Rosetta 3.4
Namespaces | Classes | Typedefs | Enumerations | Functions
protocols::features Namespace Reference

Namespaces

namespace  helixAssembly

Classes

class  AtomAtomPairFeatures
class  AtomAtomPairFeaturesCreator
 creator for the AtomAtomPairFeatures class More...
class  AtomInResidueAtomInResiduePairFeatures
class  AtomInResidueAtomInResiduePairFeaturesCreator
 creator for the AtomInResidueAtomInResiduePairFeatures class More...
class  AtomTypesFeatures
class  AtomTypesFeaturesCreator
 creator for the AtomTypesFeatures class More...
class  BetaTurnDetectionFeatures
class  BetaTurnDetectionFeaturesCreator
 creator for the BetaTurnDetectionFeatures class More...
class  DatabaseFilter
class  TopCountOfEachInput
class  TopCountOfAllInputs
class  TopPercentOfEachInput
class  TopPercentOfAllInputs
class  DatabaseJobInputter
class  DatabaseJobInputterCreator
class  DatabaseJobOutputter
class  DatabaseJobOutputterCreator
class  FeaturesReporterCreator
 The Creator class is responsible for creating a particular mover class. More...
class  FeaturesReporter
class  FeaturesReporterFactory
 Create Features Reporters. More...
class  FeaturesReporterRegistrator
 This templated class will register an instance of an FeaturesReporterCreator (class T) with the FeaturesReporterFactory. It will ensure that no FeaturesReporterCreator is registered twice, and, centralizes this registration logic so that thread safety issues can be handled in one place. More...
class  GeometricSolvationFeatures
class  GeometricSolvationFeaturesCreator
 creator for the GeometricSolvationFeatures class More...
class  HBondFeatures
class  HBondFeaturesCreator
 creator for the HBondFeatures class More...
class  HBondParameterFeatures
class  HBondParameterFeaturesCreator
 creator for the HBondParameterFeatures class More...
class  JobDataFeatures
class  JobDataFeaturesCreator
 creator for the JobDataFeatures class More...
class  LoopAnchorFeatures
class  LoopAnchorFeaturesCreator
 creator for the LoopAnchorFeatures class More...
class  OrbitalsFeatures
class  OrbitalsFeaturesCreator
 creator for the OrbitalsFeatures class More...
class  PairFeatures
class  PairFeaturesCreator
 creator for the PairFeatures class More...
class  PdbDataFeatures
class  PdbDataFeaturesCreator
 creator for the PdbDataFeatures class More...
class  PoseCommentsFeatures
class  PoseCommentsFeaturesCreator
 creator for the PoseCommentsFeatures class More...
class  PoseConformationFeatures
class  PoseConformationFeaturesCreator
 creator for the PoseConformationFeatures class More...
class  ProteinBackboneAtomAtomPairFeatures
class  ProteinBackboneAtomAtomPairFeaturesCreator
 creator for the ProteinBackboneAtomAtomPairFeatures class More...
class  ProteinBackboneTorsionAngleFeatures
class  ProteinBackboneTorsionAngleFeaturesCreator
 creator for the ProteinBackboneTorsionAngleFeatures class More...
class  ProteinResidueConformationFeatures
class  ProteinResidueConformationFeaturesCreator
 creator for the ProteinResidueConformationFeatures class More...
class  ProteinRMSDFeatures
class  ProteinRMSDFeaturesCreator
 creator for the ProteinRMSDFeatures class More...
class  ProteinSilentReport
class  ProtocolFeatures
class  ProtocolFeaturesCreator
 creator for the ProtocolFeatures class More...
class  RadiusOfGyrationFeatures
class  RadiusOfGyrationFeaturesCreator
 creator for the RadiusOfGyrationFeatures class More...
class  Report
class  ReportToDB
class  ReportToDBCreator
class  ResidueBurialFeatures
class  ResidueBurialFeaturesCreator
 creator for the ResidueBurialFeatures class More...
class  ResidueConformationFeatures
class  ResidueConformationFeaturesCreator
 creator for the ResidueConformationFeatures class More...
class  ResidueFeatures
class  ResidueFeaturesCreator
 creator for the ResidueFeatures class More...
class  ResidueScoresFeatures
class  ResidueScoresFeaturesCreator
 creator for the ResidueScoresFeatures class More...
class  ResidueSecondaryStructureFeatures
class  ResidueSecondaryStructureFeaturesCreator
 creator for the ResidueSecondaryStructureFeatures class More...
class  ResidueTypesFeatures
class  ResidueTypesFeaturesCreator
 creator for the ResidueTypesFeatures class More...
class  RotamerBoltzmannWeightFeatures
class  RotamerBoltzmannWeightFeaturesCreator
 creator for the RotamerBoltzmannWeightFeatures class More...
class  RotamerRecoveryFeatures
class  RotamerRecoveryFeaturesCreator
 creator for the RotamerRecoveryFeatures class More...
class  SaltBridgeFeatures
class  SaltBridgeFeaturesCreator
 creator for the SaltBridgeFeatures class More...
class  ScoreTypeFeatures
class  ScoreTypeFeaturesCreator
 creator for the ScoreTypeFeatures class More...
class  StructureFeatures
class  StructureFeaturesCreator
 creator for the StructureFeatures class More...
class  StructureScoresFeatures
class  StructureScoresFeaturesCreator
 creator for the StructureScoresFeatures class More...

Typedefs

typedef
utility::pointer::owning_ptr
< AtomAtomPairFeatures
AtomAtomPairFeaturesOP
typedef
utility::pointer::owning_ptr
< AtomAtomPairFeatures const > 
AtomAtomPairFeaturesCOP
typedef
utility::pointer::owning_ptr
< AtomInResidueAtomInResiduePairFeatures
AtomInResidueAtomInResiduePairFeaturesOP
typedef
utility::pointer::owning_ptr
< AtomInResidueAtomInResiduePairFeatures
const > 
AtomInResidueAtomInResiduePairFeaturesCOP
typedef
utility::pointer::owning_ptr
< AtomTypesFeatures
AtomTypesFeaturesOP
typedef
utility::pointer::owning_ptr
< AtomTypesFeatures const > 
AtomTypesFeaturesCOP
typedef
utility::pointer::owning_ptr
< BetaTurnDetectionFeatures
BetaTurnDetectionFeaturesOP
typedef
utility::pointer::owning_ptr
< BetaTurnDetectionFeatures
const > 
BetaTurnDetectionFeaturesCOP
typedef
utility::pointer::owning_ptr
< DatabaseFilter
DatabaseFilterOP
typedef
utility::pointer::owning_ptr
< DatabaseFilter const > 
DatabaseFilterCOP
typedef std::pair< bool,
utility::vector1< core::Size > > 
WriteDeletePair
typedef
utility::pointer::owning_ptr
< DatabaseJobInputter
DatabaseJobInputterOP
typedef
utility::pointer::owning_ptr
< DatabaseJobOutputter
DatabaseJobOutputterOP
typedef
utility::pointer::owning_ptr
< FeaturesReporterCreator
FeaturesReporterCreatorOP
typedef
utility::pointer::owning_ptr
< FeaturesReporterCreator
const > 
FeaturesReporterCreatorCOP
typedef
utility::pointer::owning_ptr
< FeaturesReporter
FeaturesReporterOP
typedef
utility::pointer::owning_ptr
< FeaturesReporter const > 
FeaturesReporterCOP
typedef
utility::pointer::owning_ptr
< GeometricSolvationFeatures
GeometricSolvationFeaturesOP
typedef
utility::pointer::owning_ptr
< GeometricSolvationFeatures
const > 
GeometricSolvationFeaturesCOP
typedef
utility::pointer::owning_ptr
< HBondFeatures
HBondFeaturesOP
typedef
utility::pointer::owning_ptr
< HBondFeatures const > 
HBondFeaturesCOP
typedef
utility::pointer::owning_ptr
< HBondParameterFeatures
HBondParameterFeaturesOP
typedef
utility::pointer::owning_ptr
< HBondParameterFeatures const > 
HBondParameterFeaturesCOP
typedef
utility::pointer::owning_ptr
< JobDataFeatures
JobDataFeaturesOP
typedef
utility::pointer::owning_ptr
< JobDataFeatures const > 
JobDataFeaturesCOP
typedef
utility::pointer::owning_ptr
< LoopAnchorFeatures
LoopAnchorFeaturesOP
typedef
utility::pointer::owning_ptr
< LoopAnchorFeatures const > 
LoopAnchorFeaturesCOP
typedef
utility::pointer::owning_ptr
< OrbitalsFeatures
OrbitalsFeaturesOP
typedef
utility::pointer::owning_ptr
< OrbitalsFeatures const > 
OrbitalsFeaturesCOP
typedef
utility::pointer::owning_ptr
< PairFeatures
PairFeaturesOP
typedef
utility::pointer::owning_ptr
< PairFeatures const > 
PairFeaturesCOP
typedef
utility::pointer::owning_ptr
< PdbDataFeatures
PdbDataFeaturesOP
typedef
utility::pointer::owning_ptr
< PoseCommentsFeatures
PoseCommentsFeaturesOP
typedef
utility::pointer::owning_ptr
< PoseCommentsFeatures const > 
PoseCommentsFeaturesCOP
typedef
utility::pointer::owning_ptr
< PoseConformationFeatures
PoseConformationFeaturesOP
typedef
utility::pointer::owning_ptr
< PoseConformationFeatures
const > 
PoseConformationFeaturesCOP
typedef
utility::pointer::owning_ptr
< ProteinBackboneAtomAtomPairFeatures
ProteinBackboneAtomAtomPairFeaturesOP
typedef
utility::pointer::owning_ptr
< ProteinBackboneAtomAtomPairFeatures
const > 
ProteinBackboneAtomAtomPairFeaturesCOP
typedef
utility::pointer::owning_ptr
< ProteinBackboneTorsionAngleFeatures
ProteinBackboneTorsionAngleFeaturesOP
typedef
utility::pointer::owning_ptr
< ProteinBackboneTorsionAngleFeatures
const > 
ProteinBackboneTorsionAngleFeaturesCOP
typedef
utility::pointer::owning_ptr
< ProteinResidueConformationFeatures
ProteinResidueConformationFeaturesOP
typedef
utility::pointer::owning_ptr
< ProteinResidueConformationFeatures
const > 
ProteinResidueConformationFeaturesCOP
typedef
utility::pointer::owning_ptr
< ProteinRMSDFeatures
ProteinRMSDFeaturesOP
typedef
utility::pointer::owning_ptr
< ProteinRMSDFeatures const > 
ProteinRMSDFeaturesCOP
typedef
utility::pointer::owning_ptr
< ProteinSilentReport
ProteinSilentReportOP
typedef
utility::pointer::owning_ptr
< ProteinSilentReport const > 
ProteinSilentReportCOP
typedef
utility::pointer::owning_ptr
< ProtocolFeatures
ProtocolFeaturesOP
typedef
utility::pointer::owning_ptr
< ProtocolFeatures const > 
ProtocolFeaturesCOP
typedef
utility::pointer::owning_ptr
< RadiusOfGyrationFeatures
RadiusOfGyrationFeaturesOP
typedef
utility::pointer::owning_ptr
< RadiusOfGyrationFeatures
const > 
RadiusOfGyrationFeaturesCOP
typedef
utility::pointer::owning_ptr
< Report
ReportOP
typedef
utility::pointer::owning_ptr
< Report const > 
ReportCOP
typedef
utility::pointer::owning_ptr
< ReportToDB
ReportToDBOP
typedef
utility::pointer::owning_ptr
< ReportToDB const > 
ReportToDBCOP
typedef
utility::pointer::owning_ptr
< ResidueBurialFeatures
ResidueBurialFeaturesOP
typedef
utility::pointer::owning_ptr
< ResidueBurialFeatures const > 
ResidueBurialFeaturesCOP
typedef
utility::pointer::owning_ptr
< ResidueConformationFeatures
ResidueConformationFeaturesOP
typedef
utility::pointer::owning_ptr
< ResidueConformationFeatures
const > 
ResidueConformationFeaturesCOP
typedef
utility::pointer::owning_ptr
< ResidueFeatures
ResidueFeaturesOP
typedef
utility::pointer::owning_ptr
< ResidueFeatures const > 
ResidueFeaturesCOP
typedef
utility::pointer::owning_ptr
< ResidueScoresFeatures
ResidueScoresFeaturesOP
typedef
utility::pointer::owning_ptr
< ResidueScoresFeatures const > 
ResidueScoresFeaturesCOP
typedef
utility::pointer::owning_ptr
< ResidueSecondaryStructureFeatures
ResidueSecondaryStructureFeaturesOP
typedef
utility::pointer::owning_ptr
< ResidueSecondaryStructureFeatures
const > 
ResidueSecondaryStructureFeaturesCOP
typedef
utility::pointer::owning_ptr
< ResidueTypesFeatures
ResidueTypesFeaturesOP
typedef
utility::pointer::owning_ptr
< ResidueTypesFeatures const > 
ResidueTypesFeaturesCOP
typedef
utility::pointer::owning_ptr
< RotamerBoltzmannWeightFeatures
RotamerBoltzmannWeightFeaturesOP
typedef
utility::pointer::owning_ptr
< RotamerBoltzmannWeightFeatures
const > 
RotamerBoltzmannWeightFeaturesCOP
typedef
utility::pointer::owning_ptr
< RotamerRecoveryFeatures
RotamerRecoveryFeaturesOP
typedef
utility::pointer::owning_ptr
< RotamerRecoveryFeatures
const > 
RotamerRecoveryFeaturesCOP
typedef
utility::pointer::owning_ptr
< SaltBridgeFeatures
SaltBridgeFeaturesOP
typedef
utility::pointer::owning_ptr
< SaltBridgeFeatures const > 
SaltBridgeFeaturesCOP
typedef
utility::pointer::owning_ptr
< ScoreTypeFeatures
ScoreTypeFeaturesOP
typedef
utility::pointer::owning_ptr
< ScoreTypeFeatures const > 
ScoreTypeFeaturesCOP
typedef
utility::pointer::owning_ptr
< StructureFeatures
StructureFeaturesOP
typedef
utility::pointer::owning_ptr
< StructureFeatures const > 
StructureFeaturesCOP
typedef
utility::pointer::owning_ptr
< StructureScoresFeatures
StructureScoresFeaturesOP
typedef
utility::pointer::owning_ptr
< StructureScoresFeatures
const > 
StructureScoresFeaturesCOP

Enumerations

enum  HBDefType { hbdef_NONE = 1, hbdef_ENERGY, hbdef_AHDIST, hbdef_MAX = hbdef_AHDIST }
 How a hydrogen bond should be defined See note for definition_type_ below. More...

Functions

static Tracer TR ("protocols.features.AtomAtomPairFeatures")
static Tracer TR ("protocols.features.AtomTypesFeatures")
basic::Tracer TR ("protocols.features.DatabaseFilters")
core::Real get_current_model_score (core::pose::Pose const &pose, core::Size score_type_id)
DatabaseFilterOP get_DB_filter_ptr ()
WriteDeletePair get_write_delete_pair (core::pose::Pose const &pose, utility::sql_database::sessionOP db_session, core::Size const &protocol_id, core::Size const &count, std::string const &score_term, std::string current_input="")
template<class T >
get_something_from_database (cppdb::statement statement, T)
cppdb::statement get_structure_count_statement (utility::sql_database::sessionOP db_session, std::string const &input_tag, core::Size const &protocol_id)
core::Size get_score_type_id_from_score_term (utility::sql_database::sessionOP db_session, core::Size const &protocol_id, std::string const &score_term)
cppdb::statement get_nth_lowest_score_from_job_data_statement (utility::sql_database::sessionOP db_session, std::string const &score_term, core::Size const &cutoff_index, std::string const &input_tag, core::Size const &protocol_id)
cppdb::statement get_nth_lowest_score_from_score_data_statement (utility::sql_database::sessionOP db_session, core::Size const &score_type_id, core::Size const &cutoff_index, std::string const &input_tag, core::Size const &protocol_id)
cppdb::statement get_highest_score_from_job_data_statement (utility::sql_database::sessionOP db_session, std::string const &score_term, std::string const &input_tag, core::Size const &protocol_id)
cppdb::statement get_highest_score_from_score_data_statement (utility::sql_database::sessionOP db_session, core::Size const &score_type_id, std::string const &input_tag, core::Size const &protocol_id)
core::Size get_current_structure_count (utility::sql_database::sessionOP db_session, core::Size const &protocol_id, std::string const &input_tag)
core::Size get_struct_id_with_nth_lowest_score_from_job_data (utility::sql_database::sessionOP db_session, std::string const &score_term, core::Size const &cutoff_index, core::Size const &protocol_id, std::string const &input_tag)
core::Size get_struct_id_with_nth_lowest_score_from_score_data (utility::sql_database::sessionOP db_session, core::Size const &score_type_id, core::Size const &cutoff_index, core::Size const &protocol_id, std::string const &input_tag)
core::Size get_struct_id_with_lowest_score_from_job_data (utility::sql_database::sessionOP db_session, std::string const &score_term, core::Size const &protocol_id, std::string const &input_tag)
core::Size get_struct_id_with_lowest_score_from_score_data (utility::sql_database::sessionOP db_session, core::Size const &score_type_id, core::Size const &protocol_id, std::string const &input_tag)
core::Size get_struct_id_with_highest_score_from_job_data (utility::sql_database::sessionOP db_session, std::string const &score_term, core::Size const &protocol_id, std::string const &input_tag)
core::Size get_struct_id_with_highest_score_from_score_data (utility::sql_database::sessionOP db_session, core::Size const &score_type_id, core::Size const &protocol_id, std::string const &input_tag)
core::Real get_score_for_struct_id_and_score_term_from_job_data (utility::sql_database::sessionOP db_session, core::Size const &struct_id, std::string const &score_term)
core::Real get_score_for_struct_id_and_score_term_from_score_data (utility::sql_database::sessionOP db_session, core::Size const &struct_id, core::Size const &score_type_id)
static Tracer TR ("protocols.features.FeaturesReporter")
static basic::Tracer tr ("protocols.features.FeaturesReporterFactory")
static Tracer TR ("protocols.features.HBondFeatures")
static Tracer TR ("protocols.features.HBondParameterFeatures")
static basic::Tracer TR ("protocols.features.LoopAnchorFeatures")
static basic::Tracer tr ("protocols.features.ProteinRMSDFeatures")
static Tracer TR ("protocols.features.ReportToDB")
static Tracer TR ("protocols.features.ResidueSecondaryStructureFeatures")
static Tracer TR ("protocols.features.ResidueTypesFeatures")
static Tracer TR ("protocols.features.RotamerRecoveryFeatures")

Typedef Documentation


Enumeration Type Documentation

How a hydrogen bond should be defined See note for definition_type_ below.

Enumerator:
hbdef_NONE 
hbdef_ENERGY 
hbdef_AHDIST 
hbdef_MAX 

Function Documentation

core::Real protocols::features::get_current_model_score ( core::pose::Pose const &  pose,
core::Size  score_type_id 
)
core::Size protocols::features::get_current_structure_count ( utility::sql_database::sessionOP  db_session,
core::Size const &  protocol_id,
std::string const &  input_tag 
)
DatabaseFilterOP protocols::features::get_DB_filter_ptr ( )
cppdb::statement protocols::features::get_highest_score_from_job_data_statement ( utility::sql_database::sessionOP  db_session,
std::string const &  score_term,
std::string const &  input_tag,
core::Size const &  protocol_id 
)
cppdb::statement protocols::features::get_highest_score_from_score_data_statement ( utility::sql_database::sessionOP  db_session,
core::Size const &  score_type_id,
std::string const &  input_tag,
core::Size const &  protocol_id 
)
cppdb::statement protocols::features::get_nth_lowest_score_from_job_data_statement ( utility::sql_database::sessionOP  db_session,
std::string const &  score_term,
core::Size const &  cutoff_index,
std::string const &  input_tag,
core::Size const &  protocol_id 
)
cppdb::statement protocols::features::get_nth_lowest_score_from_score_data_statement ( utility::sql_database::sessionOP  db_session,
core::Size const &  score_type_id,
core::Size const &  cutoff_index,
std::string const &  input_tag,
core::Size const &  protocol_id 
)
core::Real protocols::features::get_score_for_struct_id_and_score_term_from_job_data ( utility::sql_database::sessionOP  db_session,
core::Size const &  struct_id,
std::string const &  score_term 
)
core::Real protocols::features::get_score_for_struct_id_and_score_term_from_score_data ( utility::sql_database::sessionOP  db_session,
core::Size const &  struct_id,
core::Size const &  score_type_id 
)
core::Size protocols::features::get_score_type_id_from_score_term ( utility::sql_database::sessionOP  db_session,
core::Size const &  protocol_id,
std::string const &  score_term 
)
template<class T >
T protocols::features::get_something_from_database ( cppdb::statement  statement,
 
)
core::Size protocols::features::get_struct_id_with_highest_score_from_job_data ( utility::sql_database::sessionOP  db_session,
std::string const &  score_term,
core::Size const &  protocol_id,
std::string const &  input_tag 
)
core::Size protocols::features::get_struct_id_with_highest_score_from_score_data ( utility::sql_database::sessionOP  db_session,
core::Size const &  score_type_id,
core::Size const &  protocol_id,
std::string const &  input_tag 
)
core::Size protocols::features::get_struct_id_with_lowest_score_from_job_data ( utility::sql_database::sessionOP  db_session,
std::string const &  score_term,
core::Size const &  protocol_id,
std::string const &  input_tag 
)
core::Size protocols::features::get_struct_id_with_lowest_score_from_score_data ( utility::sql_database::sessionOP  db_session,
core::Size const &  score_type_id,
core::Size const &  protocol_id,
std::string const &  input_tag 
)
core::Size protocols::features::get_struct_id_with_nth_lowest_score_from_job_data ( utility::sql_database::sessionOP  db_session,
std::string const &  score_term,
core::Size const &  cutoff_index,
core::Size const &  protocol_id,
std::string const &  input_tag 
)
core::Size protocols::features::get_struct_id_with_nth_lowest_score_from_score_data ( utility::sql_database::sessionOP  db_session,
core::Size const &  score_type_id,
core::Size const &  cutoff_index,
core::Size const &  protocol_id,
std::string const &  input_tag 
)
cppdb::statement protocols::features::get_structure_count_statement ( utility::sql_database::sessionOP  db_session,
std::string const &  input_tag,
core::Size const &  protocol_id 
)
WriteDeletePair protocols::features::get_write_delete_pair ( core::pose::Pose const &  pose,
utility::sql_database::sessionOP  db_session,
core::Size const &  protocol_id,
core::Size const &  count,
std::string const &  score_term,
std::string  current_input = "" 
)
static Tracer protocols::features::TR ( "protocols.features.FeaturesReporter"  ) [static]
static Tracer protocols::features::TR ( "protocols.features.ResidueSecondaryStructureFeatures"  ) [static]
basic::Tracer protocols::features::TR ( "protocols.features.DatabaseFilters"  )
static basic::Tracer protocols::features::TR ( "protocols.features.LoopAnchorFeatures"  ) [static]
static Tracer protocols::features::TR ( "protocols.features.HBondParameterFeatures"  ) [static]
static Tracer protocols::features::TR ( "protocols.features.HBondFeatures"  ) [static]
static Tracer protocols::features::TR ( "protocols.features.AtomAtomPairFeatures"  ) [static]
static basic::Tracer protocols::features::tr ( "protocols.features.ProteinRMSDFeatures"  ) [static]
static Tracer protocols::features::TR ( "protocols.features.ReportToDB"  ) [static]
static Tracer protocols::features::TR ( "protocols.features.ResidueTypesFeatures"  ) [static]
static basic::Tracer protocols::features::tr ( "protocols.features.FeaturesReporterFactory"  ) [static]
static Tracer protocols::features::TR ( "protocols.features.RotamerRecoveryFeatures"  ) [static]
static Tracer protocols::features::TR ( "protocols.features.AtomTypesFeatures"  ) [static]
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