility.vector1_bool, res1: int, res2: int) bool ¶
C++: protocols::features::FeaturesReporter::check_relevant_residues_range(const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, unsigned long) const –> bool
- static class_name() str ¶
C++: protocols::features::ProteinRMSDFeatures::class_name() –> std::string
- delete_record(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, : int, : pyrosetta.rosetta.utility.sql_database.session) None ¶
C++: protocols::features::FeaturesReporter::delete_record(unsigned long, class std::shared_ptr<class utility::sql_database::session>) –> void
- features_reporter_dependencies(self: pyrosetta.rosetta.protocols.features.ProteinRMSDFeatures) pyrosetta.rosetta.utility.vector1_std_string ¶
return the set of features reporters that are required to also already be extracted by the time this one is used.
C++: protocols::features::ProteinRMSDFeatures::features_reporter_dependencies() const –> class utility::vector1<std::string, class std::allocator<std::string > >
- get_relevant_residues_mode(self: pyrosetta.rosetta.protocols.features.FeaturesReporter) pyrosetta.rosetta.protocols.features.RelevantResiduesMode.T ¶
C++: protocols::features::FeaturesReporter::get_relevant_residues_mode() const –> enum protocols::features::RelevantResiduesMode::T
- load_into_pose(self: pyrosetta.rosetta.protocols.features.FeaturesReporter, : pyrosetta.rosetta.utility.sql_database.session, : int, : pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::features::FeaturesReporter::load_into_pose(class std::shared_ptr<class utility::sql_database::session>, unsigned long, class core::pose::Pose &) –> void
- parse_my_tag(self: pyrosetta.rosetta.protocols.features.ProteinRMSDFeatures, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None ¶
C++: protocols::features::ProteinRMSDFeatures::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None ¶
C++: protocols::features::ProteinRMSDFeatures::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void
- reference_pose(*args, **kwargs)¶
Overloaded function.
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(