Rosetta Protocols  2014.35
Public Member Functions | Private Attributes | List of all members
protocols::antibody::clusters::CDRClusterFeatures Class Reference

#include <CDRClusterFeatures.hh>

Public Member Functions

 CDRClusterFeatures ()
 
virtual ~CDRClusterFeatures ()
 
std::string type_name () const
 
void write_schema_to_db (utility::sql_database::sessionOP db_session) const
 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. More...
 
utility::vector1< std::stringfeatures_reporter_dependencies () const
 return the set of features reporters that are required to also already be extracted by the time this one is used. More...
 
core::Size report_features (core::pose::Pose const &pose, utility::vector1< bool > const &residues, StructureID struct_id, utility::sql_database::sessionOP db_session)
 collect all the feature data for the pose. More...
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &, protocols::filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &)
 Specify specific CDRs to load and analyze, with cdr_definition and scheme. More...
 
void set_cdrs_to_use (vector1< CDRNameEnum > cdrs)
 Limit CDRs being analyzed. More...
 
void set_numbering_scheme (AntibodyNumberingSchemeEnum const &numbering_scheme)
 set the numbering scheme used by the pose. More...
 
- Public Member Functions inherited from protocols::features::FeaturesReporter
 FeaturesReporter ()
 
virtual ~FeaturesReporter ()
 Automatically generated virtual destructor for class deriving directly from ReferenceCount. More...
 
virtual std::string schema () const
 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 More...
 
core::Size report_features (core::pose::Pose const &, StructureID, utility::sql_database::sessionOP)
 collect all the feature data for the pose. More...
 
virtual void load_into_pose (utility::sql_database::sessionOP, StructureID, core::pose::Pose &)
 
virtual void delete_record (StructureID, utility::sql_database::sessionOP)
 
void set_relevant_residues_mode (RelevantResiduesMode::T setting)
 
RelevantResiduesMode::T get_relevant_residues_mode () const
 
bool check_relevant_residues (utility::vector1< bool > const &relevant_residues, core::Size res1) const
 
bool check_relevant_residues (utility::vector1< bool > const &relevant_residues, core::Size res1, core::Size res2) const
 
bool check_relevant_residues_range (utility::vector1< bool > const &relevant_residues, core::Size res1, core::Size res2) const
 
bool check_relevant_residues (utility::vector1< bool > const &relevant_residues, utility::vector1< core::Size > const &residues) const
 

Private Attributes

utility::vector1< CDRNameEnumcdrs_
 
AntibodyNumberingSchemeEnum numbering_scheme_
 

Additional Inherited Members

- Protected Member Functions inherited from protocols::features::FeaturesReporter
std::string find_tag (core::pose::Pose const &pose) const
 
void delete_records_from_table (std::string const &table_name, StructureID struct_id, utility::sql_database::sessionOP db_session)
 a helper function for deleting data associated with a given structure from feature database WARNING table_name must be sanitized! More...
 
- Protected Attributes inherited from protocols::features::FeaturesReporter
RelevantResiduesMode::T relevant_residues_mode_
 

Constructor & Destructor Documentation

protocols::antibody::clusters::CDRClusterFeatures::CDRClusterFeatures ( )

References cdrs_.

protocols::antibody::clusters::CDRClusterFeatures::~CDRClusterFeatures ( )
virtual

Member Function Documentation

utility::vector1< std::string > protocols::antibody::clusters::CDRClusterFeatures::features_reporter_dependencies ( ) const
virtual

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

Reimplemented from protocols::features::FeaturesReporter.

void protocols::antibody::clusters::CDRClusterFeatures::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap ,
protocols::filters::Filters_map const &  ,
protocols::moves::Movers_map const &  ,
core::pose::Pose const &   
)
virtual
core::Size protocols::antibody::clusters::CDRClusterFeatures::report_features ( core::pose::Pose const &  ,
utility::vector1< bool > const &  ,
StructureID  ,
utility::sql_database::sessionOP   
)
virtual
void protocols::antibody::clusters::CDRClusterFeatures::set_cdrs_to_use ( vector1< CDRNameEnum cdrs)

Limit CDRs being analyzed.

References cdrs_.

void protocols::antibody::clusters::CDRClusterFeatures::set_numbering_scheme ( AntibodyNumberingSchemeEnum const &  numbering_scheme)

set the numbering scheme used by the pose.

References numbering_scheme_.

Referenced by parse_my_tag().

std::string protocols::antibody::clusters::CDRClusterFeatures::type_name ( ) const
virtual
void protocols::antibody::clusters::CDRClusterFeatures::write_schema_to_db ( utility::sql_database::sessionOP  db_session) const
virtual

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.

Implements protocols::features::FeaturesReporter.

References basic::database::schema_generator::Schema::add_column(), basic::database::schema_generator::Schema::add_foreign_key(), chain, length, sequence, table, and basic::database::schema_generator::Schema::write().

Member Data Documentation

utility::vector1< CDRNameEnum > protocols::antibody::clusters::CDRClusterFeatures::cdrs_
private
AntibodyNumberingSchemeEnum protocols::antibody::clusters::CDRClusterFeatures::numbering_scheme_
private

The documentation for this class was generated from the following files: