| | |
- builtins.object
-
- BatchFeatures
- BetaTurnDetection
- DatabaseFilter
-
- TopCountOfAllInputs
- TopCountOfEachInput
- TopPercentOfAllInputs
- TopPercentOfEachInput
- FeaturesReporter
-
- AtomAtomPairFeatures
- AtomInResidueAtomInResiduePairFeatures
- AtomTypesFeatures
- BetaTurnDetectionFeatures
- ChargeChargeFeatures
- DdGFeatures
- GeometricSolvationFeatures
- HBondFeatures
- HBondParameterFeatures
- HelixCapFeatures
- InterfaceFeatures
- JobDataFeatures
- LoopAnchorFeatures
- ModelFeatures
- OrbitalsFeatures
- PairFeatures
- PdbDataFeatures
- PoseCommentsFeatures
- PoseConformationFeatures
- ProteinBackboneAtomAtomPairFeatures
- ProteinBackboneTorsionAngleFeatures
- ProteinBondGeometryFeatures
- ProteinRMSDFeatures
- ProteinRMSDNoSuperpositionFeatures
- ProteinResidueConformationFeatures
- RadiusOfGyrationFeatures
- ResidueBurialFeatures
- ResidueConformationFeatures
- ResidueFeatures
- ResidueGridScoresFeatures
- ResidueScoresFeatures
- ResidueSecondaryStructureFeatures
- ResidueTotalScoresFeatures
- ResidueTypesFeatures
- RotamerBoltzmannWeightFeatures
- RotamerFeatures
- RotamerRecoveryFeatures
- RuntimeFeatures
- SaltBridgeFeatures
- ScoreFunctionFeatures
- ScoreTypeFeatures
- ScreeningFeatures
- SecondaryStructureSegmentFeatures
- SmotifFeatures
- StructureFeatures
- StructureScoresFeatures
- TaskOperationFeatures
- TotalScoreFeatures
- TrajectoryMapFeatures
- UnrecognizedAtomFeatures
- WaterFeatures
- FeaturesReporterCreator
-
- AtomAtomPairFeaturesCreator
- AtomInResidueAtomInResiduePairFeaturesCreator
- AtomTypesFeaturesCreator
- BetaTurnDetectionFeaturesCreator
- ChargeChargeFeaturesCreator
- DdGFeaturesCreator
- GeometricSolvationFeaturesCreator
- HBondFeaturesCreator
- HBondParameterFeaturesCreator
- HelixCapFeaturesCreator
- InterfaceFeaturesCreator
- JobDataFeaturesCreator
- LoopAnchorFeaturesCreator
- ModelFeaturesCreator
- OrbitalsFeaturesCreator
- PairFeaturesCreator
- PdbDataFeaturesCreator
- PoseCommentsFeaturesCreator
- PoseConformationFeaturesCreator
- ProteinBackboneAtomAtomPairFeaturesCreator
- ProteinBackboneTorsionAngleFeaturesCreator
- ProteinBondGeometryFeaturesCreator
- ProteinRMSDFeaturesCreator
- ProteinRMSDNoSuperpositionFeaturesCreator
- ProteinResidueConformationFeaturesCreator
- RadiusOfGyrationFeaturesCreator
- ResidueBurialFeaturesCreator
- ResidueConformationFeaturesCreator
- ResidueFeaturesCreator
- ResidueGridScoresFeaturesCreator
- ResidueScoresFeaturesCreator
- ResidueSecondaryStructureFeaturesCreator
- ResidueTotalScoresFeaturesCreator
- ResidueTypesFeaturesCreator
- RotamerBoltzmannWeightFeaturesCreator
- RotamerFeaturesCreator
- RotamerRecoveryFeaturesCreator
- RuntimeFeaturesCreator
- SaltBridgeFeaturesCreator
- ScoreFunctionFeaturesCreator
- ScoreTypeFeaturesCreator
- ScreeningFeaturesCreator
- SecondaryStructureSegmentFeaturesCreator
- SmotifFeaturesCreator
- StructureFeaturesCreator
- StructureScoresFeaturesCreator
- TaskOperationFeaturesCreator
- TotalScoreFeaturesCreator
- TrajectoryMapFeaturesCreator
- UnrecognizedAtomFeaturesCreator
- WaterFeaturesCreator
- FeaturesReporterFactory
- HBDefType
- ProtocolFeatures
- RamachandranHash
- Report
-
- ProteinSilentReport
- SecondaryStructureSegment
- Segment
- clique_saver
- rosetta.protocols.jd2.FileJobOutputter(rosetta.protocols.jd2.JobOutputter)
-
- DatabaseJobOutputter
- rosetta.protocols.jd2.JobInputter(builtins.object)
-
- DatabaseJobInputter
- rosetta.protocols.jd2.JobInputterCreator(builtins.object)
-
- DatabaseJobInputterCreator
- rosetta.protocols.jd2.JobOutputterCreator(builtins.object)
-
- DatabaseJobOutputterCreator
- rosetta.protocols.moves.Mover(builtins.object)
-
- ReportToDB
-
- TrajectoryReportToDB
- rosetta.protocols.moves.MoverCreator(builtins.object)
-
- ReportToDBCreator
- TrajectoryReportToDBCreator
class AtomAtomPairFeatures(FeaturesReporter) |
| | |
- Method resolution order:
- AtomAtomPairFeatures
- FeaturesReporter
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.protocols.features.AtomAtomPairFeatures) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.features.AtomAtomPairFeatures, : rosetta.protocols.features.AtomAtomPairFeatures) -> rosetta.protocols.features.AtomAtomPairFeatures
- features_reporter_dependencies(...) from builtins.PyCapsule
- features_reporter_dependencies(rosetta.protocols.features.AtomAtomPairFeatures) -> 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.
- report_atom_pairs(...) from builtins.PyCapsule
- report_atom_pairs(self : rosetta.protocols.features.AtomAtomPairFeatures, pose : rosetta.core.pose.Pose, relevant_residues : rosetta.utility.vector1_bool, struct_id : int, db_session : rosetta.utility.sql_database.session) -> NoneType
- report_features(...) from builtins.PyCapsule
- report_features(self : rosetta.protocols.features.AtomAtomPairFeatures, pose : rosetta.core.pose.Pose, relevant_residues : rosetta.utility.vector1_bool, struct_id : int, db_session : rosetta.utility.sql_database.session) -> int
collect all the feature data for the pose
- type_name(...) from builtins.PyCapsule
- type_name(rosetta.protocols.features.AtomAtomPairFeatures) -> str
return string with class name
- write_schema_to_db(...) from builtins.PyCapsule
- write_schema_to_db(self : rosetta.protocols.features.AtomAtomPairFeatures, db_session : rosetta.utility.sql_database.session) -> NoneType
generate the table schemas and write them to the database
Methods inherited from FeaturesReporter:
- check_relevant_residues(...) from builtins.PyCapsule
- check_relevant_residues(*args, **kwargs)
Overloaded function.
1. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int) -> bool
2. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool
3. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, residues : rosetta.utility.vector1_unsigned_long) -> bool
- check_relevant_residues_range(...) from builtins.PyCapsule
- check_relevant_residues_range(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool
- delete_record(...) from builtins.PyCapsule
- delete_record(self : rosetta.protocols.features.FeaturesReporter, : int, : rosetta.utility.sql_database.session) -> NoneType
- get_relevant_residues_mode(...) from builtins.PyCapsule
- get_relevant_residues_mode(rosetta.protocols.features.FeaturesReporter) -> rosetta.protocols.features.RelevantResiduesMode.T
- load_into_pose(...) from builtins.PyCapsule
- load_into_pose(self : rosetta.protocols.features.FeaturesReporter, : rosetta.utility.sql_database.session, : int, : rosetta.core.pose.Pose) -> NoneType
- schema(...) from builtins.PyCapsule
- schema(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
- set_relevant_residues_mode(...) from builtins.PyCapsule
- set_relevant_residues_mode(self : rosetta.protocols.features.FeaturesReporter, setting : rosetta.protocols.features.RelevantResiduesMode.T) -> NoneType
|
class AtomInResidueAtomInResiduePairFeatures(FeaturesReporter) |
| | |
- Method resolution order:
- AtomInResidueAtomInResiduePairFeatures
- FeaturesReporter
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.protocols.features.AtomInResidueAtomInResiduePairFeatures) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.features.AtomInResidueAtomInResiduePairFeatures, : rosetta.protocols.features.AtomInResidueAtomInResiduePairFeatures) -> rosetta.protocols.features.AtomInResidueAtomInResiduePairFeatures
- features_reporter_dependencies(...) from builtins.PyCapsule
- features_reporter_dependencies(rosetta.protocols.features.AtomInResidueAtomInResiduePairFeatures) -> 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.
- report_atom_pairs(...) from builtins.PyCapsule
- report_atom_pairs(self : rosetta.protocols.features.AtomInResidueAtomInResiduePairFeatures, pose : rosetta.core.pose.Pose, relevant_residues : rosetta.utility.vector1_bool, struct_id : int, db_session : rosetta.utility.sql_database.session) -> NoneType
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.
- report_features(...) from builtins.PyCapsule
- report_features(self : rosetta.protocols.features.AtomInResidueAtomInResiduePairFeatures, pose : rosetta.core.pose.Pose, relevant_residues : rosetta.utility.vector1_bool, struct_id : int, db_session : rosetta.utility.sql_database.session) -> int
collect all the feature data for the pose
- type_name(...) from builtins.PyCapsule
- type_name(rosetta.protocols.features.AtomInResidueAtomInResiduePairFeatures) -> str
return string with class name
- write_schema_to_db(...) from builtins.PyCapsule
- write_schema_to_db(self : rosetta.protocols.features.AtomInResidueAtomInResiduePairFeatures, db_session : rosetta.utility.sql_database.session) -> NoneType
generate the table schemas and write them to the database
Methods inherited from FeaturesReporter:
- check_relevant_residues(...) from builtins.PyCapsule
- check_relevant_residues(*args, **kwargs)
Overloaded function.
1. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int) -> bool
2. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool
3. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, residues : rosetta.utility.vector1_unsigned_long) -> bool
- check_relevant_residues_range(...) from builtins.PyCapsule
- check_relevant_residues_range(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool
- delete_record(...) from builtins.PyCapsule
- delete_record(self : rosetta.protocols.features.FeaturesReporter, : int, : rosetta.utility.sql_database.session) -> NoneType
- get_relevant_residues_mode(...) from builtins.PyCapsule
- get_relevant_residues_mode(rosetta.protocols.features.FeaturesReporter) -> rosetta.protocols.features.RelevantResiduesMode.T
- load_into_pose(...) from builtins.PyCapsule
- load_into_pose(self : rosetta.protocols.features.FeaturesReporter, : rosetta.utility.sql_database.session, : int, : rosetta.core.pose.Pose) -> NoneType
- schema(...) from builtins.PyCapsule
- schema(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
- set_relevant_residues_mode(...) from builtins.PyCapsule
- set_relevant_residues_mode(self : rosetta.protocols.features.FeaturesReporter, setting : rosetta.protocols.features.RelevantResiduesMode.T) -> NoneType
|
class AtomTypesFeatures(FeaturesReporter) |
| | |
- Method resolution order:
- AtomTypesFeatures
- FeaturesReporter
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(handle) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.features.AtomTypesFeatures, : rosetta.protocols.features.AtomTypesFeatures) -> rosetta.protocols.features.AtomTypesFeatures
- features_reporter_dependencies(...) from builtins.PyCapsule
- features_reporter_dependencies(rosetta.protocols.features.AtomTypesFeatures) -> 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.
- report_features(...) from builtins.PyCapsule
- report_features(self : rosetta.protocols.features.AtomTypesFeatures, pose : rosetta.core.pose.Pose, relevant_residues : rosetta.utility.vector1_bool, struct_id : int, db_session : rosetta.utility.sql_database.session) -> int
collect all the feature data for the pose
- type_name(...) from builtins.PyCapsule
- type_name(rosetta.protocols.features.AtomTypesFeatures) -> str
return string with class name
- write_schema_to_db(...) from builtins.PyCapsule
- write_schema_to_db(self : rosetta.protocols.features.AtomTypesFeatures, db_session : rosetta.utility.sql_database.session) -> NoneType
generate the table schemas and write them to the database
Methods inherited from FeaturesReporter:
- check_relevant_residues(...) from builtins.PyCapsule
- check_relevant_residues(*args, **kwargs)
Overloaded function.
1. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int) -> bool
2. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool
3. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, residues : rosetta.utility.vector1_unsigned_long) -> bool
- check_relevant_residues_range(...) from builtins.PyCapsule
- check_relevant_residues_range(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool
- delete_record(...) from builtins.PyCapsule
- delete_record(self : rosetta.protocols.features.FeaturesReporter, : int, : rosetta.utility.sql_database.session) -> NoneType
- get_relevant_residues_mode(...) from builtins.PyCapsule
- get_relevant_residues_mode(rosetta.protocols.features.FeaturesReporter) -> rosetta.protocols.features.RelevantResiduesMode.T
- load_into_pose(...) from builtins.PyCapsule
- load_into_pose(self : rosetta.protocols.features.FeaturesReporter, : rosetta.utility.sql_database.session, : int, : rosetta.core.pose.Pose) -> NoneType
- schema(...) from builtins.PyCapsule
- schema(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
- set_relevant_residues_mode(...) from builtins.PyCapsule
- set_relevant_residues_mode(self : rosetta.protocols.features.FeaturesReporter, setting : rosetta.protocols.features.RelevantResiduesMode.T) -> NoneType
|
class BatchFeatures(builtins.object) |
| | |
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.protocols.features.BatchFeatures) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.features.BatchFeatures, : rosetta.protocols.features.BatchFeatures) -> rosetta.protocols.features.BatchFeatures
- features_reporter_dependencies(...) from builtins.PyCapsule
- features_reporter_dependencies(rosetta.protocols.features.BatchFeatures) -> 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.
- indices(...) from builtins.PyCapsule
- indices(rosetta.protocols.features.BatchFeatures) -> str
return sql statements that setup helpful indices on the tables
- report_features(...) from builtins.PyCapsule
- report_features(self : rosetta.protocols.features.BatchFeatures, batch_id : int, protocol_id : int, name : str, description : str, db_session : rosetta.utility.sql_database.session) -> int
- type_name(...) from builtins.PyCapsule
- type_name(rosetta.protocols.features.BatchFeatures) -> str
return string with class name
- write_schema_to_db(...) from builtins.PyCapsule
- write_schema_to_db(self : rosetta.protocols.features.BatchFeatures, db_session : rosetta.utility.sql_database.session, batch_id : int) -> NoneType
generate the table schemas and write them to the database
|
class BetaTurnDetection(builtins.object) |
| | |
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.protocols.features.BetaTurnDetection) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- all_turn_residues_are_on_the_same_chain(...) from builtins.PyCapsule
- all_turn_residues_are_on_the_same_chain(self : rosetta.protocols.features.BetaTurnDetection, pose : rosetta.core.pose.Pose, first_residue : int) -> bool
- beta_turn_distance_cutoff(...) from builtins.PyCapsule
- beta_turn_distance_cutoff(rosetta.protocols.features.BetaTurnDetection) -> float
- beta_turn_length(...) from builtins.PyCapsule
- beta_turn_length(rosetta.protocols.features.BetaTurnDetection) -> int
- beta_turn_present(...) from builtins.PyCapsule
- beta_turn_present(self : rosetta.protocols.features.BetaTurnDetection, pose : rosetta.core.pose.Pose, first_residue : int) -> bool
- beta_turn_type(...) from builtins.PyCapsule
- beta_turn_type(self : rosetta.protocols.features.BetaTurnDetection, pose : rosetta.core.pose.Pose, first_residue : int) -> str
- determine_ramachandran_hash(...) from builtins.PyCapsule
- determine_ramachandran_hash(self : rosetta.protocols.features.BetaTurnDetection, pose : rosetta.core.pose.Pose, first_residue : int) -> str
- determine_ramachandran_hash_for_residue_with_dihedrals(...) from builtins.PyCapsule
- determine_ramachandran_hash_for_residue_with_dihedrals(self : rosetta.protocols.features.BetaTurnDetection, phi : float, psi : float, omega : float) -> str
- get_conformation_to_turn_type_map(...) from builtins.PyCapsule
- get_conformation_to_turn_type_map() -> rosetta.std.map_std_string_std_string
- get_valid_ramachandran_hashes(...) from builtins.PyCapsule
- get_valid_ramachandran_hashes() -> rosetta.utility.vector1_std_string
- residue_range_is_protein(...) from builtins.PyCapsule
- residue_range_is_protein(self : rosetta.protocols.features.BetaTurnDetection, pose : rosetta.core.pose.Pose, range_begin : int, range_end : int) -> bool
- type_name(...) from builtins.PyCapsule
- type_name(rosetta.protocols.features.BetaTurnDetection) -> str
return string with class name
- validate_ramachandran_hash(...) from builtins.PyCapsule
- validate_ramachandran_hash(self : rosetta.protocols.features.BetaTurnDetection, rama_hash : str) -> NoneType
|
class BetaTurnDetectionFeatures(FeaturesReporter) |
| | |
- Method resolution order:
- BetaTurnDetectionFeatures
- FeaturesReporter
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.protocols.features.BetaTurnDetectionFeatures) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.features.BetaTurnDetectionFeatures, : rosetta.protocols.features.BetaTurnDetectionFeatures) -> rosetta.protocols.features.BetaTurnDetectionFeatures
- features_reporter_dependencies(...) from builtins.PyCapsule
- features_reporter_dependencies(rosetta.protocols.features.BetaTurnDetectionFeatures) -> 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.
- report_features(...) from builtins.PyCapsule
- report_features(self : rosetta.protocols.features.BetaTurnDetectionFeatures, pose : rosetta.core.pose.Pose, : rosetta.utility.vector1_bool, struct_id : int, db_session : rosetta.utility.sql_database.session) -> int
collect all the feature data for the pose
- type_name(...) from builtins.PyCapsule
- type_name(rosetta.protocols.features.BetaTurnDetectionFeatures) -> str
return string with class name
- write_schema_to_db(...) from builtins.PyCapsule
- write_schema_to_db(self : rosetta.protocols.features.BetaTurnDetectionFeatures, db_session : rosetta.utility.sql_database.session) -> NoneType
generate the table schemas and write them to the database
Methods inherited from FeaturesReporter:
- check_relevant_residues(...) from builtins.PyCapsule
- check_relevant_residues(*args, **kwargs)
Overloaded function.
1. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int) -> bool
2. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool
3. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, residues : rosetta.utility.vector1_unsigned_long) -> bool
- check_relevant_residues_range(...) from builtins.PyCapsule
- check_relevant_residues_range(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool
- delete_record(...) from builtins.PyCapsule
- delete_record(self : rosetta.protocols.features.FeaturesReporter, : int, : rosetta.utility.sql_database.session) -> NoneType
- get_relevant_residues_mode(...) from builtins.PyCapsule
- get_relevant_residues_mode(rosetta.protocols.features.FeaturesReporter) -> rosetta.protocols.features.RelevantResiduesMode.T
- load_into_pose(...) from builtins.PyCapsule
- load_into_pose(self : rosetta.protocols.features.FeaturesReporter, : rosetta.utility.sql_database.session, : int, : rosetta.core.pose.Pose) -> NoneType
- schema(...) from builtins.PyCapsule
- schema(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
- set_relevant_residues_mode(...) from builtins.PyCapsule
- set_relevant_residues_mode(self : rosetta.protocols.features.FeaturesReporter, setting : rosetta.protocols.features.RelevantResiduesMode.T) -> NoneType
|
class ChargeChargeFeatures(FeaturesReporter) |
| | |
- Method resolution order:
- ChargeChargeFeatures
- FeaturesReporter
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(self : handle, distance_cutoff : float) -> NoneType
3. __init__(handle, rosetta.protocols.features.ChargeChargeFeatures) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.features.ChargeChargeFeatures, : rosetta.protocols.features.ChargeChargeFeatures) -> rosetta.protocols.features.ChargeChargeFeatures
- distance_cutoff(...) from builtins.PyCapsule
- distance_cutoff(*args, **kwargs)
Overloaded function.
1. distance_cutoff(rosetta.protocols.features.ChargeChargeFeatures) -> float
2. distance_cutoff(self : rosetta.protocols.features.ChargeChargeFeatures, d : float) -> NoneType
- features_reporter_dependencies(...) from builtins.PyCapsule
- features_reporter_dependencies(rosetta.protocols.features.ChargeChargeFeatures) -> 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.
- report_features(...) from builtins.PyCapsule
- report_features(self : rosetta.protocols.features.ChargeChargeFeatures, pose : rosetta.core.pose.Pose, : rosetta.utility.vector1_bool, struct_id : int, db_session : rosetta.utility.sql_database.session) -> int
collect all the feature data for the pose
- type_name(...) from builtins.PyCapsule
- type_name(rosetta.protocols.features.ChargeChargeFeatures) -> str
return string with class name
- write_schema_to_db(...) from builtins.PyCapsule
- write_schema_to_db(self : rosetta.protocols.features.ChargeChargeFeatures, db_session : rosetta.utility.sql_database.session) -> NoneType
generate the table schemas and write them to the database
Methods inherited from FeaturesReporter:
- check_relevant_residues(...) from builtins.PyCapsule
- check_relevant_residues(*args, **kwargs)
Overloaded function.
1. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int) -> bool
2. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool
3. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, residues : rosetta.utility.vector1_unsigned_long) -> bool
- check_relevant_residues_range(...) from builtins.PyCapsule
- check_relevant_residues_range(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool
- delete_record(...) from builtins.PyCapsule
- delete_record(self : rosetta.protocols.features.FeaturesReporter, : int, : rosetta.utility.sql_database.session) -> NoneType
- get_relevant_residues_mode(...) from builtins.PyCapsule
- get_relevant_residues_mode(rosetta.protocols.features.FeaturesReporter) -> rosetta.protocols.features.RelevantResiduesMode.T
- load_into_pose(...) from builtins.PyCapsule
- load_into_pose(self : rosetta.protocols.features.FeaturesReporter, : rosetta.utility.sql_database.session, : int, : rosetta.core.pose.Pose) -> NoneType
- schema(...) from builtins.PyCapsule
- schema(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
- set_relevant_residues_mode(...) from builtins.PyCapsule
- set_relevant_residues_mode(self : rosetta.protocols.features.FeaturesReporter, setting : rosetta.protocols.features.RelevantResiduesMode.T) -> NoneType
|
class DatabaseJobInputter(rosetta.protocols.jd2.JobInputter) |
| |
This is the simplest implementation of JobInputter, which
reads from -s/-l and Database files.
|
| |
- Method resolution order:
- DatabaseJobInputter
- rosetta.protocols.jd2.JobInputter
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.protocols.features.DatabaseJobInputter) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.features.DatabaseJobInputter, : rosetta.protocols.features.DatabaseJobInputter) -> rosetta.protocols.features.DatabaseJobInputter
- fill_jobs(...) from builtins.PyCapsule
- fill_jobs(self : rosetta.protocols.features.DatabaseJobInputter, jobs : rosetta.protocols.jd2.JobsContainer) -> NoneType
this function determines what jobs exist from -in::file::silent and
-in::file::tags.
- get_database_name(...) from builtins.PyCapsule
- get_database_name(rosetta.protocols.features.DatabaseJobInputter) -> str
Get database name
- get_database_pq_schema(...) from builtins.PyCapsule
- get_database_pq_schema(rosetta.protocols.features.DatabaseJobInputter) -> str
Get database postreSQL schema
- get_scorefunction(...) from builtins.PyCapsule
- get_scorefunction(rosetta.protocols.features.DatabaseJobInputter) -> rosetta.core.scoring.ScoreFunction
Get score function
- input_source(...) from builtins.PyCapsule
- input_source(rosetta.protocols.features.DatabaseJobInputter) -> rosetta.protocols.jd2.JobInputterInputSource.Enum
Return the type of input source that the DatabaseJobInputter is currently
using.
Always DATABASE.
- load_options_from_option_system(...) from builtins.PyCapsule
- load_options_from_option_system(rosetta.protocols.features.DatabaseJobInputter) -> NoneType
load options from option sytem
- pose_from_job(...) from builtins.PyCapsule
- pose_from_job(self : rosetta.protocols.features.DatabaseJobInputter, pose : rosetta.core.pose.Pose, job : rosetta.protocols.jd2.Job) -> NoneType
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
- register_options(...) from builtins.PyCapsule
- register_options() -> NoneType
- set_database_name(...) from builtins.PyCapsule
- set_database_name(self : rosetta.protocols.features.DatabaseJobInputter, database_name : str) -> NoneType
Set database name
- set_database_pq_schema(...) from builtins.PyCapsule
- set_database_pq_schema(self : rosetta.protocols.features.DatabaseJobInputter, database_pq_schema : str) -> NoneType
Set database postreSQL schema
- set_scorefunction(...) from builtins.PyCapsule
- set_scorefunction(self : rosetta.protocols.features.DatabaseJobInputter, scorefunction : rosetta.core.scoring.ScoreFunction) -> NoneType
Set score function
- set_struct_ids_from_sql(...) from builtins.PyCapsule
- set_struct_ids_from_sql(self : rosetta.protocols.features.DatabaseJobInputter, sql : rosetta.utility.vector1_std_string) -> NoneType
set input tags using a database SELECT command
- set_struct_ids_from_strings(...) from builtins.PyCapsule
- set_struct_ids_from_strings(self : rosetta.protocols.features.DatabaseJobInputter, struct_id_strings : rosetta.utility.vector1_std_string) -> NoneType
set struct_ids from a list of strings of integer representations
Methods inherited from rosetta.protocols.jd2.JobInputter:
- get_self_ptr(...) from builtins.PyCapsule
- get_self_ptr(*args, **kwargs)
Overloaded function.
1. get_self_ptr(rosetta.protocols.jd2.JobInputter) -> rosetta.protocols.jd2.JobInputter
Get self const owning pointers.
2. get_self_ptr(rosetta.protocols.jd2.JobInputter) -> rosetta.protocols.jd2.JobInputter
Get self owning pointers.
- get_self_weak_ptr(...) from builtins.PyCapsule
- get_self_weak_ptr(*args, **kwargs)
Overloaded function.
1. get_self_weak_ptr(rosetta.protocols.jd2.JobInputter) -> rosetta.std.weak_ptr_const_protocols_jd2_JobInputter_t
Get self const weak pointers.
2. get_self_weak_ptr(rosetta.protocols.jd2.JobInputter) -> rosetta.std.weak_ptr_protocols_jd2_JobInputter_t
Get self weak pointers.
- job_inputter_input_source_to_string(...) from builtins.PyCapsule
- job_inputter_input_source_to_string(source : rosetta.protocols.jd2.JobInputterInputSource.Enum) -> str
call this with input_source() to get the input source of a
particular job inputter
- update_jobs_list(...) from builtins.PyCapsule
- update_jobs_list(self : rosetta.protocols.jd2.JobInputter, jobs : protocols::jd2::JobsContainer) -> NoneType
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.
- updates_jobs_list(...) from builtins.PyCapsule
- updates_jobs_list(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.
|
class DatabaseJobOutputter(rosetta.protocols.jd2.FileJobOutputter) |
| |
this is a implementation of JobOutputter for database-based output.
|
| |
- Method resolution order:
- DatabaseJobOutputter
- rosetta.protocols.jd2.FileJobOutputter
- rosetta.protocols.jd2.JobOutputter
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(handle) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- final_pose(...) from builtins.PyCapsule
- final_pose(self : rosetta.protocols.features.DatabaseJobOutputter, job : rosetta.protocols.jd2.Job, pose : rosetta.core.pose.Pose, tag : str) -> NoneType
this function outputs the final result of a job.
- flush(...) from builtins.PyCapsule
- flush(rosetta.protocols.features.DatabaseJobOutputter) -> NoneType
see parent class for explanation
- get_database_name(...) from builtins.PyCapsule
- get_database_name(rosetta.protocols.features.DatabaseJobOutputter) -> str
Get database name
- get_database_pq_schema(...) from builtins.PyCapsule
- get_database_pq_schema(rosetta.protocols.features.DatabaseJobOutputter) -> str
Get database postgresQL schema
- job_has_completed(...) from builtins.PyCapsule
- job_has_completed(self : rosetta.protocols.features.DatabaseJobOutputter, job : rosetta.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.
- load_options_from_option_system(...) from builtins.PyCapsule
- load_options_from_option_system(rosetta.protocols.features.DatabaseJobOutputter) -> NoneType
load options from option sytem
- other_pose(...) from builtins.PyCapsule
- other_pose(*args, **kwargs)
Overloaded function.
1. other_pose(self : rosetta.protocols.features.DatabaseJobOutputter, job : rosetta.protocols.jd2.Job, pose : rosetta.core.pose.Pose, tag : str) -> NoneType
this function is intended for saving mid-protocol poses;
for example the final centroid structure in a combined
centroid/fullatom protocol.
2. other_pose(self : rosetta.protocols.features.DatabaseJobOutputter, job : rosetta.protocols.jd2.Job, pose : rosetta.core.pose.Pose, tag : str, copy_count : int) -> NoneType
this function is intended for saving mid-protocol poses;
for example the final centroid structure in a combined
centroid/fullatom protocol.
3. other_pose(self : rosetta.protocols.features.DatabaseJobOutputter, job : rosetta.protocols.jd2.Job, pose : rosetta.core.pose.Pose, tag : str, copy_count : int, score_only : bool) -> NoneType
this function is intended for saving mid-protocol poses;
for example the final centroid structure in a combined
centroid/fullatom protocol.
- output_name(...) from builtins.PyCapsule
- output_name(self : rosetta.protocols.features.DatabaseJobOutputter, job : rosetta.protocols.jd2.Job) -> str
this is the master function for determining the
unique output identifier for a job
- register_options(...) from builtins.PyCapsule
- register_options() -> NoneType
- set_database_name(...) from builtins.PyCapsule
- set_database_name(self : rosetta.protocols.features.DatabaseJobOutputter, database_name : str) -> NoneType
Set database name
- set_database_pq_schema(...) from builtins.PyCapsule
- set_database_pq_schema(self : rosetta.protocols.features.DatabaseJobOutputter, database_pq_schema : str) -> NoneType
Set database postgreSQL schema
Methods inherited from rosetta.protocols.jd2.FileJobOutputter:
- file(...) from builtins.PyCapsule
- file(self : rosetta.protocols.jd2.FileJobOutputter, job : rosetta.protocols.jd2.Job, data : str) -> NoneType
this function takes a string and writes it to disk (separately from Tracer output).
- scorefile_name(...) from builtins.PyCapsule
- scorefile_name(rosetta.protocols.jd2.FileJobOutputter) -> rosetta.utility.file.FileName
- set_defaults(...) from builtins.PyCapsule
- set_defaults(rosetta.protocols.jd2.FileJobOutputter) -> NoneType
- write_scorefile(...) from builtins.PyCapsule
- write_scorefile(rosetta.protocols.jd2.FileJobOutputter) -> bool
Methods inherited from rosetta.protocols.jd2.JobOutputter:
- add_evaluation(...) from builtins.PyCapsule
- add_evaluation(self : rosetta.protocols.jd2.JobOutputter, : rosetta.protocols.evaluation.PoseEvaluator) -> NoneType
////////////////////////////// evaluator interface ////////////////////////////////////////////
- call_output_observers(...) from builtins.PyCapsule
- call_output_observers(self : rosetta.protocols.jd2.JobOutputter, pose : rosetta.core.pose.Pose, job : rosetta.protocols.jd2.Job) -> NoneType
call all output_observers
- clear_evaluators(...) from builtins.PyCapsule
- clear_evaluators(rosetta.protocols.jd2.JobOutputter) -> NoneType
- evaluate(...) from builtins.PyCapsule
- evaluate(self : rosetta.protocols.jd2.JobOutputter, pose : rosetta.core.pose.Pose, tag : str, pss : rosetta.core.io.silent.SilentStruct) -> NoneType
- evaluators(...) from builtins.PyCapsule
- evaluators(rosetta.protocols.jd2.JobOutputter) -> rosetta.protocols.evaluation.MetaPoseEvaluator
- filename(...) from builtins.PyCapsule
- filename(self : rosetta.protocols.jd2.JobOutputter, : rosetta.protocols.jd2.Job) -> str
- set_evaluators(...) from builtins.PyCapsule
- set_evaluators(self : rosetta.protocols.jd2.JobOutputter, : rosetta.protocols.evaluation.MetaPoseEvaluator) -> NoneType
- starting_pose(...) from builtins.PyCapsule
- starting_pose(self : rosetta.protocols.jd2.JobOutputter, : rosetta.core.pose.Pose) -> NoneType
optionally pass a starting (reference) pose to a JobOutputter for later comparison
purposes and/or as interface for initializing evaluators
|
class DdGFeatures(FeaturesReporter) |
| | |
- Method resolution order:
- DdGFeatures
- FeaturesReporter
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(self : handle, ddG_scan_mover : protocols::simple_filters::DdGScan) -> NoneType
3. __init__(handle, rosetta.protocols.features.DdGFeatures) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.features.DdGFeatures, : rosetta.protocols.features.DdGFeatures) -> rosetta.protocols.features.DdGFeatures
- features_reporter_dependencies(...) from builtins.PyCapsule
- features_reporter_dependencies(rosetta.protocols.features.DdGFeatures) -> 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.
- report_features(...) from builtins.PyCapsule
- report_features(self : rosetta.protocols.features.DdGFeatures, pose : rosetta.core.pose.Pose, relevant_residues : rosetta.utility.vector1_bool, struct_id : int, db_session : rosetta.utility.sql_database.session) -> int
collect all the feature data for the pose
- type_name(...) from builtins.PyCapsule
- type_name(rosetta.protocols.features.DdGFeatures) -> str
return string with class name
- write_ddG_table_schema(...) from builtins.PyCapsule
- write_ddG_table_schema(self : rosetta.protocols.features.DdGFeatures, db_session : rosetta.utility.sql_database.session) -> NoneType
- write_schema_to_db(...) from builtins.PyCapsule
- write_schema_to_db(self : rosetta.protocols.features.DdGFeatures, db_session : rosetta.utility.sql_database.session) -> NoneType
generate the table schemas and write them to the database
Methods inherited from FeaturesReporter:
- check_relevant_residues(...) from builtins.PyCapsule
- check_relevant_residues(*args, **kwargs)
Overloaded function.
1. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int) -> bool
2. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool
3. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, residues : rosetta.utility.vector1_unsigned_long) -> bool
- check_relevant_residues_range(...) from builtins.PyCapsule
- check_relevant_residues_range(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool
- delete_record(...) from builtins.PyCapsule
- delete_record(self : rosetta.protocols.features.FeaturesReporter, : int, : rosetta.utility.sql_database.session) -> NoneType
- get_relevant_residues_mode(...) from builtins.PyCapsule
- get_relevant_residues_mode(rosetta.protocols.features.FeaturesReporter) -> rosetta.protocols.features.RelevantResiduesMode.T
- load_into_pose(...) from builtins.PyCapsule
- load_into_pose(self : rosetta.protocols.features.FeaturesReporter, : rosetta.utility.sql_database.session, : int, : rosetta.core.pose.Pose) -> NoneType
- schema(...) from builtins.PyCapsule
- schema(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
- set_relevant_residues_mode(...) from builtins.PyCapsule
- set_relevant_residues_mode(self : rosetta.protocols.features.FeaturesReporter, setting : rosetta.protocols.features.RelevantResiduesMode.T) -> NoneType
|
class FeaturesReporter(builtins.object) |
| | |
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(rosetta.protocols.features.FeaturesReporter) -> NoneType
2. __init__(rosetta.protocols.features.FeaturesReporter, rosetta.protocols.features.FeaturesReporter) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.features.FeaturesReporter, : rosetta.protocols.features.FeaturesReporter) -> rosetta.protocols.features.FeaturesReporter
- check_relevant_residues(...) from builtins.PyCapsule
- check_relevant_residues(*args, **kwargs)
Overloaded function.
1. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int) -> bool
2. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool
3. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, residues : rosetta.utility.vector1_unsigned_long) -> bool
- check_relevant_residues_range(...) from builtins.PyCapsule
- check_relevant_residues_range(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool
- delete_record(...) from builtins.PyCapsule
- delete_record(self : rosetta.protocols.features.FeaturesReporter, : int, : rosetta.utility.sql_database.session) -> NoneType
- features_reporter_dependencies(...) from builtins.PyCapsule
- features_reporter_dependencies(rosetta.protocols.features.FeaturesReporter) -> 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.
- get_relevant_residues_mode(...) from builtins.PyCapsule
- get_relevant_residues_mode(rosetta.protocols.features.FeaturesReporter) -> rosetta.protocols.features.RelevantResiduesMode.T
- load_into_pose(...) from builtins.PyCapsule
- load_into_pose(self : rosetta.protocols.features.FeaturesReporter, : rosetta.utility.sql_database.session, : int, : rosetta.core.pose.Pose) -> NoneType
- report_features(...) from builtins.PyCapsule
- report_features(*args, **kwargs)
Overloaded function.
1. report_features(self : rosetta.protocols.features.FeaturesReporter, : rosetta.core.pose.Pose, : int, : rosetta.utility.sql_database.session) -> int
collect all the feature data for the pose.
2. report_features(self : rosetta.protocols.features.FeaturesReporter, : rosetta.core.pose.Pose, : rosetta.utility.vector1_bool, : int, : rosetta.utility.sql_database.session) -> int
collect all the feature data for the pose.
- schema(...) from builtins.PyCapsule
- schema(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
- set_relevant_residues_mode(...) from builtins.PyCapsule
- set_relevant_residues_mode(self : rosetta.protocols.features.FeaturesReporter, setting : rosetta.protocols.features.RelevantResiduesMode.T) -> NoneType
- type_name(...) from builtins.PyCapsule
- type_name(rosetta.protocols.features.FeaturesReporter) -> str
- write_schema_to_db(...) from builtins.PyCapsule
- write_schema_to_db(self : rosetta.protocols.features.FeaturesReporter, db_session : rosetta.utility.sql_database.session) -> NoneType
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
|
class GeometricSolvationFeatures(FeaturesReporter) |
| | |
- Method resolution order:
- GeometricSolvationFeatures
- FeaturesReporter
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.protocols.features.GeometricSolvationFeatures) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- features_reporter_dependencies(...) from builtins.PyCapsule
- features_reporter_dependencies(rosetta.protocols.features.GeometricSolvationFeatures) -> 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.
- report_features(...) from builtins.PyCapsule
- report_features(self : rosetta.protocols.features.GeometricSolvationFeatures, pose : rosetta.core.pose.Pose, : rosetta.utility.vector1_bool, struct_id : int, db_session : rosetta.utility.sql_database.session) -> int
collect all the feature data for the pose
- type_name(...) from builtins.PyCapsule
- type_name(rosetta.protocols.features.GeometricSolvationFeatures) -> str
return string with class name
- write_schema_to_db(...) from builtins.PyCapsule
- write_schema_to_db(self : rosetta.protocols.features.GeometricSolvationFeatures, db_session : rosetta.utility.sql_database.session) -> NoneType
generate the table schemas and write them to the database
Methods inherited from FeaturesReporter:
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.features.FeaturesReporter, : rosetta.protocols.features.FeaturesReporter) -> rosetta.protocols.features.FeaturesReporter
- check_relevant_residues(...) from builtins.PyCapsule
- check_relevant_residues(*args, **kwargs)
Overloaded function.
1. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int) -> bool
2. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool
3. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, residues : rosetta.utility.vector1_unsigned_long) -> bool
- check_relevant_residues_range(...) from builtins.PyCapsule
- check_relevant_residues_range(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool
- delete_record(...) from builtins.PyCapsule
- delete_record(self : rosetta.protocols.features.FeaturesReporter, : int, : rosetta.utility.sql_database.session) -> NoneType
- get_relevant_residues_mode(...) from builtins.PyCapsule
- get_relevant_residues_mode(rosetta.protocols.features.FeaturesReporter) -> rosetta.protocols.features.RelevantResiduesMode.T
- load_into_pose(...) from builtins.PyCapsule
- load_into_pose(self : rosetta.protocols.features.FeaturesReporter, : rosetta.utility.sql_database.session, : int, : rosetta.core.pose.Pose) -> NoneType
- schema(...) from builtins.PyCapsule
- schema(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
- set_relevant_residues_mode(...) from builtins.PyCapsule
- set_relevant_residues_mode(self : rosetta.protocols.features.FeaturesReporter, setting : rosetta.protocols.features.RelevantResiduesMode.T) -> NoneType
|
class HBondFeatures(FeaturesReporter) |
| | |
- Method resolution order:
- HBondFeatures
- FeaturesReporter
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(self : handle, scfxn : rosetta.core.scoring.ScoreFunction) -> NoneType
3. __init__(handle, rosetta.protocols.features.HBondFeatures) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.features.HBondFeatures, : rosetta.protocols.features.HBondFeatures) -> rosetta.protocols.features.HBondFeatures
- features_reporter_dependencies(...) from builtins.PyCapsule
- features_reporter_dependencies(rosetta.protocols.features.HBondFeatures) -> 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.
- insert_hbond_dehydron_row(...) from builtins.PyCapsule
- insert_hbond_dehydron_row(self : rosetta.protocols.features.HBondFeatures, pose : rosetta.core.pose.Pose, hbond : rosetta.core.scoring.hbonds.HBond, struct_id : int, hbond_id : int, db_session : rosetta.utility.sql_database.session) -> NoneType
- insert_hbond_geom_coords(...) from builtins.PyCapsule
- insert_hbond_geom_coords(self : rosetta.protocols.features.HBondFeatures, pose : rosetta.core.pose.Pose, hbond_options : rosetta.core.scoring.hbonds.HBondOptions, hbond : rosetta.core.scoring.hbonds.HBond, struct_id : int, hbond_id : int, db_session : rosetta.utility.sql_database.session) -> NoneType
- insert_hbond_lennard_jones_row(...) from builtins.PyCapsule
- insert_hbond_lennard_jones_row(self : rosetta.protocols.features.HBondFeatures, pose : rosetta.core.pose.Pose, hbond : rosetta.core.scoring.hbonds.HBond, struct_id : int, hbond_id : int, db_session : rosetta.utility.sql_database.session) -> NoneType
- insert_site_atoms_row(...) from builtins.PyCapsule
- insert_site_atoms_row(self : rosetta.protocols.features.HBondFeatures, pose : rosetta.core.pose.Pose, resNum : int, atmNum : int, struct_id : int, site_id : int, db_session : rosetta.utility.sql_database.session) -> NoneType
- insert_site_pdb_row(...) from builtins.PyCapsule
- insert_site_pdb_row(self : rosetta.protocols.features.HBondFeatures, pose : rosetta.core.pose.Pose, resNum : int, atmNum : int, heavy_atmNum : int, struct_id : int, site_id : int, db_session : rosetta.utility.sql_database.session) -> NoneType
- insert_site_row(...) from builtins.PyCapsule
- insert_site_row(self : rosetta.protocols.features.HBondFeatures, pose : rosetta.core.pose.Pose, struct_id : int, site_id : int, resNum : int, atmNum : int, is_donor : bool, db_session : rosetta.utility.sql_database.session) -> NoneType
- report_features(...) from builtins.PyCapsule
- report_features(self : rosetta.protocols.features.HBondFeatures, pose : rosetta.core.pose.Pose, relevant_residues : rosetta.utility.vector1_bool, struct_id : int, db_session : rosetta.utility.sql_database.session) -> int
collect all the feature data for the pose
- type_name(...) from builtins.PyCapsule
- type_name(rosetta.protocols.features.HBondFeatures) -> str
return string with class name
- write_schema_to_db(...) from builtins.PyCapsule
- write_schema_to_db(self : rosetta.protocols.features.HBondFeatures, db_session : rosetta.utility.sql_database.session) -> NoneType
generate the table schemas and write them to the database
Methods inherited from FeaturesReporter:
- check_relevant_residues(...) from builtins.PyCapsule
- check_relevant_residues(*args, **kwargs)
Overloaded function.
1. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int) -> bool
2. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool
3. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, residues : rosetta.utility.vector1_unsigned_long) -> bool
- check_relevant_residues_range(...) from builtins.PyCapsule
- check_relevant_residues_range(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool
- delete_record(...) from builtins.PyCapsule
- delete_record(self : rosetta.protocols.features.FeaturesReporter, : int, : rosetta.utility.sql_database.session) -> NoneType
- get_relevant_residues_mode(...) from builtins.PyCapsule
- get_relevant_residues_mode(rosetta.protocols.features.FeaturesReporter) -> rosetta.protocols.features.RelevantResiduesMode.T
- load_into_pose(...) from builtins.PyCapsule
- load_into_pose(self : rosetta.protocols.features.FeaturesReporter, : rosetta.utility.sql_database.session, : int, : rosetta.core.pose.Pose) -> NoneType
- schema(...) from builtins.PyCapsule
- schema(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
- set_relevant_residues_mode(...) from builtins.PyCapsule
- set_relevant_residues_mode(self : rosetta.protocols.features.FeaturesReporter, setting : rosetta.protocols.features.RelevantResiduesMode.T) -> NoneType
|
class HBondParameterFeatures(FeaturesReporter) |
| | |
- Method resolution order:
- HBondParameterFeatures
- FeaturesReporter
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(self : handle, scfxn : rosetta.core.scoring.ScoreFunction) -> NoneType
3. __init__(handle, rosetta.protocols.features.HBondParameterFeatures) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.features.HBondParameterFeatures, : rosetta.protocols.features.HBondParameterFeatures) -> rosetta.protocols.features.HBondParameterFeatures
- features_reporter_dependencies(...) from builtins.PyCapsule
- features_reporter_dependencies(rosetta.protocols.features.HBondParameterFeatures) -> 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.
- report_features(...) from builtins.PyCapsule
- report_features(self : rosetta.protocols.features.HBondParameterFeatures, pose : rosetta.core.pose.Pose, relevant_residues : rosetta.utility.vector1_bool, struct_id : int, db_session : rosetta.utility.sql_database.session) -> int
collect all the feature data for the pose
- type_name(...) from builtins.PyCapsule
- type_name(rosetta.protocols.features.HBondParameterFeatures) -> str
return string with class name
- write_schema_to_db(...) from builtins.PyCapsule
- write_schema_to_db(self : rosetta.protocols.features.HBondParameterFeatures, db_session : rosetta.utility.sql_database.session) -> NoneType
generate the table schemas and write them to the database
Methods inherited from FeaturesReporter:
- check_relevant_residues(...) from builtins.PyCapsule
- check_relevant_residues(*args, **kwargs)
Overloaded function.
1. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int) -> bool
2. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool
3. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, residues : rosetta.utility.vector1_unsigned_long) -> bool
- check_relevant_residues_range(...) from builtins.PyCapsule
- check_relevant_residues_range(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool
- delete_record(...) from builtins.PyCapsule
- delete_record(self : rosetta.protocols.features.FeaturesReporter, : int, : rosetta.utility.sql_database.session) -> NoneType
- get_relevant_residues_mode(...) from builtins.PyCapsule
- get_relevant_residues_mode(rosetta.protocols.features.FeaturesReporter) -> rosetta.protocols.features.RelevantResiduesMode.T
- load_into_pose(...) from builtins.PyCapsule
- load_into_pose(self : rosetta.protocols.features.FeaturesReporter, : rosetta.utility.sql_database.session, : int, : rosetta.core.pose.Pose) -> NoneType
- schema(...) from builtins.PyCapsule
- schema(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
- set_relevant_residues_mode(...) from builtins.PyCapsule
- set_relevant_residues_mode(self : rosetta.protocols.features.FeaturesReporter, setting : rosetta.protocols.features.RelevantResiduesMode.T) -> NoneType
|
class HelixCapFeatures(FeaturesReporter) |
| | |
- Method resolution order:
- HelixCapFeatures
- FeaturesReporter
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(self : handle, scfxn : rosetta.core.scoring.ScoreFunction) -> NoneType
3. __init__(handle, rosetta.protocols.features.HelixCapFeatures) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.features.HelixCapFeatures, : rosetta.protocols.features.HelixCapFeatures) -> rosetta.protocols.features.HelixCapFeatures
- features_reporter_dependencies(...) from builtins.PyCapsule
- features_reporter_dependencies(rosetta.protocols.features.HelixCapFeatures) -> 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.
- is_loop(...) from builtins.PyCapsule
- is_loop(self : rosetta.protocols.features.HelixCapFeatures, dssp_code : str) -> bool
- report_features(...) from builtins.PyCapsule
- report_features(self : rosetta.protocols.features.HelixCapFeatures, pose : rosetta.core.pose.Pose, relevant_residues : rosetta.utility.vector1_bool, struct_id : int, db_session : rosetta.utility.sql_database.session) -> int
collect all the feature data for the pose
- type_name(...) from builtins.PyCapsule
- type_name(rosetta.protocols.features.HelixCapFeatures) -> str
return string with class name
- write_schema_to_db(...) from builtins.PyCapsule
- write_schema_to_db(self : rosetta.protocols.features.HelixCapFeatures, db_session : rosetta.utility.sql_database.session) -> NoneType
generate the table schemas and write them to the database
Methods inherited from FeaturesReporter:
- check_relevant_residues(...) from builtins.PyCapsule
- check_relevant_residues(*args, **kwargs)
Overloaded function.
1. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int) -> bool
2. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool
3. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, residues : rosetta.utility.vector1_unsigned_long) -> bool
- check_relevant_residues_range(...) from builtins.PyCapsule
- check_relevant_residues_range(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool
- delete_record(...) from builtins.PyCapsule
- delete_record(self : rosetta.protocols.features.FeaturesReporter, : int, : rosetta.utility.sql_database.session) -> NoneType
- get_relevant_residues_mode(...) from builtins.PyCapsule
- get_relevant_residues_mode(rosetta.protocols.features.FeaturesReporter) -> rosetta.protocols.features.RelevantResiduesMode.T
- load_into_pose(...) from builtins.PyCapsule
- load_into_pose(self : rosetta.protocols.features.FeaturesReporter, : rosetta.utility.sql_database.session, : int, : rosetta.core.pose.Pose) -> NoneType
- schema(...) from builtins.PyCapsule
- schema(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
- set_relevant_residues_mode(...) from builtins.PyCapsule
- set_relevant_residues_mode(self : rosetta.protocols.features.FeaturesReporter, setting : rosetta.protocols.features.RelevantResiduesMode.T) -> NoneType
|
class InterfaceFeatures(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.
|
| |
- Method resolution order:
- InterfaceFeatures
- FeaturesReporter
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(self : handle, scorefxn : rosetta.core.scoring.ScoreFunction) -> NoneType
3. __init__(handle, rosetta.protocols.features.InterfaceFeatures) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.features.InterfaceFeatures, : rosetta.protocols.features.InterfaceFeatures) -> rosetta.protocols.features.InterfaceFeatures
- features_reporter_dependencies(...) from builtins.PyCapsule
- features_reporter_dependencies(rosetta.protocols.features.InterfaceFeatures) -> 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.
- make_interface_combos(...) from builtins.PyCapsule
- make_interface_combos(self : rosetta.protocols.features.InterfaceFeatures, pose : rosetta.core.pose.Pose, interfaces : rosetta.utility.vector1_std_string) -> NoneType
Gets all possible interface combinations of a given pose.
- report_all_interface_features(...) from builtins.PyCapsule
- report_all_interface_features(self : rosetta.protocols.features.InterfaceFeatures, pose : rosetta.core.pose.Pose, relevant_residues : rosetta.utility.vector1_bool, struct_id : int, db_session : rosetta.utility.sql_database.session, interface : str, db_interface : str) -> NoneType
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))
- report_features(...) from builtins.PyCapsule
- report_features(self : rosetta.protocols.features.InterfaceFeatures, pose : rosetta.core.pose.Pose, relevant_residues : rosetta.utility.vector1_bool, struct_id : int, db_session : rosetta.utility.sql_database.session) -> int
collect all the feature data for the pose
- report_interface_features(...) from builtins.PyCapsule
- report_interface_features(self : rosetta.protocols.features.InterfaceFeatures, pose : rosetta.core.pose.Pose, struct_id : int, db_session : rosetta.utility.sql_database.session, chains_side1 : str, chains_side2 : str) -> NoneType
Add interfaces table data to table
- report_interface_residue_features(...) from builtins.PyCapsule
- report_interface_residue_features(self : rosetta.protocols.features.InterfaceFeatures, pose : rosetta.core.pose.Pose, relevant_residues : rosetta.utility.vector1_bool, struct_id : int, db_session : rosetta.utility.sql_database.session, chains_side1 : str, chains_side2 : str) -> NoneType
Add interface_residues data to table
- report_interface_side_features(...) from builtins.PyCapsule
- report_interface_side_features(self : rosetta.protocols.features.InterfaceFeatures, pose : rosetta.core.pose.Pose, struct_id : int, db_session : rosetta.utility.sql_database.session, chains_side1 : str, chains_side2 : str, region : rosetta.protocols.analysis.InterfaceRegion, region_string : str) -> NoneType
Add interface_sides table data to table
- set_compute_packstat(...) from builtins.PyCapsule
- set_compute_packstat(self : rosetta.protocols.features.InterfaceFeatures, compute_packstat : bool) -> NoneType
Compute the packstat score? Default true
- set_dSASA_cutoff(...) from builtins.PyCapsule
- set_dSASA_cutoff(self : rosetta.protocols.features.InterfaceFeatures, dSASA_cutoff : float) -> NoneType
Set the reporter to only include interfaces >dSASA_cutoff.
- set_defaults(...) from builtins.PyCapsule
- set_defaults(rosetta.protocols.features.InterfaceFeatures) -> NoneType
- set_interface_chains(...) from builtins.PyCapsule
- set_interface_chains(self : rosetta.protocols.features.InterfaceFeatures, interfaces : rosetta.utility.vector1_std_string) -> NoneType
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.
- set_pack_separated(...) from builtins.PyCapsule
- set_pack_separated(self : rosetta.protocols.features.InterfaceFeatures, pack_separated : bool) -> NoneType
Pack the interface before separation? Default is false.
- set_pack_together(...) from builtins.PyCapsule
- set_pack_together(self : rosetta.protocols.features.InterfaceFeatures, pack_together : bool) -> NoneType
Pack the interface after separation? Default is true.
- set_scorefxn(...) from builtins.PyCapsule
- set_scorefxn(self : rosetta.protocols.features.InterfaceFeatures, scorefxn : rosetta.core.scoring.ScoreFunction) -> NoneType
- type_name(...) from builtins.PyCapsule
- type_name(rosetta.protocols.features.InterfaceFeatures) -> str
return string with class name
- write_interface_residues_schema_to_db(...) from builtins.PyCapsule
- write_interface_residues_schema_to_db(self : rosetta.protocols.features.InterfaceFeatures, db_session : rosetta.utility.sql_database.session) -> NoneType
- write_interface_schema_to_db(...) from builtins.PyCapsule
- write_interface_schema_to_db(self : rosetta.protocols.features.InterfaceFeatures, db_session : rosetta.utility.sql_database.session) -> NoneType
/////////////////////////////////////////////////////////////////////////
- write_interface_side_schema_to_db(...) from builtins.PyCapsule
- write_interface_side_schema_to_db(self : rosetta.protocols.features.InterfaceFeatures, db_session : rosetta.utility.sql_database.session) -> NoneType
- write_schema_to_db(...) from builtins.PyCapsule
- write_schema_to_db(self : rosetta.protocols.features.InterfaceFeatures, db_session : rosetta.utility.sql_database.session) -> NoneType
generate the table schemas and write them to the database
Methods inherited from FeaturesReporter:
- check_relevant_residues(...) from builtins.PyCapsule
- check_relevant_residues(*args, **kwargs)
Overloaded function.
1. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int) -> bool
2. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool
3. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, residues : rosetta.utility.vector1_unsigned_long) -> bool
- check_relevant_residues_range(...) from builtins.PyCapsule
- check_relevant_residues_range(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool
- delete_record(...) from builtins.PyCapsule
- delete_record(self : rosetta.protocols.features.FeaturesReporter, : int, : rosetta.utility.sql_database.session) -> NoneType
- get_relevant_residues_mode(...) from builtins.PyCapsule
- get_relevant_residues_mode(rosetta.protocols.features.FeaturesReporter) -> rosetta.protocols.features.RelevantResiduesMode.T
- load_into_pose(...) from builtins.PyCapsule
- load_into_pose(self : rosetta.protocols.features.FeaturesReporter, : rosetta.utility.sql_database.session, : int, : rosetta.core.pose.Pose) -> NoneType
- schema(...) from builtins.PyCapsule
- schema(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
- set_relevant_residues_mode(...) from builtins.PyCapsule
- set_relevant_residues_mode(self : rosetta.protocols.features.FeaturesReporter, setting : rosetta.protocols.features.RelevantResiduesMode.T) -> NoneType
|
class JobDataFeatures(FeaturesReporter) |
| | |
- Method resolution order:
- JobDataFeatures
- FeaturesReporter
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.protocols.features.JobDataFeatures) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.features.JobDataFeatures, : rosetta.protocols.features.JobDataFeatures) -> rosetta.protocols.features.JobDataFeatures
- delete_record(...) from builtins.PyCapsule
- delete_record(self : rosetta.protocols.features.JobDataFeatures, struct_id : int, db_session : rosetta.utility.sql_database.session) -> NoneType
- features_reporter_dependencies(...) from builtins.PyCapsule
- features_reporter_dependencies(rosetta.protocols.features.JobDataFeatures) -> 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.
- load_into_pose(...) from builtins.PyCapsule
- load_into_pose(self : rosetta.protocols.features.JobDataFeatures, db_session : rosetta.utility.sql_database.session, struct_id : int, pose : rosetta.core.pose.Pose) -> NoneType
- report_features(...) from builtins.PyCapsule
- report_features(self : rosetta.protocols.features.JobDataFeatures, pose : rosetta.core.pose.Pose, relevant_residues : rosetta.utility.vector1_bool, struct_id : int, db_session : rosetta.utility.sql_database.session) -> int
collect all the feature data for the pose
- type_name(...) from builtins.PyCapsule
- type_name(rosetta.protocols.features.JobDataFeatures) -> str
return string with class name
- write_schema_to_db(...) from builtins.PyCapsule
- write_schema_to_db(self : rosetta.protocols.features.JobDataFeatures, db_session : rosetta.utility.sql_database.session) -> NoneType
generate the table schemas and write them to the database
Methods inherited from FeaturesReporter:
- check_relevant_residues(...) from builtins.PyCapsule
- check_relevant_residues(*args, **kwargs)
Overloaded function.
1. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int) -> bool
2. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool
3. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, residues : rosetta.utility.vector1_unsigned_long) -> bool
- check_relevant_residues_range(...) from builtins.PyCapsule
- check_relevant_residues_range(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool
- get_relevant_residues_mode(...) from builtins.PyCapsule
- get_relevant_residues_mode(rosetta.protocols.features.FeaturesReporter) -> rosetta.protocols.features.RelevantResiduesMode.T
- schema(...) from builtins.PyCapsule
- schema(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
- set_relevant_residues_mode(...) from builtins.PyCapsule
- set_relevant_residues_mode(self : rosetta.protocols.features.FeaturesReporter, setting : rosetta.protocols.features.RelevantResiduesMode.T) -> NoneType
|
class LoopAnchorFeatures(FeaturesReporter) |
| | |
- Method resolution order:
- LoopAnchorFeatures
- FeaturesReporter
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.protocols.features.LoopAnchorFeatures) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.features.LoopAnchorFeatures, : rosetta.protocols.features.LoopAnchorFeatures) -> rosetta.protocols.features.LoopAnchorFeatures
- features_reporter_dependencies(...) from builtins.PyCapsule
- features_reporter_dependencies(rosetta.protocols.features.LoopAnchorFeatures) -> 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.
- report_features(...) from builtins.PyCapsule
- report_features(self : rosetta.protocols.features.LoopAnchorFeatures, pose : rosetta.core.pose.Pose, : rosetta.utility.vector1_bool, struct_id : int, db_session : rosetta.utility.sql_database.session) -> int
collect all the feature data for the pose
- set_use_relevant_residues_as_loop_length(...) from builtins.PyCapsule
- set_use_relevant_residues_as_loop_length(self : rosetta.protocols.features.LoopAnchorFeatures, use_relevant_residues_as_loop_length : bool) -> NoneType
- set_use_single_residue_to_define_anchor_transfrom(...) from builtins.PyCapsule
- set_use_single_residue_to_define_anchor_transfrom(self : rosetta.protocols.features.LoopAnchorFeatures, use_single_residue_to_define_anchor_transfrom : bool) -> NoneType
- type_name(...) from builtins.PyCapsule
- type_name(rosetta.protocols.features.LoopAnchorFeatures) -> str
return string with class name
- write_schema_to_db(...) from builtins.PyCapsule
- write_schema_to_db(self : rosetta.protocols.features.LoopAnchorFeatures, db_session : rosetta.utility.sql_database.session) -> NoneType
generate the table schemas and write them to the database
Methods inherited from FeaturesReporter:
- check_relevant_residues(...) from builtins.PyCapsule
- check_relevant_residues(*args, **kwargs)
Overloaded function.
1. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int) -> bool
2. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool
3. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, residues : rosetta.utility.vector1_unsigned_long) -> bool
- check_relevant_residues_range(...) from builtins.PyCapsule
- check_relevant_residues_range(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool
- delete_record(...) from builtins.PyCapsule
- delete_record(self : rosetta.protocols.features.FeaturesReporter, : int, : rosetta.utility.sql_database.session) -> NoneType
- get_relevant_residues_mode(...) from builtins.PyCapsule
- get_relevant_residues_mode(rosetta.protocols.features.FeaturesReporter) -> rosetta.protocols.features.RelevantResiduesMode.T
- load_into_pose(...) from builtins.PyCapsule
- load_into_pose(self : rosetta.protocols.features.FeaturesReporter, : rosetta.utility.sql_database.session, : int, : rosetta.core.pose.Pose) -> NoneType
- schema(...) from builtins.PyCapsule
- schema(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
- set_relevant_residues_mode(...) from builtins.PyCapsule
- set_relevant_residues_mode(self : rosetta.protocols.features.FeaturesReporter, setting : rosetta.protocols.features.RelevantResiduesMode.T) -> NoneType
|
class ModelFeatures(FeaturesReporter) |
| | |
- Method resolution order:
- ModelFeatures
- FeaturesReporter
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(handle) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.features.ModelFeatures, : rosetta.protocols.features.ModelFeatures) -> rosetta.protocols.features.ModelFeatures
- features_reporter_dependencies(...) from builtins.PyCapsule
- features_reporter_dependencies(rosetta.protocols.features.ModelFeatures) -> 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.
- report_features(...) from builtins.PyCapsule
- report_features(self : rosetta.protocols.features.ModelFeatures, pose : rosetta.core.pose.Pose, relevant_residues : rosetta.utility.vector1_bool, struct_id : int, db_session : rosetta.utility.sql_database.session) -> int
collect all the feature data for the pose
- trim_pose(...) from builtins.PyCapsule
- trim_pose(self : rosetta.protocols.features.ModelFeatures, pose : rosetta.core.pose.Pose, resnums : rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t) -> NoneType
for testing purposes only
- type_name(...) from builtins.PyCapsule
- type_name(rosetta.protocols.features.ModelFeatures) -> str
- write_clique_to_db(...) from builtins.PyCapsule
- write_clique_to_db(self : rosetta.protocols.features.ModelFeatures, clique : rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t, struct_id : int, db_session : rosetta.utility.sql_database.session) -> NoneType
- write_schema_to_db(...) from builtins.PyCapsule
- write_schema_to_db(self : rosetta.protocols.features.ModelFeatures, db_session : rosetta.utility.sql_database.session) -> NoneType
generate the table schemas and write them to the database
Methods inherited from FeaturesReporter:
- check_relevant_residues(...) from builtins.PyCapsule
- check_relevant_residues(*args, **kwargs)
Overloaded function.
1. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int) -> bool
2. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool
3. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, residues : rosetta.utility.vector1_unsigned_long) -> bool
- check_relevant_residues_range(...) from builtins.PyCapsule
- check_relevant_residues_range(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool
- delete_record(...) from builtins.PyCapsule
- delete_record(self : rosetta.protocols.features.FeaturesReporter, : int, : rosetta.utility.sql_database.session) -> NoneType
- get_relevant_residues_mode(...) from builtins.PyCapsule
- get_relevant_residues_mode(rosetta.protocols.features.FeaturesReporter) -> rosetta.protocols.features.RelevantResiduesMode.T
- load_into_pose(...) from builtins.PyCapsule
- load_into_pose(self : rosetta.protocols.features.FeaturesReporter, : rosetta.utility.sql_database.session, : int, : rosetta.core.pose.Pose) -> NoneType
- schema(...) from builtins.PyCapsule
- schema(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
- set_relevant_residues_mode(...) from builtins.PyCapsule
- set_relevant_residues_mode(self : rosetta.protocols.features.FeaturesReporter, setting : rosetta.protocols.features.RelevantResiduesMode.T) -> NoneType
|
class OrbitalsFeatures(FeaturesReporter) |
| | |
- Method resolution order:
- OrbitalsFeatures
- FeaturesReporter
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.protocols.features.OrbitalsFeatures) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.features.OrbitalsFeatures, : rosetta.protocols.features.OrbitalsFeatures) -> rosetta.protocols.features.OrbitalsFeatures
- features_reporter_dependencies(...) from builtins.PyCapsule
- features_reporter_dependencies(rosetta.protocols.features.OrbitalsFeatures) -> 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.
- report_features(...) from builtins.PyCapsule
- report_features(self : rosetta.protocols.features.OrbitalsFeatures, pose : rosetta.core.pose.Pose, relevant_residues : rosetta.utility.vector1_bool, struct_id : int, db_session : rosetta.utility.sql_database.session) -> int
collect all the feature data for the pose
- report_haro_orbital_interactions(...) from builtins.PyCapsule
- report_haro_orbital_interactions(self : rosetta.protocols.features.OrbitalsFeatures, pose : rosetta.core.pose.Pose, relevant_residues : rosetta.utility.vector1_bool, struct_id : int, db_session : rosetta.utility.sql_database.session) -> NoneType
- report_hpol_orbital_interactions(...) from builtins.PyCapsule
- report_hpol_orbital_interactions(self : rosetta.protocols.features.OrbitalsFeatures, pose : rosetta.core.pose.Pose, relevant_residues : rosetta.utility.vector1_bool, struct_id : int, db_session : rosetta.utility.sql_database.session) -> NoneType
- set_OrbH_features_data(...) from builtins.PyCapsule
- set_OrbH_features_data(self : rosetta.protocols.features.OrbitalsFeatures, res1 : rosetta.core.conformation.Residue, res2 : rosetta.core.conformation.Residue, Aindex : int, Hindex : int, Orbindex : int, Orbxyz : 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) -> NoneType
- set_OrbOrb_features_data(...) from builtins.PyCapsule
- set_OrbOrb_features_data(self : rosetta.protocols.features.OrbitalsFeatures, res1 : rosetta.core.conformation.Residue, res2 : rosetta.core.conformation.Residue, Aindex : int, Dindex : int, Orbindex1 : int, Orbindex2 : int, Orbxyz1 : rosetta.numeric.xyzVector_double_t, Orbxyz2 : 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) -> NoneType
- type_name(...) from builtins.PyCapsule
- type_name(rosetta.protocols.features.OrbitalsFeatures) -> str
return string with class name
- write_schema_to_db(...) from builtins.PyCapsule
- write_schema_to_db(self : rosetta.protocols.features.OrbitalsFeatures, db_session : rosetta.utility.sql_database.session) -> NoneType
generate the table schemas and write them to the database
Methods inherited from FeaturesReporter:
- check_relevant_residues(...) from builtins.PyCapsule
- check_relevant_residues(*args, **kwargs)
Overloaded function.
1. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int) -> bool
2. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool
3. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, residues : rosetta.utility.vector1_unsigned_long) -> bool
- check_relevant_residues_range(...) from builtins.PyCapsule
- check_relevant_residues_range(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool
- delete_record(...) from builtins.PyCapsule
- delete_record(self : rosetta.protocols.features.FeaturesReporter, : int, : rosetta.utility.sql_database.session) -> NoneType
- get_relevant_residues_mode(...) from builtins.PyCapsule
- get_relevant_residues_mode(rosetta.protocols.features.FeaturesReporter) -> rosetta.protocols.features.RelevantResiduesMode.T
- load_into_pose(...) from builtins.PyCapsule
- load_into_pose(self : rosetta.protocols.features.FeaturesReporter, : rosetta.utility.sql_database.session, : int, : rosetta.core.pose.Pose) -> NoneType
- schema(...) from builtins.PyCapsule
- schema(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
- set_relevant_residues_mode(...) from builtins.PyCapsule
- set_relevant_residues_mode(self : rosetta.protocols.features.FeaturesReporter, setting : rosetta.protocols.features.RelevantResiduesMode.T) -> NoneType
|
class PairFeatures(FeaturesReporter) |
| | |
- Method resolution order:
- PairFeatures
- FeaturesReporter
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.protocols.features.PairFeatures) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.features.PairFeatures, : rosetta.protocols.features.PairFeatures) -> rosetta.protocols.features.PairFeatures
- features_reporter_dependencies(...) from builtins.PyCapsule
- features_reporter_dependencies(rosetta.protocols.features.PairFeatures) -> 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.
- report_features(...) from builtins.PyCapsule
- report_features(self : rosetta.protocols.features.PairFeatures, pose : rosetta.core.pose.Pose, relevant_residues : rosetta.utility.vector1_bool, struct_id : int, db_session : rosetta.utility.sql_database.session) -> int
collect all the feature data for the pose
- report_residue_pairs(...) from builtins.PyCapsule
- report_residue_pairs(self : rosetta.protocols.features.PairFeatures, pose : rosetta.core.pose.Pose, relevant_residues : rosetta.utility.vector1_bool, struct_id : int, db_session : rosetta.utility.sql_database.session) -> NoneType
- type_name(...) from builtins.PyCapsule
- type_name(rosetta.protocols.features.PairFeatures) -> str
return string with class name
- write_schema_to_db(...) from builtins.PyCapsule
- write_schema_to_db(self : rosetta.protocols.features.PairFeatures, db_session : rosetta.utility.sql_database.session) -> NoneType
generate the table schemas and write them to the database
Methods inherited from FeaturesReporter:
- check_relevant_residues(...) from builtins.PyCapsule
- check_relevant_residues(*args, **kwargs)
Overloaded function.
1. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int) -> bool
2. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool
3. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, residues : rosetta.utility.vector1_unsigned_long) -> bool
- check_relevant_residues_range(...) from builtins.PyCapsule
- check_relevant_residues_range(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool
- delete_record(...) from builtins.PyCapsule
- delete_record(self : rosetta.protocols.features.FeaturesReporter, : int, : rosetta.utility.sql_database.session) -> NoneType
- get_relevant_residues_mode(...) from builtins.PyCapsule
- get_relevant_residues_mode(rosetta.protocols.features.FeaturesReporter) -> rosetta.protocols.features.RelevantResiduesMode.T
- load_into_pose(...) from builtins.PyCapsule
- load_into_pose(self : rosetta.protocols.features.FeaturesReporter, : rosetta.utility.sql_database.session, : int, : rosetta.core.pose.Pose) -> NoneType
- schema(...) from builtins.PyCapsule
- schema(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
- set_relevant_residues_mode(...) from builtins.PyCapsule
- set_relevant_residues_mode(self : rosetta.protocols.features.FeaturesReporter, setting : rosetta.protocols.features.RelevantResiduesMode.T) -> NoneType
|
class PdbDataFeatures(FeaturesReporter) |
| | |
- Method resolution order:
- PdbDataFeatures
- FeaturesReporter
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.protocols.features.PdbDataFeatures) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.features.PdbDataFeatures, : rosetta.protocols.features.PdbDataFeatures) -> rosetta.protocols.features.PdbDataFeatures
- delete_record(...) from builtins.PyCapsule
- delete_record(self : rosetta.protocols.features.PdbDataFeatures, struct_id : int, db_session : rosetta.utility.sql_database.session) -> NoneType
- features_reporter_dependencies(...) from builtins.PyCapsule
- features_reporter_dependencies(rosetta.protocols.features.PdbDataFeatures) -> 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.
- load_into_pose(...) from builtins.PyCapsule
- load_into_pose(self : rosetta.protocols.features.PdbDataFeatures, db_session : rosetta.utility.sql_database.session, struct_id : int, pose : rosetta.core.pose.Pose) -> NoneType
- report_features(...) from builtins.PyCapsule
- report_features(self : rosetta.protocols.features.PdbDataFeatures, pose : rosetta.core.pose.Pose, relevant_residues : rosetta.utility.vector1_bool, struct_id : int, db_session : rosetta.utility.sql_database.session) -> int
collect all the feature data for the pose
- type_name(...) from builtins.PyCapsule
- type_name(rosetta.protocols.features.PdbDataFeatures) -> str
return string with class name
- write_schema_to_db(...) from builtins.PyCapsule
- write_schema_to_db(self : rosetta.protocols.features.PdbDataFeatures, db_session : rosetta.utility.sql_database.session) -> NoneType
generate the table schemas and write them to the database
Methods inherited from FeaturesReporter:
- check_relevant_residues(...) from builtins.PyCapsule
- check_relevant_residues(*args, **kwargs)
Overloaded function.
1. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int) -> bool
2. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool
3. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, residues : rosetta.utility.vector1_unsigned_long) -> bool
- check_relevant_residues_range(...) from builtins.PyCapsule
- check_relevant_residues_range(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool
- get_relevant_residues_mode(...) from builtins.PyCapsule
- get_relevant_residues_mode(rosetta.protocols.features.FeaturesReporter) -> rosetta.protocols.features.RelevantResiduesMode.T
- schema(...) from builtins.PyCapsule
- schema(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
- set_relevant_residues_mode(...) from builtins.PyCapsule
- set_relevant_residues_mode(self : rosetta.protocols.features.FeaturesReporter, setting : rosetta.protocols.features.RelevantResiduesMode.T) -> NoneType
|
class PoseCommentsFeatures(FeaturesReporter) |
| | |
- Method resolution order:
- PoseCommentsFeatures
- FeaturesReporter
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.protocols.features.PoseCommentsFeatures) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.features.PoseCommentsFeatures, : rosetta.protocols.features.PoseCommentsFeatures) -> rosetta.protocols.features.PoseCommentsFeatures
- delete_record(...) from builtins.PyCapsule
- delete_record(self : rosetta.protocols.features.PoseCommentsFeatures, struct_id : int, db_session : rosetta.utility.sql_database.session) -> NoneType
- features_reporter_dependencies(...) from builtins.PyCapsule
- features_reporter_dependencies(rosetta.protocols.features.PoseCommentsFeatures) -> 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.
- load_into_pose(...) from builtins.PyCapsule
- load_into_pose(self : rosetta.protocols.features.PoseCommentsFeatures, db_session : rosetta.utility.sql_database.session, struct_id : int, pose : rosetta.core.pose.Pose) -> NoneType
- report_features(...) from builtins.PyCapsule
- report_features(self : rosetta.protocols.features.PoseCommentsFeatures, pose : rosetta.core.pose.Pose, : rosetta.utility.vector1_bool, struct_id : int, db_session : rosetta.utility.sql_database.session) -> int
collect all the feature data for the pose
- type_name(...) from builtins.PyCapsule
- type_name(rosetta.protocols.features.PoseCommentsFeatures) -> str
return string with class name
- write_schema_to_db(...) from builtins.PyCapsule
- write_schema_to_db(self : rosetta.protocols.features.PoseCommentsFeatures, db_session : rosetta.utility.sql_database.session) -> NoneType
generate the table schemas and write them to the database
Methods inherited from FeaturesReporter:
- check_relevant_residues(...) from builtins.PyCapsule
- check_relevant_residues(*args, **kwargs)
Overloaded function.
1. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int) -> bool
2. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool
3. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, residues : rosetta.utility.vector1_unsigned_long) -> bool
- check_relevant_residues_range(...) from builtins.PyCapsule
- check_relevant_residues_range(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool
- get_relevant_residues_mode(...) from builtins.PyCapsule
- get_relevant_residues_mode(rosetta.protocols.features.FeaturesReporter) -> rosetta.protocols.features.RelevantResiduesMode.T
- schema(...) from builtins.PyCapsule
- schema(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
- set_relevant_residues_mode(...) from builtins.PyCapsule
- set_relevant_residues_mode(self : rosetta.protocols.features.FeaturesReporter, setting : rosetta.protocols.features.RelevantResiduesMode.T) -> NoneType
|
class PoseConformationFeatures(FeaturesReporter) |
| | |
- Method resolution order:
- PoseConformationFeatures
- FeaturesReporter
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.protocols.features.PoseConformationFeatures) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.features.PoseConformationFeatures, : rosetta.protocols.features.PoseConformationFeatures) -> rosetta.protocols.features.PoseConformationFeatures
- delete_record(...) from builtins.PyCapsule
- delete_record(self : rosetta.protocols.features.PoseConformationFeatures, struct_id : int, db_session : rosetta.utility.sql_database.session) -> NoneType
- features_reporter_dependencies(...) from builtins.PyCapsule
- features_reporter_dependencies(rosetta.protocols.features.PoseConformationFeatures) -> 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.
- load_into_pose(...) from builtins.PyCapsule
- load_into_pose(self : rosetta.protocols.features.PoseConformationFeatures, db_session : rosetta.utility.sql_database.session, struct_id : int, pose : rosetta.core.pose.Pose, ideal : bool) -> NoneType
Load information from pose_conformations into pose
- true if structure is ideal, false if not
- report_features(...) from builtins.PyCapsule
- report_features(self : rosetta.protocols.features.PoseConformationFeatures, pose : rosetta.core.pose.Pose, relevant_residues : rosetta.utility.vector1_bool, struct_id : int, db_session : rosetta.utility.sql_database.session) -> int
collect all the feature data for the pose
- type_name(...) from builtins.PyCapsule
- type_name(rosetta.protocols.features.PoseConformationFeatures) -> str
return string with class name
- write_schema_to_db(...) from builtins.PyCapsule
- write_schema_to_db(self : rosetta.protocols.features.PoseConformationFeatures, db_session : rosetta.utility.sql_database.session) -> NoneType
generate the table schemas and write them to the database
Methods inherited from FeaturesReporter:
- check_relevant_residues(...) from builtins.PyCapsule
- check_relevant_residues(*args, **kwargs)
Overloaded function.
1. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int) -> bool
2. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool
3. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, residues : rosetta.utility.vector1_unsigned_long) -> bool
- check_relevant_residues_range(...) from builtins.PyCapsule
- check_relevant_residues_range(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool
- get_relevant_residues_mode(...) from builtins.PyCapsule
- get_relevant_residues_mode(rosetta.protocols.features.FeaturesReporter) -> rosetta.protocols.features.RelevantResiduesMode.T
- schema(...) from builtins.PyCapsule
- schema(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
- set_relevant_residues_mode(...) from builtins.PyCapsule
- set_relevant_residues_mode(self : rosetta.protocols.features.FeaturesReporter, setting : rosetta.protocols.features.RelevantResiduesMode.T) -> NoneType
|
class ProteinBackboneAtomAtomPairFeatures(FeaturesReporter) |
| | |
- Method resolution order:
- ProteinBackboneAtomAtomPairFeatures
- FeaturesReporter
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.protocols.features.ProteinBackboneAtomAtomPairFeatures) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.features.ProteinBackboneAtomAtomPairFeatures, : rosetta.protocols.features.ProteinBackboneAtomAtomPairFeatures) -> rosetta.protocols.features.ProteinBackboneAtomAtomPairFeatures
- features_reporter_dependencies(...) from builtins.PyCapsule
- features_reporter_dependencies(rosetta.protocols.features.ProteinBackboneAtomAtomPairFeatures) -> 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.
- report_features(...) from builtins.PyCapsule
- report_features(self : rosetta.protocols.features.ProteinBackboneAtomAtomPairFeatures, pose : rosetta.core.pose.Pose, relevant_residues : rosetta.utility.vector1_bool, struct_id : int, db_session : rosetta.utility.sql_database.session) -> int
collect all the feature data for the pose
- type_name(...) from builtins.PyCapsule
- type_name(rosetta.protocols.features.ProteinBackboneAtomAtomPairFeatures) -> str
return string with class name
- write_schema_to_db(...) from builtins.PyCapsule
- write_schema_to_db(self : rosetta.protocols.features.ProteinBackboneAtomAtomPairFeatures, db_session : rosetta.utility.sql_database.session) -> NoneType
generate the table schemas and write them to the database
Methods inherited from FeaturesReporter:
- check_relevant_residues(...) from builtins.PyCapsule
- check_relevant_residues(*args, **kwargs)
Overloaded function.
1. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int) -> bool
2. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool
3. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, residues : rosetta.utility.vector1_unsigned_long) -> bool
- check_relevant_residues_range(...) from builtins.PyCapsule
- check_relevant_residues_range(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool
- delete_record(...) from builtins.PyCapsule
- delete_record(self : rosetta.protocols.features.FeaturesReporter, : int, : rosetta.utility.sql_database.session) -> NoneType
- get_relevant_residues_mode(...) from builtins.PyCapsule
- get_relevant_residues_mode(rosetta.protocols.features.FeaturesReporter) -> rosetta.protocols.features.RelevantResiduesMode.T
- load_into_pose(...) from builtins.PyCapsule
- load_into_pose(self : rosetta.protocols.features.FeaturesReporter, : rosetta.utility.sql_database.session, : int, : rosetta.core.pose.Pose) -> NoneType
- schema(...) from builtins.PyCapsule
- schema(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
- set_relevant_residues_mode(...) from builtins.PyCapsule
- set_relevant_residues_mode(self : rosetta.protocols.features.FeaturesReporter, setting : rosetta.protocols.features.RelevantResiduesMode.T) -> NoneType
|
class ProteinBackboneTorsionAngleFeatures(FeaturesReporter) |
| | |
- Method resolution order:
- ProteinBackboneTorsionAngleFeatures
- FeaturesReporter
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.protocols.features.ProteinBackboneTorsionAngleFeatures) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.features.ProteinBackboneTorsionAngleFeatures, : rosetta.protocols.features.ProteinBackboneTorsionAngleFeatures) -> rosetta.protocols.features.ProteinBackboneTorsionAngleFeatures
- features_reporter_dependencies(...) from builtins.PyCapsule
- features_reporter_dependencies(rosetta.protocols.features.ProteinBackboneTorsionAngleFeatures) -> 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.
- report_features(...) from builtins.PyCapsule
- report_features(self : rosetta.protocols.features.ProteinBackboneTorsionAngleFeatures, pose : rosetta.core.pose.Pose, relevant_residues : rosetta.utility.vector1_bool, struct_id : int, db_session : rosetta.utility.sql_database.session) -> int
collect all the feature data for the pose
- type_name(...) from builtins.PyCapsule
- type_name(rosetta.protocols.features.ProteinBackboneTorsionAngleFeatures) -> str
return string with class name
- write_schema_to_db(...) from builtins.PyCapsule
- write_schema_to_db(self : rosetta.protocols.features.ProteinBackboneTorsionAngleFeatures, db_session : rosetta.utility.sql_database.session) -> NoneType
generate the table schemas and write them to the database
Methods inherited from FeaturesReporter:
- check_relevant_residues(...) from builtins.PyCapsule
- check_relevant_residues(*args, **kwargs)
Overloaded function.
1. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int) -> bool
2. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool
3. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, residues : rosetta.utility.vector1_unsigned_long) -> bool
- check_relevant_residues_range(...) from builtins.PyCapsule
- check_relevant_residues_range(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool
- delete_record(...) from builtins.PyCapsule
- delete_record(self : rosetta.protocols.features.FeaturesReporter, : int, : rosetta.utility.sql_database.session) -> NoneType
- get_relevant_residues_mode(...) from builtins.PyCapsule
- get_relevant_residues_mode(rosetta.protocols.features.FeaturesReporter) -> rosetta.protocols.features.RelevantResiduesMode.T
- load_into_pose(...) from builtins.PyCapsule
- load_into_pose(self : rosetta.protocols.features.FeaturesReporter, : rosetta.utility.sql_database.session, : int, : rosetta.core.pose.Pose) -> NoneType
- schema(...) from builtins.PyCapsule
- schema(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
- set_relevant_residues_mode(...) from builtins.PyCapsule
- set_relevant_residues_mode(self : rosetta.protocols.features.FeaturesReporter, setting : rosetta.protocols.features.RelevantResiduesMode.T) -> NoneType
|
class ProteinBondGeometryFeatures(FeaturesReporter) |
| | |
- Method resolution order:
- ProteinBondGeometryFeatures
- FeaturesReporter
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.protocols.features.ProteinBondGeometryFeatures) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.features.ProteinBondGeometryFeatures, : rosetta.protocols.features.ProteinBondGeometryFeatures) -> rosetta.protocols.features.ProteinBondGeometryFeatures
- features_reporter_dependencies(...) from builtins.PyCapsule
- features_reporter_dependencies(rosetta.protocols.features.ProteinBondGeometryFeatures) -> 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.
- report_features(...) from builtins.PyCapsule
- report_features(self : rosetta.protocols.features.ProteinBondGeometryFeatures, pose : rosetta.core.pose.Pose, relevant_residues : rosetta.utility.vector1_bool, struct_id : int, db_session : rosetta.utility.sql_database.session) -> int
collect all the feature data for the pose
- report_interres_angles(...) from builtins.PyCapsule
- report_interres_angles(self : rosetta.protocols.features.ProteinBondGeometryFeatures, pose : rosetta.core.pose.Pose, relevant_residues : rosetta.utility.vector1_bool, struct_id : int, db_session : rosetta.utility.sql_database.session) -> NoneType
- report_interres_lengths(...) from builtins.PyCapsule
- report_interres_lengths(self : rosetta.protocols.features.ProteinBondGeometryFeatures, pose : rosetta.core.pose.Pose, relevant_residues : rosetta.utility.vector1_bool, struct_id : int, db_session : rosetta.utility.sql_database.session) -> NoneType
- report_intrares_angles(...) from builtins.PyCapsule
- report_intrares_angles(self : rosetta.protocols.features.ProteinBondGeometryFeatures, pose : rosetta.core.pose.Pose, relevant_residues : rosetta.utility.vector1_bool, struct_id : int, db_session : rosetta.utility.sql_database.session) -> NoneType
- report_intrares_lengths(...) from builtins.PyCapsule
- report_intrares_lengths(self : rosetta.protocols.features.ProteinBondGeometryFeatures, pose : rosetta.core.pose.Pose, relevant_residues : rosetta.utility.vector1_bool, struct_id : int, db_session : rosetta.utility.sql_database.session) -> NoneType
- report_intrares_torsions(...) from builtins.PyCapsule
- report_intrares_torsions(self : rosetta.protocols.features.ProteinBondGeometryFeatures, pose : rosetta.core.pose.Pose, relevant_residues : rosetta.utility.vector1_bool, struct_id : int, db_session : rosetta.utility.sql_database.session) -> NoneType
- type_name(...) from builtins.PyCapsule
- type_name(rosetta.protocols.features.ProteinBondGeometryFeatures) -> str
return string with class name
- write_schema_to_db(...) from builtins.PyCapsule
- write_schema_to_db(self : rosetta.protocols.features.ProteinBondGeometryFeatures, db_session : rosetta.utility.sql_database.session) -> NoneType
generate the table schemas and write them to the database
Methods inherited from FeaturesReporter:
- check_relevant_residues(...) from builtins.PyCapsule
- check_relevant_residues(*args, **kwargs)
Overloaded function.
1. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int) -> bool
2. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool
3. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, residues : rosetta.utility.vector1_unsigned_long) -> bool
- check_relevant_residues_range(...) from builtins.PyCapsule
- check_relevant_residues_range(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool
- delete_record(...) from builtins.PyCapsule
- delete_record(self : rosetta.protocols.features.FeaturesReporter, : int, : rosetta.utility.sql_database.session) -> NoneType
- get_relevant_residues_mode(...) from builtins.PyCapsule
- get_relevant_residues_mode(rosetta.protocols.features.FeaturesReporter) -> rosetta.protocols.features.RelevantResiduesMode.T
- load_into_pose(...) from builtins.PyCapsule
- load_into_pose(self : rosetta.protocols.features.FeaturesReporter, : rosetta.utility.sql_database.session, : int, : rosetta.core.pose.Pose) -> NoneType
- schema(...) from builtins.PyCapsule
- schema(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
- set_relevant_residues_mode(...) from builtins.PyCapsule
- set_relevant_residues_mode(self : rosetta.protocols.features.FeaturesReporter, setting : rosetta.protocols.features.RelevantResiduesMode.T) -> NoneType
|
class ProteinRMSDFeatures(FeaturesReporter) |
| | |
- Method resolution order:
- ProteinRMSDFeatures
- FeaturesReporter
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(self : handle, reference_pose : rosetta.core.pose.Pose) -> NoneType
3. __init__(handle, rosetta.protocols.features.ProteinRMSDFeatures) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.features.ProteinRMSDFeatures, : rosetta.protocols.features.ProteinRMSDFeatures) -> rosetta.protocols.features.ProteinRMSDFeatures
- features_reporter_dependencies(...) from builtins.PyCapsule
- features_reporter_dependencies(rosetta.protocols.features.ProteinRMSDFeatures) -> 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.
- reference_pose(...) from builtins.PyCapsule
- reference_pose(*args, **kwargs)
Overloaded function.
1. reference_pose(rosetta.protocols.features.ProteinRMSDFeatures) -> rosetta.core.pose.Pose
2. reference_pose(self : rosetta.protocols.features.ProteinRMSDFeatures, : rosetta.core.pose.Pose) -> NoneType
- report_features(...) from builtins.PyCapsule
- report_features(self : rosetta.protocols.features.ProteinRMSDFeatures, pose : rosetta.core.pose.Pose, relevant_residues : rosetta.utility.vector1_bool, struct_id : int, db_session : rosetta.utility.sql_database.session) -> int
collect all the feature data for the pose
- type_name(...) from builtins.PyCapsule
- type_name(rosetta.protocols.features.ProteinRMSDFeatures) -> str
return string with class name
- write_schema_to_db(...) from builtins.PyCapsule
- write_schema_to_db(self : rosetta.protocols.features.ProteinRMSDFeatures, db_session : rosetta.utility.sql_database.session) -> NoneType
generate the table schemas and write them to the database
Methods inherited from FeaturesReporter:
- check_relevant_residues(...) from builtins.PyCapsule
- check_relevant_residues(*args, **kwargs)
Overloaded function.
1. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int) -> bool
2. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool
3. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, residues : rosetta.utility.vector1_unsigned_long) -> bool
- check_relevant_residues_range(...) from builtins.PyCapsule
- check_relevant_residues_range(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool
- delete_record(...) from builtins.PyCapsule
- delete_record(self : rosetta.protocols.features.FeaturesReporter, : int, : rosetta.utility.sql_database.session) -> NoneType
- get_relevant_residues_mode(...) from builtins.PyCapsule
- get_relevant_residues_mode(rosetta.protocols.features.FeaturesReporter) -> rosetta.protocols.features.RelevantResiduesMode.T
- load_into_pose(...) from builtins.PyCapsule
- load_into_pose(self : rosetta.protocols.features.FeaturesReporter, : rosetta.utility.sql_database.session, : int, : rosetta.core.pose.Pose) -> NoneType
- schema(...) from builtins.PyCapsule
- schema(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
- set_relevant_residues_mode(...) from builtins.PyCapsule
- set_relevant_residues_mode(self : rosetta.protocols.features.FeaturesReporter, setting : rosetta.protocols.features.RelevantResiduesMode.T) -> NoneType
|
class ProteinRMSDNoSuperpositionFeatures(FeaturesReporter) |
| | |
- Method resolution order:
- ProteinRMSDNoSuperpositionFeatures
- FeaturesReporter
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(self : handle, reference_pose : rosetta.core.pose.Pose) -> NoneType
3. __init__(handle, rosetta.protocols.features.ProteinRMSDNoSuperpositionFeatures) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.features.ProteinRMSDNoSuperpositionFeatures, : rosetta.protocols.features.ProteinRMSDNoSuperpositionFeatures) -> rosetta.protocols.features.ProteinRMSDNoSuperpositionFeatures
- features_reporter_dependencies(...) from builtins.PyCapsule
- features_reporter_dependencies(rosetta.protocols.features.ProteinRMSDNoSuperpositionFeatures) -> 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.
- reference_pose(...) from builtins.PyCapsule
- reference_pose(*args, **kwargs)
Overloaded function.
1. reference_pose(rosetta.protocols.features.ProteinRMSDNoSuperpositionFeatures) -> rosetta.core.pose.Pose
2. reference_pose(self : rosetta.protocols.features.ProteinRMSDNoSuperpositionFeatures, : rosetta.core.pose.Pose) -> NoneType
- reference_pose_from_options(...) from builtins.PyCapsule
- reference_pose_from_options(self : rosetta.protocols.features.ProteinRMSDNoSuperpositionFeatures, pose : rosetta.core.pose.Pose) -> NoneType
Sets the native pose to the native pose if set, or the starting pose otherwise
- report_features(...) from builtins.PyCapsule
- report_features(self : rosetta.protocols.features.ProteinRMSDNoSuperpositionFeatures, pose : rosetta.core.pose.Pose, relevant_residues : rosetta.utility.vector1_bool, struct_id : int, db_session : rosetta.utility.sql_database.session) -> int
collect all the feature data for the pose
- type_name(...) from builtins.PyCapsule
- type_name(rosetta.protocols.features.ProteinRMSDNoSuperpositionFeatures) -> str
return string with class name
- write_schema_to_db(...) from builtins.PyCapsule
- write_schema_to_db(self : rosetta.protocols.features.ProteinRMSDNoSuperpositionFeatures, db_session : rosetta.utility.sql_database.session) -> NoneType
generate the table schemas and write them to the database
Methods inherited from FeaturesReporter:
- check_relevant_residues(...) from builtins.PyCapsule
- check_relevant_residues(*args, **kwargs)
Overloaded function.
1. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int) -> bool
2. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool
3. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, residues : rosetta.utility.vector1_unsigned_long) -> bool
- check_relevant_residues_range(...) from builtins.PyCapsule
- check_relevant_residues_range(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool
- delete_record(...) from builtins.PyCapsule
- delete_record(self : rosetta.protocols.features.FeaturesReporter, : int, : rosetta.utility.sql_database.session) -> NoneType
- get_relevant_residues_mode(...) from builtins.PyCapsule
- get_relevant_residues_mode(rosetta.protocols.features.FeaturesReporter) -> rosetta.protocols.features.RelevantResiduesMode.T
- load_into_pose(...) from builtins.PyCapsule
- load_into_pose(self : rosetta.protocols.features.FeaturesReporter, : rosetta.utility.sql_database.session, : int, : rosetta.core.pose.Pose) -> NoneType
- schema(...) from builtins.PyCapsule
- schema(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
- set_relevant_residues_mode(...) from builtins.PyCapsule
- set_relevant_residues_mode(self : rosetta.protocols.features.FeaturesReporter, setting : rosetta.protocols.features.RelevantResiduesMode.T) -> NoneType
|
class ProteinResidueConformationFeatures(FeaturesReporter) |
| | |
- Method resolution order:
- ProteinResidueConformationFeatures
- FeaturesReporter
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.protocols.features.ProteinResidueConformationFeatures) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.features.ProteinResidueConformationFeatures, : rosetta.protocols.features.ProteinResidueConformationFeatures) -> rosetta.protocols.features.ProteinResidueConformationFeatures
- delete_record(...) from builtins.PyCapsule
- delete_record(self : rosetta.protocols.features.ProteinResidueConformationFeatures, struct_id : int, db_session : rosetta.utility.sql_database.session) -> NoneType
- features_reporter_dependencies(...) from builtins.PyCapsule
- features_reporter_dependencies(rosetta.protocols.features.ProteinResidueConformationFeatures) -> 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.
- load_conformation(...) from builtins.PyCapsule
- load_conformation(self : rosetta.protocols.features.ProteinResidueConformationFeatures, db_session : rosetta.utility.sql_database.session, struct_id : int, pose : rosetta.core.pose.Pose, ideal : bool) -> NoneType
- Is the input structure ideal? If so, load backbone torsions into pose
- load_into_pose(...) from builtins.PyCapsule
- load_into_pose(self : rosetta.protocols.features.ProteinResidueConformationFeatures, db_session : rosetta.utility.sql_database.session, struct_id : int, pose : rosetta.core.pose.Pose, ideal : bool) -> NoneType
- Is the input structure ideal?
- report_features(...) from builtins.PyCapsule
- report_features(self : rosetta.protocols.features.ProteinResidueConformationFeatures, pose : rosetta.core.pose.Pose, relevant_residues : rosetta.utility.vector1_bool, struct_id : int, db_session : rosetta.utility.sql_database.session) -> int
collect all the feature data for the pose
- type_name(...) from builtins.PyCapsule
- type_name(rosetta.protocols.features.ProteinResidueConformationFeatures) -> str
return string with class name
- write_schema_to_db(...) from builtins.PyCapsule
- write_schema_to_db(self : rosetta.protocols.features.ProteinResidueConformationFeatures, db_session : rosetta.utility.sql_database.session) -> NoneType
generate the table schemas and write them to the database
Methods inherited from FeaturesReporter:
- check_relevant_residues(...) from builtins.PyCapsule
- check_relevant_residues(*args, **kwargs)
Overloaded function.
1. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int) -> bool
2. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool
3. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, residues : rosetta.utility.vector1_unsigned_long) -> bool
- check_relevant_residues_range(...) from builtins.PyCapsule
- check_relevant_residues_range(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool
- get_relevant_residues_mode(...) from builtins.PyCapsule
- get_relevant_residues_mode(rosetta.protocols.features.FeaturesReporter) -> rosetta.protocols.features.RelevantResiduesMode.T
- schema(...) from builtins.PyCapsule
- schema(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
- set_relevant_residues_mode(...) from builtins.PyCapsule
- set_relevant_residues_mode(self : rosetta.protocols.features.FeaturesReporter, setting : rosetta.protocols.features.RelevantResiduesMode.T) -> NoneType
|
class ProteinSilentReport(Report) |
| | |
- Method resolution order:
- ProteinSilentReport
- Report
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.protocols.features.ProteinSilentReport) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- apply(...) from builtins.PyCapsule
- apply(*args, **kwargs)
Overloaded function.
1. apply(self : rosetta.protocols.features.ProteinSilentReport, pose : rosetta.core.pose.Pose, db_sesion : rosetta.utility.sql_database.session) -> NoneType
2. apply(self : rosetta.protocols.features.ProteinSilentReport, pose : rosetta.core.pose.Pose, db_sesion : rosetta.utility.sql_database.session, tag : str) -> NoneType
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.features.ProteinSilentReport, : rosetta.protocols.features.ProteinSilentReport) -> rosetta.protocols.features.ProteinSilentReport
- delete_pose(...) from builtins.PyCapsule
- delete_pose(self : rosetta.protocols.features.ProteinSilentReport, db_session : rosetta.utility.sql_database.session, struct_id : int) -> NoneType
- delete_pose_from_tag(...) from builtins.PyCapsule
- delete_pose_from_tag(self : rosetta.protocols.features.ProteinSilentReport, db_session : rosetta.utility.sql_database.session, tag : str) -> NoneType
- get_batch_id(...) from builtins.PyCapsule
- get_batch_id(rosetta.protocols.features.ProteinSilentReport) -> int
- get_protocol_id(...) from builtins.PyCapsule
- get_protocol_id(rosetta.protocols.features.ProteinSilentReport) -> int
- initialize(...) from builtins.PyCapsule
- initialize(self : rosetta.protocols.features.ProteinSilentReport, db_session : rosetta.utility.sql_database.session) -> NoneType
- is_initialized(...) from builtins.PyCapsule
- is_initialized(rosetta.protocols.features.ProteinSilentReport) -> bool
- load_pose(...) from builtins.PyCapsule
- load_pose(*args, **kwargs)
Overloaded function.
1. load_pose(self : rosetta.protocols.features.ProteinSilentReport, db_session : rosetta.utility.sql_database.session, struct_id : int, pose : rosetta.core.pose.Pose) -> NoneType
2. load_pose(self : rosetta.protocols.features.ProteinSilentReport, db_session : rosetta.utility.sql_database.session, struct_id : int, residue_numbers : rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t, pose : rosetta.core.pose.Pose) -> NoneType
- version(...) from builtins.PyCapsule
- version(rosetta.protocols.features.ProteinSilentReport) -> int
- write_schema_to_db(...) from builtins.PyCapsule
- write_schema_to_db(self : rosetta.protocols.features.ProteinSilentReport, db_session : rosetta.utility.sql_database.session) -> NoneType
|
class RadiusOfGyrationFeatures(FeaturesReporter) |
| | |
- Method resolution order:
- RadiusOfGyrationFeatures
- FeaturesReporter
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.protocols.features.RadiusOfGyrationFeatures) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.features.RadiusOfGyrationFeatures, : rosetta.protocols.features.RadiusOfGyrationFeatures) -> rosetta.protocols.features.RadiusOfGyrationFeatures
- features_reporter_dependencies(...) from builtins.PyCapsule
- features_reporter_dependencies(rosetta.protocols.features.RadiusOfGyrationFeatures) -> 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.
- report_features(...) from builtins.PyCapsule
- report_features(self : rosetta.protocols.features.RadiusOfGyrationFeatures, pose : rosetta.core.pose.Pose, relevant_residues : rosetta.utility.vector1_bool, stuct_id : int, db_interface : rosetta.utility.sql_database.session) -> int
collect all the feature data for the pose
- type_name(...) from builtins.PyCapsule
- type_name(rosetta.protocols.features.RadiusOfGyrationFeatures) -> str
return string with class name
- write_schema_to_db(...) from builtins.PyCapsule
- write_schema_to_db(self : rosetta.protocols.features.RadiusOfGyrationFeatures, db_session : rosetta.utility.sql_database.session) -> NoneType
generate the table schemas and write them to the database
Methods inherited from FeaturesReporter:
- check_relevant_residues(...) from builtins.PyCapsule
- check_relevant_residues(*args, **kwargs)
Overloaded function.
1. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int) -> bool
2. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool
3. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, residues : rosetta.utility.vector1_unsigned_long) -> bool
- check_relevant_residues_range(...) from builtins.PyCapsule
- check_relevant_residues_range(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool
- delete_record(...) from builtins.PyCapsule
- delete_record(self : rosetta.protocols.features.FeaturesReporter, : int, : rosetta.utility.sql_database.session) -> NoneType
- get_relevant_residues_mode(...) from builtins.PyCapsule
- get_relevant_residues_mode(rosetta.protocols.features.FeaturesReporter) -> rosetta.protocols.features.RelevantResiduesMode.T
- load_into_pose(...) from builtins.PyCapsule
- load_into_pose(self : rosetta.protocols.features.FeaturesReporter, : rosetta.utility.sql_database.session, : int, : rosetta.core.pose.Pose) -> NoneType
- schema(...) from builtins.PyCapsule
- schema(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
- set_relevant_residues_mode(...) from builtins.PyCapsule
- set_relevant_residues_mode(self : rosetta.protocols.features.FeaturesReporter, setting : rosetta.protocols.features.RelevantResiduesMode.T) -> NoneType
|
class ReportToDB(rosetta.protocols.moves.Mover) |
| | |
- Method resolution order:
- ReportToDB
- rosetta.protocols.moves.Mover
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(self : handle, name : str) -> NoneType
3. __init__(handle, rosetta.utility.sql_database.session, str, str) -> NoneType
doc
4. __init__(handle, rosetta.utility.sql_database.session, str, str, bool) -> NoneType
doc
5. __init__(self : handle, db_session : rosetta.utility.sql_database.session, batch_name : str, batch_description : str, use_transactions : bool, cache_size : int) -> NoneType
6. __init__(handle, str, rosetta.utility.sql_database.session, str, str) -> NoneType
doc
7. __init__(handle, str, rosetta.utility.sql_database.session, str, str, bool) -> NoneType
doc
8. __init__(self : handle, name : str, db_session : rosetta.utility.sql_database.session, batch_name : str, batch_description : str, use_transactions : bool, cache_size : int) -> NoneType
9. __init__(handle, rosetta.protocols.features.ReportToDB) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- add_features_reporter(...) from builtins.PyCapsule
- add_features_reporter(self : rosetta.protocols.features.ReportToDB, features_reporter : rosetta.protocols.features.FeaturesReporter) -> NoneType
- apply(...) from builtins.PyCapsule
- apply(self : rosetta.protocols.features.ReportToDB, pose : rosetta.core.pose.Pose) -> NoneType
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.features.ReportToDB, : rosetta.protocols.features.ReportToDB) -> rosetta.protocols.features.ReportToDB
- check_features_reporter_dependencies(...) from builtins.PyCapsule
- check_features_reporter_dependencies(self : rosetta.protocols.features.ReportToDB, test_feature_reporter : rosetta.protocols.features.FeaturesReporter) -> NoneType
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.features.ReportToDB) -> rosetta.protocols.moves.Mover
- fresh_instance(...) from builtins.PyCapsule
- fresh_instance(rosetta.protocols.features.ReportToDB) -> rosetta.protocols.moves.Mover
- get_batch_description(...) from builtins.PyCapsule
- get_batch_description(rosetta.protocols.features.ReportToDB) -> str
- get_batch_name(...) from builtins.PyCapsule
- get_batch_name(rosetta.protocols.features.ReportToDB) -> str
- get_last_struct_id(...) from builtins.PyCapsule
- get_last_struct_id(rosetta.protocols.features.ReportToDB) -> int
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.features.ReportToDB) -> str
- get_relevant_residues(...) from builtins.PyCapsule
- get_relevant_residues(rosetta.protocols.features.ReportToDB) -> rosetta.utility.vector1_bool
- get_relevant_residues_mode(...) from builtins.PyCapsule
- get_relevant_residues_mode(rosetta.protocols.features.ReportToDB) -> rosetta.protocols.features.RelevantResiduesMode.T
- get_relevant_residues_task_factory(...) from builtins.PyCapsule
- get_relevant_residues_task_factory(rosetta.protocols.features.ReportToDB) -> rosetta.core.pack.task.TaskFactory
- get_structure_input_tag(...) from builtins.PyCapsule
- get_structure_input_tag(rosetta.protocols.features.ReportToDB) -> str
- get_structure_tag(...) from builtins.PyCapsule
- get_structure_tag(rosetta.protocols.features.ReportToDB) -> str
- initialize_database(...) from builtins.PyCapsule
- initialize_database(rosetta.protocols.features.ReportToDB) -> NoneType
- initialize_pose(...) from builtins.PyCapsule
- initialize_pose(self : rosetta.protocols.features.ReportToDB, pose : rosetta.core.pose.Pose) -> NoneType
initialize the pose and set the relevant residues
- initialize_relevant_residues(...) from builtins.PyCapsule
- initialize_relevant_residues(self : rosetta.protocols.features.ReportToDB, pose : rosetta.core.pose.Pose) -> rosetta.utility.vector1_bool
initialize the relevant residues of the pose and store save for later.
- initialize_reporters(...) from builtins.PyCapsule
- initialize_reporters(rosetta.protocols.features.ReportToDB) -> NoneType
- name(...) from builtins.PyCapsule
- name(rosetta.protocols.features.ReportToDB) -> str
- parse_batch_description_tag_item(...) from builtins.PyCapsule
- parse_batch_description_tag_item(self : rosetta.protocols.features.ReportToDB, tag : rosetta.utility.tag.Tag) -> NoneType
- parse_batch_id_tag_item(...) from builtins.PyCapsule
- parse_batch_id_tag_item(self : rosetta.protocols.features.ReportToDB, tag : rosetta.utility.tag.Tag) -> NoneType
- parse_batch_name_tag_item(...) from builtins.PyCapsule
- parse_batch_name_tag_item(self : rosetta.protocols.features.ReportToDB, tag : rosetta.utility.tag.Tag) -> NoneType
- parse_cache_size_tag_item(...) from builtins.PyCapsule
- parse_cache_size_tag_item(self : rosetta.protocols.features.ReportToDB, tag : rosetta.utility.tag.Tag) -> NoneType
- parse_protocol_id_tag_item(...) from builtins.PyCapsule
- parse_protocol_id_tag_item(self : rosetta.protocols.features.ReportToDB, tag : rosetta.utility.tag.Tag) -> NoneType
- parse_relevant_residues_mode_tag_item(...) from builtins.PyCapsule
- parse_relevant_residues_mode_tag_item(self : rosetta.protocols.features.ReportToDB, tag : rosetta.utility.tag.Tag) -> NoneType
- parse_remove_xray_virt_tag_item(...) from builtins.PyCapsule
- parse_remove_xray_virt_tag_item(self : rosetta.protocols.features.ReportToDB, tag : rosetta.utility.tag.Tag) -> NoneType
- parse_use_transactions_tag_item(...) from builtins.PyCapsule
- parse_use_transactions_tag_item(self : rosetta.protocols.features.ReportToDB, tag : rosetta.utility.tag.Tag) -> NoneType
- register_options(...) from builtins.PyCapsule
- register_options(rosetta.protocols.features.ReportToDB) -> NoneType
- report_features(...) from builtins.PyCapsule
- report_features(self : rosetta.protocols.features.ReportToDB, pose : rosetta.core.pose.Pose, struct_id : int, relevant_residues : rosetta.utility.vector1_bool) -> NoneType
- report_structure_features(...) from builtins.PyCapsule
- report_structure_features(rosetta.protocols.features.ReportToDB) -> int
- set_batch_description(...) from builtins.PyCapsule
- set_batch_description(self : rosetta.protocols.features.ReportToDB, batch_description : str) -> NoneType
- set_batch_name(...) from builtins.PyCapsule
- set_batch_name(self : rosetta.protocols.features.ReportToDB, batch_name : str) -> NoneType
- set_relevant_residues(...) from builtins.PyCapsule
- set_relevant_residues(self : rosetta.protocols.features.ReportToDB, relevant_residues : rosetta.utility.vector1_bool) -> NoneType
- set_relevant_residues_mode(...) from builtins.PyCapsule
- set_relevant_residues_mode(self : rosetta.protocols.features.ReportToDB, setting : rosetta.protocols.features.RelevantResiduesMode.T) -> NoneType
- set_relevant_residues_task_factory(...) from builtins.PyCapsule
- set_relevant_residues_task_factory(self : rosetta.protocols.features.ReportToDB, task_factory : rosetta.core.pack.task.TaskFactory) -> NoneType
- set_structure_input_tag(...) from builtins.PyCapsule
- set_structure_input_tag(self : rosetta.protocols.features.ReportToDB, setting : str) -> NoneType
- set_structure_tag(...) from builtins.PyCapsule
- set_structure_tag(self : rosetta.protocols.features.ReportToDB, setting : str) -> NoneType
Methods inherited from rosetta.protocols.moves.Mover:
- clear_info(...) from builtins.PyCapsule
- clear_info(rosetta.protocols.moves.Mover) -> NoneType
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
- create(...) from builtins.PyCapsule
- create(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
- get_additional_output(...) from builtins.PyCapsule
- get_additional_output(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
fpd
Mechanism by which a mover may return multiple output poses from a single input pose.
- get_current_job(...) from builtins.PyCapsule
- get_current_job(rosetta.protocols.moves.Mover) -> protocols::jobdist::BasicJob
- get_current_tag(...) from builtins.PyCapsule
- get_current_tag(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.
- get_input_pose(...) from builtins.PyCapsule
- get_input_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
- get_last_move_status(...) from builtins.PyCapsule
- get_last_move_status(rosetta.protocols.moves.Mover) -> 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.
- get_native_pose(...) from builtins.PyCapsule
- get_native_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
- get_self_ptr(...) from builtins.PyCapsule
- get_self_ptr(*args, **kwargs)
Overloaded function.
1. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
2. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
- get_self_weak_ptr(...) from builtins.PyCapsule
- get_self_weak_ptr(*args, **kwargs)
Overloaded function.
1. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_const_protocols_moves_Mover_t
2. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_protocols_moves_Mover_t
- get_type(...) from builtins.PyCapsule
- get_type(rosetta.protocols.moves.Mover) -> str
- info(...) from builtins.PyCapsule
- info(*args, **kwargs)
Overloaded function.
1. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t
non-const accessor
2. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t
const accessor
- last_proposal_density_ratio(...) from builtins.PyCapsule
- last_proposal_density_ratio(rosetta.protocols.moves.Mover) -> float
- reinitialize_for_each_job(...) from builtins.PyCapsule
- reinitialize_for_each_job(rosetta.protocols.moves.Mover) -> bool
Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on
each use.
- reinitialize_for_new_input(...) from builtins.PyCapsule
- reinitialize_for_new_input(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).
- reset_status(...) from builtins.PyCapsule
- reset_status(rosetta.protocols.moves.Mover) -> NoneType
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.
- set_current_job(...) from builtins.PyCapsule
- set_current_job(self : rosetta.protocols.moves.Mover, job : protocols::jobdist::BasicJob) -> NoneType
////////////////////////////end Job Distributor interface////////////////////////////////////////
- set_current_tag(...) from builtins.PyCapsule
- set_current_tag(self : rosetta.protocols.moves.Mover, new_tag : str) -> NoneType
- set_input_pose(...) from builtins.PyCapsule
- set_input_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
setter for poses contained for rms
- set_native_pose(...) from builtins.PyCapsule
- set_native_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
setter for native poses contained for rms ---- we should get rid of this method? it is widely used, but a bit unsafe
- set_type(...) from builtins.PyCapsule
- set_type(self : rosetta.protocols.moves.Mover, setting : str) -> NoneType
- test_move(...) from builtins.PyCapsule
- test_move(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
: Unit test support function. Apply one move to a given pose.
Allows extra test specific functions to be called before applying
- type(...) from builtins.PyCapsule
- type(*args, **kwargs)
Overloaded function.
1. type(rosetta.protocols.moves.Mover) -> str
2. type(self : rosetta.protocols.moves.Mover, type_in : str) -> NoneType
|
class ResidueBurialFeatures(FeaturesReporter) |
| | |
- Method resolution order:
- ResidueBurialFeatures
- FeaturesReporter
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.protocols.features.ResidueBurialFeatures) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.features.ResidueBurialFeatures, : rosetta.protocols.features.ResidueBurialFeatures) -> rosetta.protocols.features.ResidueBurialFeatures
- features_reporter_dependencies(...) from builtins.PyCapsule
- features_reporter_dependencies(rosetta.protocols.features.ResidueBurialFeatures) -> 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.
- report_features(...) from builtins.PyCapsule
- report_features(self : rosetta.protocols.features.ResidueBurialFeatures, pose : rosetta.core.pose.Pose, relevant_residues : rosetta.utility.vector1_bool, struct_id : int, db_session : rosetta.utility.sql_database.session) -> int
collect all the feature data for the pose
- type_name(...) from builtins.PyCapsule
- type_name(rosetta.protocols.features.ResidueBurialFeatures) -> str
return string with class name
- write_schema_to_db(...) from builtins.PyCapsule
- write_schema_to_db(self : rosetta.protocols.features.ResidueBurialFeatures, db_session : rosetta.utility.sql_database.session) -> NoneType
generate the table schemas and write them to the database
Methods inherited from FeaturesReporter:
- check_relevant_residues(...) from builtins.PyCapsule
- check_relevant_residues(*args, **kwargs)
Overloaded function.
1. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int) -> bool
2. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool
3. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, residues : rosetta.utility.vector1_unsigned_long) -> bool
- check_relevant_residues_range(...) from builtins.PyCapsule
- check_relevant_residues_range(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool
- delete_record(...) from builtins.PyCapsule
- delete_record(self : rosetta.protocols.features.FeaturesReporter, : int, : rosetta.utility.sql_database.session) -> NoneType
- get_relevant_residues_mode(...) from builtins.PyCapsule
- get_relevant_residues_mode(rosetta.protocols.features.FeaturesReporter) -> rosetta.protocols.features.RelevantResiduesMode.T
- load_into_pose(...) from builtins.PyCapsule
- load_into_pose(self : rosetta.protocols.features.FeaturesReporter, : rosetta.utility.sql_database.session, : int, : rosetta.core.pose.Pose) -> NoneType
- schema(...) from builtins.PyCapsule
- schema(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
- set_relevant_residues_mode(...) from builtins.PyCapsule
- set_relevant_residues_mode(self : rosetta.protocols.features.FeaturesReporter, setting : rosetta.protocols.features.RelevantResiduesMode.T) -> NoneType
|
class ResidueConformationFeatures(FeaturesReporter) |
| | |
- Method resolution order:
- ResidueConformationFeatures
- FeaturesReporter
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.protocols.features.ResidueConformationFeatures) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.features.ResidueConformationFeatures, : rosetta.protocols.features.ResidueConformationFeatures) -> rosetta.protocols.features.ResidueConformationFeatures
- delete_record(...) from builtins.PyCapsule
- delete_record(self : rosetta.protocols.features.ResidueConformationFeatures, struct_id : int, : rosetta.utility.sql_database.session) -> NoneType
- features_reporter_dependencies(...) from builtins.PyCapsule
- features_reporter_dependencies(rosetta.protocols.features.ResidueConformationFeatures) -> 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.
- load_conformation(...) from builtins.PyCapsule
- load_conformation(self : rosetta.protocols.features.ResidueConformationFeatures, db_session : rosetta.utility.sql_database.session, struct_id : int, pose : rosetta.core.pose.Pose) -> NoneType
- load_into_pose(...) from builtins.PyCapsule
- load_into_pose(self : rosetta.protocols.features.ResidueConformationFeatures, db_session : rosetta.utility.sql_database.session, struct_id : int, pose : rosetta.core.pose.Pose) -> NoneType
- report_features(...) from builtins.PyCapsule
- report_features(self : rosetta.protocols.features.ResidueConformationFeatures, pose : rosetta.core.pose.Pose, relevant_residues : rosetta.utility.vector1_bool, struct_id : int, db_session : rosetta.utility.sql_database.session) -> int
collect all the feature data for the pose
- type_name(...) from builtins.PyCapsule
- type_name(rosetta.protocols.features.ResidueConformationFeatures) -> str
return string with class name
- write_schema_to_db(...) from builtins.PyCapsule
- write_schema_to_db(self : rosetta.protocols.features.ResidueConformationFeatures, db_session : rosetta.utility.sql_database.session) -> NoneType
generate the table schemas and write them to the database
Methods inherited from FeaturesReporter:
- check_relevant_residues(...) from builtins.PyCapsule
- check_relevant_residues(*args, **kwargs)
Overloaded function.
1. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int) -> bool
2. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool
3. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, residues : rosetta.utility.vector1_unsigned_long) -> bool
- check_relevant_residues_range(...) from builtins.PyCapsule
- check_relevant_residues_range(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool
- get_relevant_residues_mode(...) from builtins.PyCapsule
- get_relevant_residues_mode(rosetta.protocols.features.FeaturesReporter) -> rosetta.protocols.features.RelevantResiduesMode.T
- schema(...) from builtins.PyCapsule
- schema(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
- set_relevant_residues_mode(...) from builtins.PyCapsule
- set_relevant_residues_mode(self : rosetta.protocols.features.FeaturesReporter, setting : rosetta.protocols.features.RelevantResiduesMode.T) -> NoneType
|
class ResidueFeatures(FeaturesReporter) |
| | |
- Method resolution order:
- ResidueFeatures
- FeaturesReporter
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.protocols.features.ResidueFeatures) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.features.ResidueFeatures, : rosetta.protocols.features.ResidueFeatures) -> rosetta.protocols.features.ResidueFeatures
- delete_record(...) from builtins.PyCapsule
- delete_record(self : rosetta.protocols.features.ResidueFeatures, struct_id : int, db_sesion : rosetta.utility.sql_database.session) -> NoneType
- features_reporter_dependencies(...) from builtins.PyCapsule
- features_reporter_dependencies(rosetta.protocols.features.ResidueFeatures) -> 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.
- insert_residue_rows(...) from builtins.PyCapsule
- insert_residue_rows(self : rosetta.protocols.features.ResidueFeatures, pose : rosetta.core.pose.Pose, relevant_residues : rosetta.utility.vector1_bool, struct_id : int, db_session : rosetta.utility.sql_database.session) -> NoneType
- report_features(...) from builtins.PyCapsule
- report_features(self : rosetta.protocols.features.ResidueFeatures, pose : rosetta.core.pose.Pose, relevant_residues : rosetta.utility.vector1_bool, struct_id : int, db_session : rosetta.utility.sql_database.session) -> int
collect all the feature data for the pose
- type_name(...) from builtins.PyCapsule
- type_name(rosetta.protocols.features.ResidueFeatures) -> str
return string with class name
- write_schema_to_db(...) from builtins.PyCapsule
- write_schema_to_db(self : rosetta.protocols.features.ResidueFeatures, db_session : rosetta.utility.sql_database.session) -> NoneType
generate the table schemas and write them to the database
Methods inherited from FeaturesReporter:
- check_relevant_residues(...) from builtins.PyCapsule
- check_relevant_residues(*args, **kwargs)
Overloaded function.
1. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int) -> bool
2. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool
3. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, residues : rosetta.utility.vector1_unsigned_long) -> bool
- check_relevant_residues_range(...) from builtins.PyCapsule
- check_relevant_residues_range(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool
- get_relevant_residues_mode(...) from builtins.PyCapsule
- get_relevant_residues_mode(rosetta.protocols.features.FeaturesReporter) -> rosetta.protocols.features.RelevantResiduesMode.T
- load_into_pose(...) from builtins.PyCapsule
- load_into_pose(self : rosetta.protocols.features.FeaturesReporter, : rosetta.utility.sql_database.session, : int, : rosetta.core.pose.Pose) -> NoneType
- schema(...) from builtins.PyCapsule
- schema(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
- set_relevant_residues_mode(...) from builtins.PyCapsule
- set_relevant_residues_mode(self : rosetta.protocols.features.FeaturesReporter, setting : rosetta.protocols.features.RelevantResiduesMode.T) -> NoneType
|
class ResidueGridScoresFeatures(FeaturesReporter) |
| | |
- Method resolution order:
- ResidueGridScoresFeatures
- FeaturesReporter
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.protocols.features.ResidueGridScoresFeatures) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.features.ResidueGridScoresFeatures, : rosetta.protocols.features.ResidueGridScoresFeatures) -> rosetta.protocols.features.ResidueGridScoresFeatures
- features_reporter_dependencies(...) from builtins.PyCapsule
- features_reporter_dependencies(rosetta.protocols.features.ResidueGridScoresFeatures) -> 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.
- report_features(...) from builtins.PyCapsule
- report_features(self : rosetta.protocols.features.ResidueGridScoresFeatures, pose : rosetta.core.pose.Pose, relevant_residues : rosetta.utility.vector1_bool, struct_id : int, db_session : rosetta.utility.sql_database.session) -> int
collect all the feature data for the pose
- type_name(...) from builtins.PyCapsule
- type_name(rosetta.protocols.features.ResidueGridScoresFeatures) -> str
return string with class name
- write_schema_to_db(...) from builtins.PyCapsule
- write_schema_to_db(self : rosetta.protocols.features.ResidueGridScoresFeatures, db_session : rosetta.utility.sql_database.session) -> NoneType
generate the table schemas and write them to the database
Methods inherited from FeaturesReporter:
- check_relevant_residues(...) from builtins.PyCapsule
- check_relevant_residues(*args, **kwargs)
Overloaded function.
1. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int) -> bool
2. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool
3. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, residues : rosetta.utility.vector1_unsigned_long) -> bool
- check_relevant_residues_range(...) from builtins.PyCapsule
- check_relevant_residues_range(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool
- delete_record(...) from builtins.PyCapsule
- delete_record(self : rosetta.protocols.features.FeaturesReporter, : int, : rosetta.utility.sql_database.session) -> NoneType
- get_relevant_residues_mode(...) from builtins.PyCapsule
- get_relevant_residues_mode(rosetta.protocols.features.FeaturesReporter) -> rosetta.protocols.features.RelevantResiduesMode.T
- load_into_pose(...) from builtins.PyCapsule
- load_into_pose(self : rosetta.protocols.features.FeaturesReporter, : rosetta.utility.sql_database.session, : int, : rosetta.core.pose.Pose) -> NoneType
- schema(...) from builtins.PyCapsule
- schema(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
- set_relevant_residues_mode(...) from builtins.PyCapsule
- set_relevant_residues_mode(self : rosetta.protocols.features.FeaturesReporter, setting : rosetta.protocols.features.RelevantResiduesMode.T) -> NoneType
|
class ResidueScoresFeatures(FeaturesReporter) |
| | |
- Method resolution order:
- ResidueScoresFeatures
- FeaturesReporter
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(self : handle, scfxn : rosetta.core.scoring.ScoreFunction) -> NoneType
3. __init__(handle, rosetta.protocols.features.ResidueScoresFeatures) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.features.ResidueScoresFeatures, : rosetta.protocols.features.ResidueScoresFeatures) -> rosetta.protocols.features.ResidueScoresFeatures
- features_reporter_dependencies(...) from builtins.PyCapsule
- features_reporter_dependencies(rosetta.protocols.features.ResidueScoresFeatures) -> 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.
- report_features(...) from builtins.PyCapsule
- report_features(self : rosetta.protocols.features.ResidueScoresFeatures, pose : rosetta.core.pose.Pose, relevant_residues : rosetta.utility.vector1_bool, struct_id : int, db_session : rosetta.utility.sql_database.session) -> int
collect all the feature data for the pose
- type_name(...) from builtins.PyCapsule
- type_name(rosetta.protocols.features.ResidueScoresFeatures) -> str
return string with class name
- write_schema_to_db(...) from builtins.PyCapsule
- write_schema_to_db(self : rosetta.protocols.features.ResidueScoresFeatures, db_session : rosetta.utility.sql_database.session) -> NoneType
generate the table schemas and write them to the database
Methods inherited from FeaturesReporter:
- check_relevant_residues(...) from builtins.PyCapsule
- check_relevant_residues(*args, **kwargs)
Overloaded function.
1. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int) -> bool
2. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool
3. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, residues : rosetta.utility.vector1_unsigned_long) -> bool
- check_relevant_residues_range(...) from builtins.PyCapsule
- check_relevant_residues_range(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool
- delete_record(...) from builtins.PyCapsule
- delete_record(self : rosetta.protocols.features.FeaturesReporter, : int, : rosetta.utility.sql_database.session) -> NoneType
- get_relevant_residues_mode(...) from builtins.PyCapsule
- get_relevant_residues_mode(rosetta.protocols.features.FeaturesReporter) -> rosetta.protocols.features.RelevantResiduesMode.T
- load_into_pose(...) from builtins.PyCapsule
- load_into_pose(self : rosetta.protocols.features.FeaturesReporter, : rosetta.utility.sql_database.session, : int, : rosetta.core.pose.Pose) -> NoneType
- schema(...) from builtins.PyCapsule
- schema(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
- set_relevant_residues_mode(...) from builtins.PyCapsule
- set_relevant_residues_mode(self : rosetta.protocols.features.FeaturesReporter, setting : rosetta.protocols.features.RelevantResiduesMode.T) -> NoneType
|
class ResidueSecondaryStructureFeatures(FeaturesReporter) |
| | |
- Method resolution order:
- ResidueSecondaryStructureFeatures
- FeaturesReporter
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.protocols.features.ResidueSecondaryStructureFeatures) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.features.ResidueSecondaryStructureFeatures, : rosetta.protocols.features.ResidueSecondaryStructureFeatures) -> rosetta.protocols.features.ResidueSecondaryStructureFeatures
- features_reporter_dependencies(...) from builtins.PyCapsule
- features_reporter_dependencies(rosetta.protocols.features.ResidueSecondaryStructureFeatures) -> 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.
- report_features(...) from builtins.PyCapsule
- report_features(self : rosetta.protocols.features.ResidueSecondaryStructureFeatures, pose : rosetta.core.pose.Pose, relevant_residues : rosetta.utility.vector1_bool, struct_id : int, db_session : rosetta.utility.sql_database.session) -> int
collect all the feature data for the pose
- type_name(...) from builtins.PyCapsule
- type_name(rosetta.protocols.features.ResidueSecondaryStructureFeatures) -> str
return string with class name
- write_schema_to_db(...) from builtins.PyCapsule
- write_schema_to_db(self : rosetta.protocols.features.ResidueSecondaryStructureFeatures, db_session : rosetta.utility.sql_database.session) -> NoneType
generate the table schemas and write them to the database
Methods inherited from FeaturesReporter:
- check_relevant_residues(...) from builtins.PyCapsule
- check_relevant_residues(*args, **kwargs)
Overloaded function.
1. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int) -> bool
2. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool
3. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, residues : rosetta.utility.vector1_unsigned_long) -> bool
- check_relevant_residues_range(...) from builtins.PyCapsule
- check_relevant_residues_range(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool
- delete_record(...) from builtins.PyCapsule
- delete_record(self : rosetta.protocols.features.FeaturesReporter, : int, : rosetta.utility.sql_database.session) -> NoneType
- get_relevant_residues_mode(...) from builtins.PyCapsule
- get_relevant_residues_mode(rosetta.protocols.features.FeaturesReporter) -> rosetta.protocols.features.RelevantResiduesMode.T
- load_into_pose(...) from builtins.PyCapsule
- load_into_pose(self : rosetta.protocols.features.FeaturesReporter, : rosetta.utility.sql_database.session, : int, : rosetta.core.pose.Pose) -> NoneType
- schema(...) from builtins.PyCapsule
- schema(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
- set_relevant_residues_mode(...) from builtins.PyCapsule
- set_relevant_residues_mode(self : rosetta.protocols.features.FeaturesReporter, setting : rosetta.protocols.features.RelevantResiduesMode.T) -> NoneType
|
class ResidueTotalScoresFeatures(FeaturesReporter) |
| | |
- Method resolution order:
- ResidueTotalScoresFeatures
- FeaturesReporter
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(self : handle, scfxn : rosetta.core.scoring.ScoreFunction) -> NoneType
3. __init__(handle, rosetta.protocols.features.ResidueTotalScoresFeatures) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.features.ResidueTotalScoresFeatures, : rosetta.protocols.features.ResidueTotalScoresFeatures) -> rosetta.protocols.features.ResidueTotalScoresFeatures
- features_reporter_dependencies(...) from builtins.PyCapsule
- features_reporter_dependencies(rosetta.protocols.features.ResidueTotalScoresFeatures) -> 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.
- report_features(...) from builtins.PyCapsule
- report_features(self : rosetta.protocols.features.ResidueTotalScoresFeatures, pose : rosetta.core.pose.Pose, relevant_residues : rosetta.utility.vector1_bool, struct_id : int, db_session : rosetta.utility.sql_database.session) -> int
collect all the feature data for the pose
- type_name(...) from builtins.PyCapsule
- type_name(rosetta.protocols.features.ResidueTotalScoresFeatures) -> str
return string with class name
- write_schema_to_db(...) from builtins.PyCapsule
- write_schema_to_db(self : rosetta.protocols.features.ResidueTotalScoresFeatures, db_session : rosetta.utility.sql_database.session) -> NoneType
generate the table schemas and write them to the database
Methods inherited from FeaturesReporter:
- check_relevant_residues(...) from builtins.PyCapsule
- check_relevant_residues(*args, **kwargs)
Overloaded function.
1. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int) -> bool
2. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool
3. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, residues : rosetta.utility.vector1_unsigned_long) -> bool
- check_relevant_residues_range(...) from builtins.PyCapsule
- check_relevant_residues_range(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool
- delete_record(...) from builtins.PyCapsule
- delete_record(self : rosetta.protocols.features.FeaturesReporter, : int, : rosetta.utility.sql_database.session) -> NoneType
- get_relevant_residues_mode(...) from builtins.PyCapsule
- get_relevant_residues_mode(rosetta.protocols.features.FeaturesReporter) -> rosetta.protocols.features.RelevantResiduesMode.T
- load_into_pose(...) from builtins.PyCapsule
- load_into_pose(self : rosetta.protocols.features.FeaturesReporter, : rosetta.utility.sql_database.session, : int, : rosetta.core.pose.Pose) -> NoneType
- schema(...) from builtins.PyCapsule
- schema(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
- set_relevant_residues_mode(...) from builtins.PyCapsule
- set_relevant_residues_mode(self : rosetta.protocols.features.FeaturesReporter, setting : rosetta.protocols.features.RelevantResiduesMode.T) -> NoneType
|
class ResidueTypesFeatures(FeaturesReporter) |
| | |
- Method resolution order:
- ResidueTypesFeatures
- FeaturesReporter
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(handle) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.features.ResidueTypesFeatures, : rosetta.protocols.features.ResidueTypesFeatures) -> rosetta.protocols.features.ResidueTypesFeatures
- features_reporter_dependencies(...) from builtins.PyCapsule
- features_reporter_dependencies(rosetta.protocols.features.ResidueTypesFeatures) -> 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.
- report_features(...) from builtins.PyCapsule
- report_features(self : rosetta.protocols.features.ResidueTypesFeatures, pose : rosetta.core.pose.Pose, relevant_residues : rosetta.utility.vector1_bool, struct_id : int, db_session : rosetta.utility.sql_database.session) -> int
collect all the feature data for the pose
- type_name(...) from builtins.PyCapsule
- type_name(rosetta.protocols.features.ResidueTypesFeatures) -> str
return string with class name
- write_schema_to_db(...) from builtins.PyCapsule
- write_schema_to_db(self : rosetta.protocols.features.ResidueTypesFeatures, db_session : rosetta.utility.sql_database.session) -> NoneType
generate the table schemas and write them to the database
Methods inherited from FeaturesReporter:
- check_relevant_residues(...) from builtins.PyCapsule
- check_relevant_residues(*args, **kwargs)
Overloaded function.
1. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int) -> bool
2. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool
3. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, residues : rosetta.utility.vector1_unsigned_long) -> bool
- check_relevant_residues_range(...) from builtins.PyCapsule
- check_relevant_residues_range(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool
- delete_record(...) from builtins.PyCapsule
- delete_record(self : rosetta.protocols.features.FeaturesReporter, : int, : rosetta.utility.sql_database.session) -> NoneType
- get_relevant_residues_mode(...) from builtins.PyCapsule
- get_relevant_residues_mode(rosetta.protocols.features.FeaturesReporter) -> rosetta.protocols.features.RelevantResiduesMode.T
- load_into_pose(...) from builtins.PyCapsule
- load_into_pose(self : rosetta.protocols.features.FeaturesReporter, : rosetta.utility.sql_database.session, : int, : rosetta.core.pose.Pose) -> NoneType
- schema(...) from builtins.PyCapsule
- schema(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
- set_relevant_residues_mode(...) from builtins.PyCapsule
- set_relevant_residues_mode(self : rosetta.protocols.features.FeaturesReporter, setting : rosetta.protocols.features.RelevantResiduesMode.T) -> NoneType
|
class RotamerBoltzmannWeightFeatures(FeaturesReporter) |
| | |
- Method resolution order:
- RotamerBoltzmannWeightFeatures
- FeaturesReporter
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(self : handle, scfxn : rosetta.core.scoring.ScoreFunction) -> NoneType
3. __init__(handle, rosetta.protocols.features.RotamerBoltzmannWeightFeatures) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.features.RotamerBoltzmannWeightFeatures, : rosetta.protocols.features.RotamerBoltzmannWeightFeatures) -> rosetta.protocols.features.RotamerBoltzmannWeightFeatures
- features_reporter_dependencies(...) from builtins.PyCapsule
- features_reporter_dependencies(rosetta.protocols.features.RotamerBoltzmannWeightFeatures) -> 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.
- report_features(...) from builtins.PyCapsule
- report_features(self : rosetta.protocols.features.RotamerBoltzmannWeightFeatures, pose : rosetta.core.pose.Pose, relevant_residues : rosetta.utility.vector1_bool, struct_id : int, db_session : rosetta.utility.sql_database.session) -> int
collect all the feature data for the pose
- type_name(...) from builtins.PyCapsule
- type_name(rosetta.protocols.features.RotamerBoltzmannWeightFeatures) -> str
return string with class name
- write_schema_to_db(...) from builtins.PyCapsule
- write_schema_to_db(self : rosetta.protocols.features.RotamerBoltzmannWeightFeatures, db_session : rosetta.utility.sql_database.session) -> NoneType
generate the table schemas and write them to the database
Methods inherited from FeaturesReporter:
- check_relevant_residues(...) from builtins.PyCapsule
- check_relevant_residues(*args, **kwargs)
Overloaded function.
1. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int) -> bool
2. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool
3. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, residues : rosetta.utility.vector1_unsigned_long) -> bool
- check_relevant_residues_range(...) from builtins.PyCapsule
- check_relevant_residues_range(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool
- delete_record(...) from builtins.PyCapsule
- delete_record(self : rosetta.protocols.features.FeaturesReporter, : int, : rosetta.utility.sql_database.session) -> NoneType
- get_relevant_residues_mode(...) from builtins.PyCapsule
- get_relevant_residues_mode(rosetta.protocols.features.FeaturesReporter) -> rosetta.protocols.features.RelevantResiduesMode.T
- load_into_pose(...) from builtins.PyCapsule
- load_into_pose(self : rosetta.protocols.features.FeaturesReporter, : rosetta.utility.sql_database.session, : int, : rosetta.core.pose.Pose) -> NoneType
- schema(...) from builtins.PyCapsule
- schema(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
- set_relevant_residues_mode(...) from builtins.PyCapsule
- set_relevant_residues_mode(self : rosetta.protocols.features.FeaturesReporter, setting : rosetta.protocols.features.RelevantResiduesMode.T) -> NoneType
|
class RotamerFeatures(FeaturesReporter) |
| | |
- Method resolution order:
- RotamerFeatures
- FeaturesReporter
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.protocols.features.RotamerFeatures) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.features.RotamerFeatures, : rosetta.protocols.features.RotamerFeatures) -> rosetta.protocols.features.RotamerFeatures
- delete_record(...) from builtins.PyCapsule
- delete_record(self : rosetta.protocols.features.RotamerFeatures, struct_id : int, db_session : rosetta.utility.sql_database.session) -> NoneType
- features_reporter_dependencies(...) from builtins.PyCapsule
- features_reporter_dependencies(rosetta.protocols.features.RotamerFeatures) -> 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.
- report_features(...) from builtins.PyCapsule
- report_features(self : rosetta.protocols.features.RotamerFeatures, pose : rosetta.core.pose.Pose, relevant_residues : rosetta.utility.vector1_bool, struct_id : int, db_session : rosetta.utility.sql_database.session) -> int
collect all the feature data for the pose
- type_name(...) from builtins.PyCapsule
- type_name(rosetta.protocols.features.RotamerFeatures) -> str
return string with class name
- write_schema_to_db(...) from builtins.PyCapsule
- write_schema_to_db(self : rosetta.protocols.features.RotamerFeatures, db_session : rosetta.utility.sql_database.session) -> NoneType
generate the table schemas and write them to the database
Methods inherited from FeaturesReporter:
- check_relevant_residues(...) from builtins.PyCapsule
- check_relevant_residues(*args, **kwargs)
Overloaded function.
1. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int) -> bool
2. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool
3. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, residues : rosetta.utility.vector1_unsigned_long) -> bool
- check_relevant_residues_range(...) from builtins.PyCapsule
- check_relevant_residues_range(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool
- get_relevant_residues_mode(...) from builtins.PyCapsule
- get_relevant_residues_mode(rosetta.protocols.features.FeaturesReporter) -> rosetta.protocols.features.RelevantResiduesMode.T
- load_into_pose(...) from builtins.PyCapsule
- load_into_pose(self : rosetta.protocols.features.FeaturesReporter, : rosetta.utility.sql_database.session, : int, : rosetta.core.pose.Pose) -> NoneType
- schema(...) from builtins.PyCapsule
- schema(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
- set_relevant_residues_mode(...) from builtins.PyCapsule
- set_relevant_residues_mode(self : rosetta.protocols.features.FeaturesReporter, setting : rosetta.protocols.features.RelevantResiduesMode.T) -> NoneType
|
class RotamerRecoveryFeatures(FeaturesReporter) |
| | |
- Method resolution order:
- RotamerRecoveryFeatures
- FeaturesReporter
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(self : handle, scfxn : rosetta.core.scoring.ScoreFunction) -> NoneType
3. __init__(handle, rosetta.protocols.features.RotamerRecoveryFeatures) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.features.RotamerRecoveryFeatures, : rosetta.protocols.features.RotamerRecoveryFeatures) -> rosetta.protocols.features.RotamerRecoveryFeatures
- features_reporter_dependencies(...) from builtins.PyCapsule
- features_reporter_dependencies(rosetta.protocols.features.RotamerRecoveryFeatures) -> 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.
- initialize_task_factory(...) from builtins.PyCapsule
- initialize_task_factory(self : rosetta.protocols.features.RotamerRecoveryFeatures, task_factory : rosetta.core.pack.task.TaskFactory) -> NoneType
- report_features(...) from builtins.PyCapsule
- report_features(self : rosetta.protocols.features.RotamerRecoveryFeatures, pose : rosetta.core.pose.Pose, relevant_residues : rosetta.utility.vector1_bool, struct_id : int, db_session : rosetta.utility.sql_database.session) -> int
collect all the feature data for the pose
- type_name(...) from builtins.PyCapsule
- type_name(rosetta.protocols.features.RotamerRecoveryFeatures) -> str
return string with class name
- write_schema_to_db(...) from builtins.PyCapsule
- write_schema_to_db(self : rosetta.protocols.features.RotamerRecoveryFeatures, db_session : rosetta.utility.sql_database.session) -> NoneType
generate the table schemas and write them to the database
Methods inherited from FeaturesReporter:
- check_relevant_residues(...) from builtins.PyCapsule
- check_relevant_residues(*args, **kwargs)
Overloaded function.
1. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int) -> bool
2. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool
3. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, residues : rosetta.utility.vector1_unsigned_long) -> bool
- check_relevant_residues_range(...) from builtins.PyCapsule
- check_relevant_residues_range(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool
- delete_record(...) from builtins.PyCapsule
- delete_record(self : rosetta.protocols.features.FeaturesReporter, : int, : rosetta.utility.sql_database.session) -> NoneType
- get_relevant_residues_mode(...) from builtins.PyCapsule
- get_relevant_residues_mode(rosetta.protocols.features.FeaturesReporter) -> rosetta.protocols.features.RelevantResiduesMode.T
- load_into_pose(...) from builtins.PyCapsule
- load_into_pose(self : rosetta.protocols.features.FeaturesReporter, : rosetta.utility.sql_database.session, : int, : rosetta.core.pose.Pose) -> NoneType
- schema(...) from builtins.PyCapsule
- schema(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
- set_relevant_residues_mode(...) from builtins.PyCapsule
- set_relevant_residues_mode(self : rosetta.protocols.features.FeaturesReporter, setting : rosetta.protocols.features.RelevantResiduesMode.T) -> NoneType
|
class RuntimeFeatures(FeaturesReporter) |
| | |
- Method resolution order:
- RuntimeFeatures
- FeaturesReporter
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(handle) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.features.RuntimeFeatures, : rosetta.protocols.features.RuntimeFeatures) -> rosetta.protocols.features.RuntimeFeatures
- features_reporter_dependencies(...) from builtins.PyCapsule
- features_reporter_dependencies(rosetta.protocols.features.RuntimeFeatures) -> rosetta.utility.vector1_std_string
The runtime features links to a structure ID, so the
StructureFeatures reporter must also be present.
- report_features(...) from builtins.PyCapsule
- report_features(self : rosetta.protocols.features.RuntimeFeatures, pose : rosetta.core.pose.Pose, relevant_residues : rosetta.utility.vector1_bool, struct_id : int, db_session : rosetta.utility.sql_database.session) -> int
Report runtime information for the current job.
- type_name(...) from builtins.PyCapsule
- type_name(rosetta.protocols.features.RuntimeFeatures) -> str
FeaturesReporter::get_name
- write_schema_to_db(...) from builtins.PyCapsule
- write_schema_to_db(self : rosetta.protocols.features.RuntimeFeatures, db_session : rosetta.utility.sql_database.session) -> NoneType
FeaturesReporter::write_schema_to_db
Methods inherited from FeaturesReporter:
- check_relevant_residues(...) from builtins.PyCapsule
- check_relevant_residues(*args, **kwargs)
Overloaded function.
1. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int) -> bool
2. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool
3. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, residues : rosetta.utility.vector1_unsigned_long) -> bool
- check_relevant_residues_range(...) from builtins.PyCapsule
- check_relevant_residues_range(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool
- delete_record(...) from builtins.PyCapsule
- delete_record(self : rosetta.protocols.features.FeaturesReporter, : int, : rosetta.utility.sql_database.session) -> NoneType
- get_relevant_residues_mode(...) from builtins.PyCapsule
- get_relevant_residues_mode(rosetta.protocols.features.FeaturesReporter) -> rosetta.protocols.features.RelevantResiduesMode.T
- load_into_pose(...) from builtins.PyCapsule
- load_into_pose(self : rosetta.protocols.features.FeaturesReporter, : rosetta.utility.sql_database.session, : int, : rosetta.core.pose.Pose) -> NoneType
- schema(...) from builtins.PyCapsule
- schema(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
- set_relevant_residues_mode(...) from builtins.PyCapsule
- set_relevant_residues_mode(self : rosetta.protocols.features.FeaturesReporter, setting : rosetta.protocols.features.RelevantResiduesMode.T) -> NoneType
|
class SaltBridgeFeatures(FeaturesReporter) |
| | |
- Method resolution order:
- SaltBridgeFeatures
- FeaturesReporter
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(self : handle, distance_cutoff : float) -> NoneType
3. __init__(handle, rosetta.protocols.features.SaltBridgeFeatures) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.features.SaltBridgeFeatures, : rosetta.protocols.features.SaltBridgeFeatures) -> rosetta.protocols.features.SaltBridgeFeatures
- distance_cutoff(...) from builtins.PyCapsule
- distance_cutoff(*args, **kwargs)
Overloaded function.
1. distance_cutoff(rosetta.protocols.features.SaltBridgeFeatures) -> float
2. distance_cutoff(self : rosetta.protocols.features.SaltBridgeFeatures, d : float) -> NoneType
- features_reporter_dependencies(...) from builtins.PyCapsule
- features_reporter_dependencies(rosetta.protocols.features.SaltBridgeFeatures) -> 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.
- report_features(...) from builtins.PyCapsule
- report_features(self : rosetta.protocols.features.SaltBridgeFeatures, pose : rosetta.core.pose.Pose, : rosetta.utility.vector1_bool, struct_id : int, db_session : rosetta.utility.sql_database.session) -> int
collect all the feature data for the pose
- type_name(...) from builtins.PyCapsule
- type_name(rosetta.protocols.features.SaltBridgeFeatures) -> str
return string with class name
- write_schema_to_db(...) from builtins.PyCapsule
- write_schema_to_db(self : rosetta.protocols.features.SaltBridgeFeatures, db_session : rosetta.utility.sql_database.session) -> NoneType
generate the table schemas and write them to the database
Methods inherited from FeaturesReporter:
- check_relevant_residues(...) from builtins.PyCapsule
- check_relevant_residues(*args, **kwargs)
Overloaded function.
1. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int) -> bool
2. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool
3. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, residues : rosetta.utility.vector1_unsigned_long) -> bool
- check_relevant_residues_range(...) from builtins.PyCapsule
- check_relevant_residues_range(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool
- delete_record(...) from builtins.PyCapsule
- delete_record(self : rosetta.protocols.features.FeaturesReporter, : int, : rosetta.utility.sql_database.session) -> NoneType
- get_relevant_residues_mode(...) from builtins.PyCapsule
- get_relevant_residues_mode(rosetta.protocols.features.FeaturesReporter) -> rosetta.protocols.features.RelevantResiduesMode.T
- load_into_pose(...) from builtins.PyCapsule
- load_into_pose(self : rosetta.protocols.features.FeaturesReporter, : rosetta.utility.sql_database.session, : int, : rosetta.core.pose.Pose) -> NoneType
- schema(...) from builtins.PyCapsule
- schema(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
- set_relevant_residues_mode(...) from builtins.PyCapsule
- set_relevant_residues_mode(self : rosetta.protocols.features.FeaturesReporter, setting : rosetta.protocols.features.RelevantResiduesMode.T) -> NoneType
|
class ScoreFunctionFeatures(FeaturesReporter) |
| | |
- Method resolution order:
- ScoreFunctionFeatures
- FeaturesReporter
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(self : handle, scfxn : rosetta.core.scoring.ScoreFunction, scfxn_name : str) -> NoneType
3. __init__(handle, rosetta.protocols.features.ScoreFunctionFeatures) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.features.ScoreFunctionFeatures, : rosetta.protocols.features.ScoreFunctionFeatures) -> rosetta.protocols.features.ScoreFunctionFeatures
- delete_record(...) from builtins.PyCapsule
- delete_record(self : rosetta.protocols.features.ScoreFunctionFeatures, struct_id : int, db_session : rosetta.utility.sql_database.session) -> NoneType
- features_reporter_dependencies(...) from builtins.PyCapsule
- features_reporter_dependencies(rosetta.protocols.features.ScoreFunctionFeatures) -> 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.
- insert_score_function_weights_rows(...) from builtins.PyCapsule
- insert_score_function_weights_rows(self : rosetta.protocols.features.ScoreFunctionFeatures, batch_id : int, db_session : rosetta.utility.sql_database.session) -> NoneType
- report_features(...) from builtins.PyCapsule
- report_features(self : rosetta.protocols.features.ScoreFunctionFeatures, pose : rosetta.core.pose.Pose, relevant_residues : rosetta.utility.vector1_bool, struct_id : int, db_session : rosetta.utility.sql_database.session) -> int
collect all the feature data for the pose
- type_name(...) from builtins.PyCapsule
- type_name(rosetta.protocols.features.ScoreFunctionFeatures) -> str
return string with class name
- write_schema_to_db(...) from builtins.PyCapsule
- write_schema_to_db(self : rosetta.protocols.features.ScoreFunctionFeatures, db_session : rosetta.utility.sql_database.session) -> NoneType
generate the table schemas and write them to the database
Methods inherited from FeaturesReporter:
- check_relevant_residues(...) from builtins.PyCapsule
- check_relevant_residues(*args, **kwargs)
Overloaded function.
1. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int) -> bool
2. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool
3. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, residues : rosetta.utility.vector1_unsigned_long) -> bool
- check_relevant_residues_range(...) from builtins.PyCapsule
- check_relevant_residues_range(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool
- get_relevant_residues_mode(...) from builtins.PyCapsule
- get_relevant_residues_mode(rosetta.protocols.features.FeaturesReporter) -> rosetta.protocols.features.RelevantResiduesMode.T
- load_into_pose(...) from builtins.PyCapsule
- load_into_pose(self : rosetta.protocols.features.FeaturesReporter, : rosetta.utility.sql_database.session, : int, : rosetta.core.pose.Pose) -> NoneType
- schema(...) from builtins.PyCapsule
- schema(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
- set_relevant_residues_mode(...) from builtins.PyCapsule
- set_relevant_residues_mode(self : rosetta.protocols.features.FeaturesReporter, setting : rosetta.protocols.features.RelevantResiduesMode.T) -> NoneType
|
class ScoreTypeFeatures(FeaturesReporter) |
| | |
- Method resolution order:
- ScoreTypeFeatures
- FeaturesReporter
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(self : handle, scfxn : rosetta.core.scoring.ScoreFunction) -> NoneType
3. __init__(handle, rosetta.protocols.features.ScoreTypeFeatures) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.features.ScoreTypeFeatures, : rosetta.protocols.features.ScoreTypeFeatures) -> rosetta.protocols.features.ScoreTypeFeatures
- delete_record(...) from builtins.PyCapsule
- delete_record(self : rosetta.protocols.features.ScoreTypeFeatures, struct_id : int, db_session : rosetta.utility.sql_database.session) -> NoneType
- features_reporter_dependencies(...) from builtins.PyCapsule
- features_reporter_dependencies(rosetta.protocols.features.ScoreTypeFeatures) -> 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.
- report_features(...) from builtins.PyCapsule
- report_features(*args, **kwargs)
Overloaded function.
1. report_features(self : rosetta.protocols.features.ScoreTypeFeatures, : rosetta.core.pose.Pose, : rosetta.utility.vector1_bool, struct_id : int, db_session : rosetta.utility.sql_database.session) -> int
2. report_features(self : rosetta.protocols.features.ScoreTypeFeatures, batch_id : int, db_session : rosetta.utility.sql_database.session) -> int
- type_name(...) from builtins.PyCapsule
- type_name(rosetta.protocols.features.ScoreTypeFeatures) -> str
return string with class name
- write_schema_to_db(...) from builtins.PyCapsule
- write_schema_to_db(self : rosetta.protocols.features.ScoreTypeFeatures, db_session : rosetta.utility.sql_database.session) -> NoneType
generate the table schemas and write them to the database
Methods inherited from FeaturesReporter:
- check_relevant_residues(...) from builtins.PyCapsule
- check_relevant_residues(*args, **kwargs)
Overloaded function.
1. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int) -> bool
2. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool
3. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, residues : rosetta.utility.vector1_unsigned_long) -> bool
- check_relevant_residues_range(...) from builtins.PyCapsule
- check_relevant_residues_range(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool
- get_relevant_residues_mode(...) from builtins.PyCapsule
- get_relevant_residues_mode(rosetta.protocols.features.FeaturesReporter) -> rosetta.protocols.features.RelevantResiduesMode.T
- load_into_pose(...) from builtins.PyCapsule
- load_into_pose(self : rosetta.protocols.features.FeaturesReporter, : rosetta.utility.sql_database.session, : int, : rosetta.core.pose.Pose) -> NoneType
- schema(...) from builtins.PyCapsule
- schema(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
- set_relevant_residues_mode(...) from builtins.PyCapsule
- set_relevant_residues_mode(self : rosetta.protocols.features.FeaturesReporter, setting : rosetta.protocols.features.RelevantResiduesMode.T) -> NoneType
|
class ScreeningFeatures(FeaturesReporter) |
| | |
- Method resolution order:
- ScreeningFeatures
- FeaturesReporter
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.protocols.features.ScreeningFeatures) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.features.ScreeningFeatures, : rosetta.protocols.features.ScreeningFeatures) -> rosetta.protocols.features.ScreeningFeatures
- features_reporter_dependencies(...) from builtins.PyCapsule
- features_reporter_dependencies(rosetta.protocols.features.ScreeningFeatures) -> rosetta.utility.vector1_std_string
- report_features(...) from builtins.PyCapsule
- report_features(self : rosetta.protocols.features.ScreeningFeatures, pose : rosetta.core.pose.Pose, : rosetta.utility.vector1_bool, struct_id : int, db_session : rosetta.utility.sql_database.session) -> int
- type_name(...) from builtins.PyCapsule
- type_name(rosetta.protocols.features.ScreeningFeatures) -> str
- write_schema_to_db(...) from builtins.PyCapsule
- write_schema_to_db(self : rosetta.protocols.features.ScreeningFeatures, db_session : rosetta.utility.sql_database.session) -> NoneType
Methods inherited from FeaturesReporter:
- check_relevant_residues(...) from builtins.PyCapsule
- check_relevant_residues(*args, **kwargs)
Overloaded function.
1. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int) -> bool
2. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool
3. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, residues : rosetta.utility.vector1_unsigned_long) -> bool
- check_relevant_residues_range(...) from builtins.PyCapsule
- check_relevant_residues_range(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool
- delete_record(...) from builtins.PyCapsule
- delete_record(self : rosetta.protocols.features.FeaturesReporter, : int, : rosetta.utility.sql_database.session) -> NoneType
- get_relevant_residues_mode(...) from builtins.PyCapsule
- get_relevant_residues_mode(rosetta.protocols.features.FeaturesReporter) -> rosetta.protocols.features.RelevantResiduesMode.T
- load_into_pose(...) from builtins.PyCapsule
- load_into_pose(self : rosetta.protocols.features.FeaturesReporter, : rosetta.utility.sql_database.session, : int, : rosetta.core.pose.Pose) -> NoneType
- schema(...) from builtins.PyCapsule
- schema(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
- set_relevant_residues_mode(...) from builtins.PyCapsule
- set_relevant_residues_mode(self : rosetta.protocols.features.FeaturesReporter, setting : rosetta.protocols.features.RelevantResiduesMode.T) -> NoneType
|
class SecondaryStructureSegmentFeatures(FeaturesReporter) |
| | |
- Method resolution order:
- SecondaryStructureSegmentFeatures
- FeaturesReporter
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(self : handle, scfxn : rosetta.core.scoring.ScoreFunction) -> NoneType
3. __init__(handle, rosetta.protocols.features.SecondaryStructureSegmentFeatures) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.features.SecondaryStructureSegmentFeatures, : rosetta.protocols.features.SecondaryStructureSegmentFeatures) -> rosetta.protocols.features.SecondaryStructureSegmentFeatures
- features_reporter_dependencies(...) from builtins.PyCapsule
- features_reporter_dependencies(rosetta.protocols.features.SecondaryStructureSegmentFeatures) -> 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.
- is_helix(...) from builtins.PyCapsule
- is_helix(self : rosetta.protocols.features.SecondaryStructureSegmentFeatures, dssp_code : str) -> bool
- is_loop(...) from builtins.PyCapsule
- is_loop(self : rosetta.protocols.features.SecondaryStructureSegmentFeatures, dssp_code : str) -> bool
- report_features(...) from builtins.PyCapsule
- report_features(self : rosetta.protocols.features.SecondaryStructureSegmentFeatures, pose : rosetta.core.pose.Pose, relevant_residues : rosetta.utility.vector1_bool, struct_id : int, db_session : rosetta.utility.sql_database.session) -> int
collect all the feature data for the pose
- type_name(...) from builtins.PyCapsule
- type_name(rosetta.protocols.features.SecondaryStructureSegmentFeatures) -> str
return string with class name
- write_schema_to_db(...) from builtins.PyCapsule
- write_schema_to_db(self : rosetta.protocols.features.SecondaryStructureSegmentFeatures, db_session : rosetta.utility.sql_database.session) -> NoneType
generate the table schemas and write them to the database
Methods inherited from FeaturesReporter:
- check_relevant_residues(...) from builtins.PyCapsule
- check_relevant_residues(*args, **kwargs)
Overloaded function.
1. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int) -> bool
2. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool
3. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, residues : rosetta.utility.vector1_unsigned_long) -> bool
- check_relevant_residues_range(...) from builtins.PyCapsule
- check_relevant_residues_range(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool
- delete_record(...) from builtins.PyCapsule
- delete_record(self : rosetta.protocols.features.FeaturesReporter, : int, : rosetta.utility.sql_database.session) -> NoneType
- get_relevant_residues_mode(...) from builtins.PyCapsule
- get_relevant_residues_mode(rosetta.protocols.features.FeaturesReporter) -> rosetta.protocols.features.RelevantResiduesMode.T
- load_into_pose(...) from builtins.PyCapsule
- load_into_pose(self : rosetta.protocols.features.FeaturesReporter, : rosetta.utility.sql_database.session, : int, : rosetta.core.pose.Pose) -> NoneType
- schema(...) from builtins.PyCapsule
- schema(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
- set_relevant_residues_mode(...) from builtins.PyCapsule
- set_relevant_residues_mode(self : rosetta.protocols.features.FeaturesReporter, setting : rosetta.protocols.features.RelevantResiduesMode.T) -> NoneType
|
class SmotifFeatures(FeaturesReporter) |
| | |
- Method resolution order:
- SmotifFeatures
- FeaturesReporter
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(self : handle, scfxn : rosetta.core.scoring.ScoreFunction) -> NoneType
3. __init__(handle, rosetta.protocols.features.SmotifFeatures) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.features.SmotifFeatures, : rosetta.protocols.features.SmotifFeatures) -> rosetta.protocols.features.SmotifFeatures
- calculate_angles(...) from builtins.PyCapsule
- calculate_angles(self : rosetta.protocols.features.SmotifFeatures, ss1_coords : rosetta.utility.vector1_numeric_xyzVector_double_t, ss2_coords : rosetta.utility.vector1_numeric_xyzVector_double_t, distance : float, hoist_angle_degrees : float, packing_angle_degrees : float, meridian_angle_degrees : float) -> NoneType
- features_reporter_dependencies(...) from builtins.PyCapsule
- features_reporter_dependencies(rosetta.protocols.features.SmotifFeatures) -> 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.
- report_features(...) from builtins.PyCapsule
- report_features(self : rosetta.protocols.features.SmotifFeatures, pose : rosetta.core.pose.Pose, relevant_residues : rosetta.utility.vector1_bool, struct_id : int, db_session : rosetta.utility.sql_database.session) -> int
collect all the feature data for the pose
- type_name(...) from builtins.PyCapsule
- type_name(rosetta.protocols.features.SmotifFeatures) -> str
return string with class name
- write_schema_to_db(...) from builtins.PyCapsule
- write_schema_to_db(self : rosetta.protocols.features.SmotifFeatures, db_session : rosetta.utility.sql_database.session) -> NoneType
generate the table schemas and write them to the database
Methods inherited from FeaturesReporter:
- check_relevant_residues(...) from builtins.PyCapsule
- check_relevant_residues(*args, **kwargs)
Overloaded function.
1. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int) -> bool
2. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool
3. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, residues : rosetta.utility.vector1_unsigned_long) -> bool
- check_relevant_residues_range(...) from builtins.PyCapsule
- check_relevant_residues_range(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool
- delete_record(...) from builtins.PyCapsule
- delete_record(self : rosetta.protocols.features.FeaturesReporter, : int, : rosetta.utility.sql_database.session) -> NoneType
- get_relevant_residues_mode(...) from builtins.PyCapsule
- get_relevant_residues_mode(rosetta.protocols.features.FeaturesReporter) -> rosetta.protocols.features.RelevantResiduesMode.T
- load_into_pose(...) from builtins.PyCapsule
- load_into_pose(self : rosetta.protocols.features.FeaturesReporter, : rosetta.utility.sql_database.session, : int, : rosetta.core.pose.Pose) -> NoneType
- schema(...) from builtins.PyCapsule
- schema(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
- set_relevant_residues_mode(...) from builtins.PyCapsule
- set_relevant_residues_mode(self : rosetta.protocols.features.FeaturesReporter, setting : rosetta.protocols.features.RelevantResiduesMode.T) -> NoneType
|
class StructureFeatures(FeaturesReporter) |
| | |
- Method resolution order:
- StructureFeatures
- FeaturesReporter
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.protocols.features.StructureFeatures) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.features.StructureFeatures, : rosetta.protocols.features.StructureFeatures) -> rosetta.protocols.features.StructureFeatures
- delete_record(...) from builtins.PyCapsule
- delete_record(self : rosetta.protocols.features.StructureFeatures, struct_id : int, db_session : rosetta.utility.sql_database.session) -> NoneType
- features_reporter_dependencies(...) from builtins.PyCapsule
- features_reporter_dependencies(rosetta.protocols.features.StructureFeatures) -> 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.
- get_struct_id(...) from builtins.PyCapsule
- get_struct_id(self : rosetta.protocols.features.StructureFeatures, db_session : rosetta.utility.sql_database.session, tag : str, protocol_id : int) -> int
- load_into_pose(...) from builtins.PyCapsule
- load_into_pose(self : rosetta.protocols.features.StructureFeatures, db_session : rosetta.utility.sql_database.session, struct_id : int, pose : rosetta.core.pose.Pose) -> NoneType
- load_tag(...) from builtins.PyCapsule
- load_tag(self : rosetta.protocols.features.StructureFeatures, db_session : rosetta.utility.sql_database.session, struct_id : int, pose : rosetta.core.pose.Pose) -> NoneType
- mark_structure_as_sampled(...) from builtins.PyCapsule
- mark_structure_as_sampled(self : rosetta.protocols.features.StructureFeatures, batch_id : int, tag : str, input_tag : str, db_session : rosetta.utility.sql_database.session) -> NoneType
- report_features(...) from builtins.PyCapsule
- report_features(*args, **kwargs)
Overloaded function.
1. report_features(self : rosetta.protocols.features.StructureFeatures, : rosetta.core.pose.Pose, : rosetta.utility.vector1_bool, : int, : rosetta.utility.sql_database.session) -> int
collect all the feature data for the pose
2. report_features(self : rosetta.protocols.features.StructureFeatures, batch_id : int, db_session : rosetta.utility.sql_database.session, tag : str, input_tag : str) -> int
collect all the feature data for the pose use
This version allows the tag and the input tag to be specificed
- type_name(...) from builtins.PyCapsule
- type_name(rosetta.protocols.features.StructureFeatures) -> str
return string with class name
- write_schema_to_db(...) from builtins.PyCapsule
- write_schema_to_db(self : rosetta.protocols.features.StructureFeatures, db_session : rosetta.utility.sql_database.session) -> NoneType
generate the table schemas and write them to the database
Methods inherited from FeaturesReporter:
- check_relevant_residues(...) from builtins.PyCapsule
- check_relevant_residues(*args, **kwargs)
Overloaded function.
1. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int) -> bool
2. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool
3. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, residues : rosetta.utility.vector1_unsigned_long) -> bool
- check_relevant_residues_range(...) from builtins.PyCapsule
- check_relevant_residues_range(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool
- get_relevant_residues_mode(...) from builtins.PyCapsule
- get_relevant_residues_mode(rosetta.protocols.features.FeaturesReporter) -> rosetta.protocols.features.RelevantResiduesMode.T
- schema(...) from builtins.PyCapsule
- schema(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
- set_relevant_residues_mode(...) from builtins.PyCapsule
- set_relevant_residues_mode(self : rosetta.protocols.features.FeaturesReporter, setting : rosetta.protocols.features.RelevantResiduesMode.T) -> NoneType
|
class StructureScoresFeatures(FeaturesReporter) |
| | |
- Method resolution order:
- StructureScoresFeatures
- FeaturesReporter
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(self : handle, scfxn : rosetta.core.scoring.ScoreFunction) -> NoneType
3. __init__(handle, rosetta.protocols.features.StructureScoresFeatures) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.features.StructureScoresFeatures, : rosetta.protocols.features.StructureScoresFeatures) -> rosetta.protocols.features.StructureScoresFeatures
- compute_energies(...) from builtins.PyCapsule
- compute_energies(self : rosetta.protocols.features.StructureScoresFeatures, pose_in : rosetta.core.pose.Pose, relevant_residues : rosetta.utility.vector1_bool, emap : rosetta.core.scoring.EMapVector) -> NoneType
- delete_record(...) from builtins.PyCapsule
- delete_record(self : rosetta.protocols.features.StructureScoresFeatures, struct_id : int, db_session : rosetta.utility.sql_database.session) -> NoneType
- features_reporter_dependencies(...) from builtins.PyCapsule
- features_reporter_dependencies(rosetta.protocols.features.StructureScoresFeatures) -> 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.
- insert_structure_score_rows(...) from builtins.PyCapsule
- insert_structure_score_rows(self : rosetta.protocols.features.StructureScoresFeatures, pose : rosetta.core.pose.Pose, relevant_residues : rosetta.utility.vector1_bool, struct_id : int, db_session : rosetta.utility.sql_database.session) -> NoneType
- report_features(...) from builtins.PyCapsule
- report_features(self : rosetta.protocols.features.StructureScoresFeatures, pose : rosetta.core.pose.Pose, relevant_residues : rosetta.utility.vector1_bool, struct_id : int, db_session : rosetta.utility.sql_database.session) -> int
collect all the feature data for the pose
- type_name(...) from builtins.PyCapsule
- type_name(rosetta.protocols.features.StructureScoresFeatures) -> str
return string with class name
- write_schema_to_db(...) from builtins.PyCapsule
- write_schema_to_db(self : rosetta.protocols.features.StructureScoresFeatures, db_session : rosetta.utility.sql_database.session) -> NoneType
generate the table schemas and write them to the database
Methods inherited from FeaturesReporter:
- check_relevant_residues(...) from builtins.PyCapsule
- check_relevant_residues(*args, **kwargs)
Overloaded function.
1. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int) -> bool
2. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool
3. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, residues : rosetta.utility.vector1_unsigned_long) -> bool
- check_relevant_residues_range(...) from builtins.PyCapsule
- check_relevant_residues_range(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool
- get_relevant_residues_mode(...) from builtins.PyCapsule
- get_relevant_residues_mode(rosetta.protocols.features.FeaturesReporter) -> rosetta.protocols.features.RelevantResiduesMode.T
- load_into_pose(...) from builtins.PyCapsule
- load_into_pose(self : rosetta.protocols.features.FeaturesReporter, : rosetta.utility.sql_database.session, : int, : rosetta.core.pose.Pose) -> NoneType
- schema(...) from builtins.PyCapsule
- schema(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
- set_relevant_residues_mode(...) from builtins.PyCapsule
- set_relevant_residues_mode(self : rosetta.protocols.features.FeaturesReporter, setting : rosetta.protocols.features.RelevantResiduesMode.T) -> NoneType
|
class TaskOperationFeatures(FeaturesReporter) |
| | |
- Method resolution order:
- TaskOperationFeatures
- FeaturesReporter
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.protocols.features.TaskOperationFeatures) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.features.TaskOperationFeatures, : rosetta.protocols.features.TaskOperationFeatures) -> rosetta.protocols.features.TaskOperationFeatures
- features_reporter_dependencies(...) from builtins.PyCapsule
- features_reporter_dependencies(rosetta.protocols.features.TaskOperationFeatures) -> rosetta.utility.vector1_std_string
- insert_task_operation_residue_effects_row(...) from builtins.PyCapsule
- insert_task_operation_residue_effects_row(self : rosetta.protocols.features.TaskOperationFeatures, struct_id : int, resNum : int, taskop_id : int, pack : bool, design : bool, db_session : rosetta.utility.sql_database.session) -> NoneType
- insert_task_operations_row(...) from builtins.PyCapsule
- insert_task_operations_row(self : rosetta.protocols.features.TaskOperationFeatures, taskop_id : int, taskop_name : str, db_session : rosetta.utility.sql_database.session) -> NoneType
- report_features(...) from builtins.PyCapsule
- report_features(self : rosetta.protocols.features.TaskOperationFeatures, pose : rosetta.core.pose.Pose, relevant_residues : rosetta.utility.vector1_bool, struct_id : int, db_session : rosetta.utility.sql_database.session) -> int
collect all the feature data for the pose
- type_name(...) from builtins.PyCapsule
- type_name(rosetta.protocols.features.TaskOperationFeatures) -> str
return string with class name
- write_schema_to_db(...) from builtins.PyCapsule
- write_schema_to_db(self : rosetta.protocols.features.TaskOperationFeatures, db_session : rosetta.utility.sql_database.session) -> NoneType
generate the table schemas and write them to the database
Methods inherited from FeaturesReporter:
- check_relevant_residues(...) from builtins.PyCapsule
- check_relevant_residues(*args, **kwargs)
Overloaded function.
1. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int) -> bool
2. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool
3. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, residues : rosetta.utility.vector1_unsigned_long) -> bool
- check_relevant_residues_range(...) from builtins.PyCapsule
- check_relevant_residues_range(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool
- delete_record(...) from builtins.PyCapsule
- delete_record(self : rosetta.protocols.features.FeaturesReporter, : int, : rosetta.utility.sql_database.session) -> NoneType
- get_relevant_residues_mode(...) from builtins.PyCapsule
- get_relevant_residues_mode(rosetta.protocols.features.FeaturesReporter) -> rosetta.protocols.features.RelevantResiduesMode.T
- load_into_pose(...) from builtins.PyCapsule
- load_into_pose(self : rosetta.protocols.features.FeaturesReporter, : rosetta.utility.sql_database.session, : int, : rosetta.core.pose.Pose) -> NoneType
- schema(...) from builtins.PyCapsule
- schema(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
- set_relevant_residues_mode(...) from builtins.PyCapsule
- set_relevant_residues_mode(self : rosetta.protocols.features.FeaturesReporter, setting : rosetta.protocols.features.RelevantResiduesMode.T) -> NoneType
|
class TotalScoreFeatures(FeaturesReporter) |
| | |
- Method resolution order:
- TotalScoreFeatures
- FeaturesReporter
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(self : handle, scorefxn : rosetta.core.scoring.ScoreFunction) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.features.TotalScoreFeatures, : rosetta.protocols.features.TotalScoreFeatures) -> rosetta.protocols.features.TotalScoreFeatures
- report_features(...) from builtins.PyCapsule
- report_features(self : rosetta.protocols.features.TotalScoreFeatures, pose : rosetta.core.pose.Pose, relevant_residues : rosetta.utility.vector1_bool, struct_id : int, db_session : rosetta.utility.sql_database.session) -> int
FeaturesReporter::report_features
- scorefxn(...) from builtins.PyCapsule
- scorefxn(*args, **kwargs)
Overloaded function.
1. scorefxn(rosetta.protocols.features.TotalScoreFeatures) -> rosetta.core.scoring.ScoreFunction
Get the score function being reported by this object.
2. scorefxn(self : rosetta.protocols.features.TotalScoreFeatures, scorefxn : rosetta.core.scoring.ScoreFunction) -> NoneType
Set the score function being reported by this object.
- type_name(...) from builtins.PyCapsule
- type_name(rosetta.protocols.features.TotalScoreFeatures) -> str
FeaturesReporter::type_name
- write_schema_to_db(...) from builtins.PyCapsule
- write_schema_to_db(self : rosetta.protocols.features.TotalScoreFeatures, db_session : rosetta.utility.sql_database.session) -> NoneType
FeaturesReporter::write_schema_to_db
Methods inherited from FeaturesReporter:
- check_relevant_residues(...) from builtins.PyCapsule
- check_relevant_residues(*args, **kwargs)
Overloaded function.
1. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int) -> bool
2. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool
3. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, residues : rosetta.utility.vector1_unsigned_long) -> bool
- check_relevant_residues_range(...) from builtins.PyCapsule
- check_relevant_residues_range(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool
- delete_record(...) from builtins.PyCapsule
- delete_record(self : rosetta.protocols.features.FeaturesReporter, : int, : rosetta.utility.sql_database.session) -> NoneType
- features_reporter_dependencies(...) from builtins.PyCapsule
- features_reporter_dependencies(rosetta.protocols.features.FeaturesReporter) -> 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.
- get_relevant_residues_mode(...) from builtins.PyCapsule
- get_relevant_residues_mode(rosetta.protocols.features.FeaturesReporter) -> rosetta.protocols.features.RelevantResiduesMode.T
- load_into_pose(...) from builtins.PyCapsule
- load_into_pose(self : rosetta.protocols.features.FeaturesReporter, : rosetta.utility.sql_database.session, : int, : rosetta.core.pose.Pose) -> NoneType
- schema(...) from builtins.PyCapsule
- schema(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
- set_relevant_residues_mode(...) from builtins.PyCapsule
- set_relevant_residues_mode(self : rosetta.protocols.features.FeaturesReporter, setting : rosetta.protocols.features.RelevantResiduesMode.T) -> NoneType
|
class TrajectoryMapFeatures(FeaturesReporter) |
| | |
- Method resolution order:
- TrajectoryMapFeatures
- FeaturesReporter
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.protocols.features.TrajectoryMapFeatures) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.features.TrajectoryMapFeatures, : rosetta.protocols.features.TrajectoryMapFeatures) -> rosetta.protocols.features.TrajectoryMapFeatures
- delete_record(...) from builtins.PyCapsule
- delete_record(self : rosetta.protocols.features.TrajectoryMapFeatures, struct_id : int, db_sesion : rosetta.utility.sql_database.session) -> NoneType
- features_reporter_dependencies(...) from builtins.PyCapsule
- features_reporter_dependencies(rosetta.protocols.features.TrajectoryMapFeatures) -> 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.
- get_current_cycle(...) from builtins.PyCapsule
- get_current_cycle(rosetta.protocols.features.TrajectoryMapFeatures) -> int
- report_features(...) from builtins.PyCapsule
- report_features(self : rosetta.protocols.features.TrajectoryMapFeatures, pose : rosetta.core.pose.Pose, relevant_residues : rosetta.utility.vector1_bool, struct_id : int, db_session : rosetta.utility.sql_database.session) -> int
collect all the feature data for the pose
- set_current_cycle(...) from builtins.PyCapsule
- set_current_cycle(self : rosetta.protocols.features.TrajectoryMapFeatures, stride : int) -> NoneType
- type_name(...) from builtins.PyCapsule
- type_name(rosetta.protocols.features.TrajectoryMapFeatures) -> str
return string with class name
- write_schema_to_db(...) from builtins.PyCapsule
- write_schema_to_db(self : rosetta.protocols.features.TrajectoryMapFeatures, db_session : rosetta.utility.sql_database.session) -> NoneType
generate the table schemas and write them to the database
Methods inherited from FeaturesReporter:
- check_relevant_residues(...) from builtins.PyCapsule
- check_relevant_residues(*args, **kwargs)
Overloaded function.
1. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int) -> bool
2. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool
3. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, residues : rosetta.utility.vector1_unsigned_long) -> bool
- check_relevant_residues_range(...) from builtins.PyCapsule
- check_relevant_residues_range(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool
- get_relevant_residues_mode(...) from builtins.PyCapsule
- get_relevant_residues_mode(rosetta.protocols.features.FeaturesReporter) -> rosetta.protocols.features.RelevantResiduesMode.T
- load_into_pose(...) from builtins.PyCapsule
- load_into_pose(self : rosetta.protocols.features.FeaturesReporter, : rosetta.utility.sql_database.session, : int, : rosetta.core.pose.Pose) -> NoneType
- schema(...) from builtins.PyCapsule
- schema(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
- set_relevant_residues_mode(...) from builtins.PyCapsule
- set_relevant_residues_mode(self : rosetta.protocols.features.FeaturesReporter, setting : rosetta.protocols.features.RelevantResiduesMode.T) -> NoneType
|
class TrajectoryReportToDB(ReportToDB) |
| | |
- Method resolution order:
- TrajectoryReportToDB
- ReportToDB
- rosetta.protocols.moves.Mover
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(self : handle, stride : int) -> NoneType
3. __init__(self : handle, name : str) -> NoneType
4. __init__(handle, rosetta.utility.sql_database.session, str, str) -> NoneType
doc
5. __init__(handle, rosetta.utility.sql_database.session, str, str, bool) -> NoneType
doc
6. __init__(self : handle, db_session : rosetta.utility.sql_database.session, batch_name : str, batch_description : str, use_transactions : bool, cache_size : int) -> NoneType
7. __init__(handle, rosetta.protocols.features.TrajectoryReportToDB) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- apply(...) from builtins.PyCapsule
- apply(self : rosetta.protocols.features.TrajectoryReportToDB, pose : rosetta.core.pose.Pose) -> NoneType
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.features.TrajectoryReportToDB, : rosetta.protocols.features.TrajectoryReportToDB) -> rosetta.protocols.features.TrajectoryReportToDB
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.features.TrajectoryReportToDB) -> rosetta.protocols.moves.Mover
- fresh_instance(...) from builtins.PyCapsule
- fresh_instance(rosetta.protocols.features.TrajectoryReportToDB) -> rosetta.protocols.moves.Mover
- get_cycle_counts(...) from builtins.PyCapsule
- get_cycle_counts(rosetta.protocols.features.TrajectoryReportToDB) -> rosetta.std.map_std_string_unsigned_long
Probably only needed for unit testing
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.features.TrajectoryReportToDB) -> str
- get_stride(...) from builtins.PyCapsule
- get_stride(rosetta.protocols.features.TrajectoryReportToDB) -> int
- name(...) from builtins.PyCapsule
- name(rosetta.protocols.features.TrajectoryReportToDB) -> str
- parse_stride_tag_item(...) from builtins.PyCapsule
- parse_stride_tag_item(self : rosetta.protocols.features.TrajectoryReportToDB, tag : rosetta.utility.tag.Tag) -> NoneType
- set_stride(...) from builtins.PyCapsule
- set_stride(self : rosetta.protocols.features.TrajectoryReportToDB, stride : int) -> NoneType
Methods inherited from ReportToDB:
- add_features_reporter(...) from builtins.PyCapsule
- add_features_reporter(self : rosetta.protocols.features.ReportToDB, features_reporter : rosetta.protocols.features.FeaturesReporter) -> NoneType
- check_features_reporter_dependencies(...) from builtins.PyCapsule
- check_features_reporter_dependencies(self : rosetta.protocols.features.ReportToDB, test_feature_reporter : rosetta.protocols.features.FeaturesReporter) -> NoneType
- get_batch_description(...) from builtins.PyCapsule
- get_batch_description(rosetta.protocols.features.ReportToDB) -> str
- get_batch_name(...) from builtins.PyCapsule
- get_batch_name(rosetta.protocols.features.ReportToDB) -> str
- get_last_struct_id(...) from builtins.PyCapsule
- get_last_struct_id(rosetta.protocols.features.ReportToDB) -> int
- get_relevant_residues(...) from builtins.PyCapsule
- get_relevant_residues(rosetta.protocols.features.ReportToDB) -> rosetta.utility.vector1_bool
- get_relevant_residues_mode(...) from builtins.PyCapsule
- get_relevant_residues_mode(rosetta.protocols.features.ReportToDB) -> rosetta.protocols.features.RelevantResiduesMode.T
- get_relevant_residues_task_factory(...) from builtins.PyCapsule
- get_relevant_residues_task_factory(rosetta.protocols.features.ReportToDB) -> rosetta.core.pack.task.TaskFactory
- get_structure_input_tag(...) from builtins.PyCapsule
- get_structure_input_tag(rosetta.protocols.features.ReportToDB) -> str
- get_structure_tag(...) from builtins.PyCapsule
- get_structure_tag(rosetta.protocols.features.ReportToDB) -> str
- initialize_database(...) from builtins.PyCapsule
- initialize_database(rosetta.protocols.features.ReportToDB) -> NoneType
- initialize_pose(...) from builtins.PyCapsule
- initialize_pose(self : rosetta.protocols.features.ReportToDB, pose : rosetta.core.pose.Pose) -> NoneType
initialize the pose and set the relevant residues
- initialize_relevant_residues(...) from builtins.PyCapsule
- initialize_relevant_residues(self : rosetta.protocols.features.ReportToDB, pose : rosetta.core.pose.Pose) -> rosetta.utility.vector1_bool
initialize the relevant residues of the pose and store save for later.
- initialize_reporters(...) from builtins.PyCapsule
- initialize_reporters(rosetta.protocols.features.ReportToDB) -> NoneType
- parse_batch_description_tag_item(...) from builtins.PyCapsule
- parse_batch_description_tag_item(self : rosetta.protocols.features.ReportToDB, tag : rosetta.utility.tag.Tag) -> NoneType
- parse_batch_id_tag_item(...) from builtins.PyCapsule
- parse_batch_id_tag_item(self : rosetta.protocols.features.ReportToDB, tag : rosetta.utility.tag.Tag) -> NoneType
- parse_batch_name_tag_item(...) from builtins.PyCapsule
- parse_batch_name_tag_item(self : rosetta.protocols.features.ReportToDB, tag : rosetta.utility.tag.Tag) -> NoneType
- parse_cache_size_tag_item(...) from builtins.PyCapsule
- parse_cache_size_tag_item(self : rosetta.protocols.features.ReportToDB, tag : rosetta.utility.tag.Tag) -> NoneType
- parse_protocol_id_tag_item(...) from builtins.PyCapsule
- parse_protocol_id_tag_item(self : rosetta.protocols.features.ReportToDB, tag : rosetta.utility.tag.Tag) -> NoneType
- parse_relevant_residues_mode_tag_item(...) from builtins.PyCapsule
- parse_relevant_residues_mode_tag_item(self : rosetta.protocols.features.ReportToDB, tag : rosetta.utility.tag.Tag) -> NoneType
- parse_remove_xray_virt_tag_item(...) from builtins.PyCapsule
- parse_remove_xray_virt_tag_item(self : rosetta.protocols.features.ReportToDB, tag : rosetta.utility.tag.Tag) -> NoneType
- parse_use_transactions_tag_item(...) from builtins.PyCapsule
- parse_use_transactions_tag_item(self : rosetta.protocols.features.ReportToDB, tag : rosetta.utility.tag.Tag) -> NoneType
- register_options(...) from builtins.PyCapsule
- register_options(rosetta.protocols.features.ReportToDB) -> NoneType
- report_features(...) from builtins.PyCapsule
- report_features(self : rosetta.protocols.features.ReportToDB, pose : rosetta.core.pose.Pose, struct_id : int, relevant_residues : rosetta.utility.vector1_bool) -> NoneType
- report_structure_features(...) from builtins.PyCapsule
- report_structure_features(rosetta.protocols.features.ReportToDB) -> int
- set_batch_description(...) from builtins.PyCapsule
- set_batch_description(self : rosetta.protocols.features.ReportToDB, batch_description : str) -> NoneType
- set_batch_name(...) from builtins.PyCapsule
- set_batch_name(self : rosetta.protocols.features.ReportToDB, batch_name : str) -> NoneType
- set_relevant_residues(...) from builtins.PyCapsule
- set_relevant_residues(self : rosetta.protocols.features.ReportToDB, relevant_residues : rosetta.utility.vector1_bool) -> NoneType
- set_relevant_residues_mode(...) from builtins.PyCapsule
- set_relevant_residues_mode(self : rosetta.protocols.features.ReportToDB, setting : rosetta.protocols.features.RelevantResiduesMode.T) -> NoneType
- set_relevant_residues_task_factory(...) from builtins.PyCapsule
- set_relevant_residues_task_factory(self : rosetta.protocols.features.ReportToDB, task_factory : rosetta.core.pack.task.TaskFactory) -> NoneType
- set_structure_input_tag(...) from builtins.PyCapsule
- set_structure_input_tag(self : rosetta.protocols.features.ReportToDB, setting : str) -> NoneType
- set_structure_tag(...) from builtins.PyCapsule
- set_structure_tag(self : rosetta.protocols.features.ReportToDB, setting : str) -> NoneType
Methods inherited from rosetta.protocols.moves.Mover:
- clear_info(...) from builtins.PyCapsule
- clear_info(rosetta.protocols.moves.Mover) -> NoneType
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
- create(...) from builtins.PyCapsule
- create(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
- get_additional_output(...) from builtins.PyCapsule
- get_additional_output(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
fpd
Mechanism by which a mover may return multiple output poses from a single input pose.
- get_current_job(...) from builtins.PyCapsule
- get_current_job(rosetta.protocols.moves.Mover) -> protocols::jobdist::BasicJob
- get_current_tag(...) from builtins.PyCapsule
- get_current_tag(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.
- get_input_pose(...) from builtins.PyCapsule
- get_input_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
- get_last_move_status(...) from builtins.PyCapsule
- get_last_move_status(rosetta.protocols.moves.Mover) -> 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.
- get_native_pose(...) from builtins.PyCapsule
- get_native_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
- get_self_ptr(...) from builtins.PyCapsule
- get_self_ptr(*args, **kwargs)
Overloaded function.
1. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
2. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
- get_self_weak_ptr(...) from builtins.PyCapsule
- get_self_weak_ptr(*args, **kwargs)
Overloaded function.
1. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_const_protocols_moves_Mover_t
2. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_protocols_moves_Mover_t
- get_type(...) from builtins.PyCapsule
- get_type(rosetta.protocols.moves.Mover) -> str
- info(...) from builtins.PyCapsule
- info(*args, **kwargs)
Overloaded function.
1. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t
non-const accessor
2. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t
const accessor
- last_proposal_density_ratio(...) from builtins.PyCapsule
- last_proposal_density_ratio(rosetta.protocols.moves.Mover) -> float
- reinitialize_for_each_job(...) from builtins.PyCapsule
- reinitialize_for_each_job(rosetta.protocols.moves.Mover) -> bool
Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on
each use.
- reinitialize_for_new_input(...) from builtins.PyCapsule
- reinitialize_for_new_input(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).
- reset_status(...) from builtins.PyCapsule
- reset_status(rosetta.protocols.moves.Mover) -> NoneType
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.
- set_current_job(...) from builtins.PyCapsule
- set_current_job(self : rosetta.protocols.moves.Mover, job : protocols::jobdist::BasicJob) -> NoneType
////////////////////////////end Job Distributor interface////////////////////////////////////////
- set_current_tag(...) from builtins.PyCapsule
- set_current_tag(self : rosetta.protocols.moves.Mover, new_tag : str) -> NoneType
- set_input_pose(...) from builtins.PyCapsule
- set_input_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
setter for poses contained for rms
- set_native_pose(...) from builtins.PyCapsule
- set_native_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
setter for native poses contained for rms ---- we should get rid of this method? it is widely used, but a bit unsafe
- set_type(...) from builtins.PyCapsule
- set_type(self : rosetta.protocols.moves.Mover, setting : str) -> NoneType
- test_move(...) from builtins.PyCapsule
- test_move(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
: Unit test support function. Apply one move to a given pose.
Allows extra test specific functions to be called before applying
- type(...) from builtins.PyCapsule
- type(*args, **kwargs)
Overloaded function.
1. type(rosetta.protocols.moves.Mover) -> str
2. type(self : rosetta.protocols.moves.Mover, type_in : str) -> NoneType
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class UnrecognizedAtomFeatures(FeaturesReporter) |
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- Method resolution order:
- UnrecognizedAtomFeatures
- FeaturesReporter
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(self : handle, neighbor_distance_cutoff : float) -> NoneType
3. __init__(handle, rosetta.protocols.features.UnrecognizedAtomFeatures) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.features.UnrecognizedAtomFeatures, : rosetta.protocols.features.UnrecognizedAtomFeatures) -> rosetta.protocols.features.UnrecognizedAtomFeatures
- delete_record(...) from builtins.PyCapsule
- delete_record(self : rosetta.protocols.features.UnrecognizedAtomFeatures, struct_id : int, db_sesion : rosetta.utility.sql_database.session) -> NoneType
- features_reporter_dependencies(...) from builtins.PyCapsule
- features_reporter_dependencies(rosetta.protocols.features.UnrecognizedAtomFeatures) -> 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.
- report_features(...) from builtins.PyCapsule
- report_features(self : rosetta.protocols.features.UnrecognizedAtomFeatures, pose : rosetta.core.pose.Pose, relevant_residues : rosetta.utility.vector1_bool, struct_id : int, db_session : rosetta.utility.sql_database.session) -> int
collect all the feature data for the pose
- type_name(...) from builtins.PyCapsule
- type_name(rosetta.protocols.features.UnrecognizedAtomFeatures) -> str
return string with class name
- write_schema_to_db(...) from builtins.PyCapsule
- write_schema_to_db(self : rosetta.protocols.features.UnrecognizedAtomFeatures, db_session : rosetta.utility.sql_database.session) -> NoneType
generate the table schemas and write them to the database
Methods inherited from FeaturesReporter:
- check_relevant_residues(...) from builtins.PyCapsule
- check_relevant_residues(*args, **kwargs)
Overloaded function.
1. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int) -> bool
2. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool
3. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, residues : rosetta.utility.vector1_unsigned_long) -> bool
- check_relevant_residues_range(...) from builtins.PyCapsule
- check_relevant_residues_range(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool
- get_relevant_residues_mode(...) from builtins.PyCapsule
- get_relevant_residues_mode(rosetta.protocols.features.FeaturesReporter) -> rosetta.protocols.features.RelevantResiduesMode.T
- load_into_pose(...) from builtins.PyCapsule
- load_into_pose(self : rosetta.protocols.features.FeaturesReporter, : rosetta.utility.sql_database.session, : int, : rosetta.core.pose.Pose) -> NoneType
- schema(...) from builtins.PyCapsule
- schema(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
- set_relevant_residues_mode(...) from builtins.PyCapsule
- set_relevant_residues_mode(self : rosetta.protocols.features.FeaturesReporter, setting : rosetta.protocols.features.RelevantResiduesMode.T) -> NoneType
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class WaterFeatures(FeaturesReporter) |
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- Method resolution order:
- WaterFeatures
- FeaturesReporter
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(self : handle, acc_dist_cutoff : float, don_dist_cutoff : float) -> NoneType
3. __init__(handle, rosetta.protocols.features.WaterFeatures) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- acc_dist_cutoff(...) from builtins.PyCapsule
- acc_dist_cutoff(*args, **kwargs)
Overloaded function.
1. acc_dist_cutoff(rosetta.protocols.features.WaterFeatures) -> float
2. acc_dist_cutoff(self : rosetta.protocols.features.WaterFeatures, d : float) -> NoneType
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.features.WaterFeatures, : rosetta.protocols.features.WaterFeatures) -> rosetta.protocols.features.WaterFeatures
- don_dist_cutoff(...) from builtins.PyCapsule
- don_dist_cutoff(*args, **kwargs)
Overloaded function.
1. don_dist_cutoff(rosetta.protocols.features.WaterFeatures) -> float
2. don_dist_cutoff(self : rosetta.protocols.features.WaterFeatures, d : float) -> NoneType
- features_reporter_dependencies(...) from builtins.PyCapsule
- features_reporter_dependencies(rosetta.protocols.features.WaterFeatures) -> 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.
- report_features(...) from builtins.PyCapsule
- report_features(self : rosetta.protocols.features.WaterFeatures, pose : rosetta.core.pose.Pose, : rosetta.utility.vector1_bool, struct_id : int, db_session : rosetta.utility.sql_database.session) -> int
collect all the feature data for the pose
- type_name(...) from builtins.PyCapsule
- type_name(rosetta.protocols.features.WaterFeatures) -> str
return string with class name
- write_schema_to_db(...) from builtins.PyCapsule
- write_schema_to_db(self : rosetta.protocols.features.WaterFeatures, db_session : rosetta.utility.sql_database.session) -> NoneType
generate the table schemas and write them to the database
Methods inherited from FeaturesReporter:
- check_relevant_residues(...) from builtins.PyCapsule
- check_relevant_residues(*args, **kwargs)
Overloaded function.
1. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int) -> bool
2. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool
3. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, residues : rosetta.utility.vector1_unsigned_long) -> bool
- check_relevant_residues_range(...) from builtins.PyCapsule
- check_relevant_residues_range(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool
- delete_record(...) from builtins.PyCapsule
- delete_record(self : rosetta.protocols.features.FeaturesReporter, : int, : rosetta.utility.sql_database.session) -> NoneType
- get_relevant_residues_mode(...) from builtins.PyCapsule
- get_relevant_residues_mode(rosetta.protocols.features.FeaturesReporter) -> rosetta.protocols.features.RelevantResiduesMode.T
- load_into_pose(...) from builtins.PyCapsule
- load_into_pose(self : rosetta.protocols.features.FeaturesReporter, : rosetta.utility.sql_database.session, : int, : rosetta.core.pose.Pose) -> NoneType
- schema(...) from builtins.PyCapsule
- schema(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
- set_relevant_residues_mode(...) from builtins.PyCapsule
- set_relevant_residues_mode(self : rosetta.protocols.features.FeaturesReporter, setting : rosetta.protocols.features.RelevantResiduesMode.T) -> NoneType
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class clique_saver(builtins.object) |
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Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(self : rosetta.protocols.features.clique_saver, cliques : rosetta.std.set_std_set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_std_less_std_set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_std_allocator_std_set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
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