#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::string >	features_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< CDRNameEnum >	cdrs_

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

Specify specific CDRs to load and analyze, with cdr_definition and scheme.

Reimplemented from protocols::features::FeaturesReporter.

References protocols::antibody::AntibodyEnumManager::cdr_name_is_present(), protocols::antibody::AntibodyEnumManager::cdr_name_string_to_enum(), cdrs_, protocols::antibody::AntibodyEnumManager::numbering_scheme_is_present(), protocols::antibody::AntibodyEnumManager::numbering_scheme_string_to_enum(), set_numbering_scheme(), and utility::string_split().

core::Size protocols::antibody::clusters::CDRClusterFeatures::report_features	(	core::pose::Pose const &	,
		utility::vector1< bool > const &	,
		StructureID	,
		utility::sql_database::sessionOP
	)

virtual

collect all the feature data for the pose.

Implements protocols::features::FeaturesReporter.

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

Reimplemented from protocols::features::FeaturesReporter.

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

Referenced by CDRClusterFeatures(), parse_my_tag(), report_features(), and set_cdrs_to_use().

AntibodyNumberingSchemeEnum protocols::antibody::clusters::CDRClusterFeatures::numbering_scheme_

private

Referenced by report_features(), and set_numbering_scheme().

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

src/protocols/antibody/clusters/CDRClusterFeatures.hh
src/protocols/antibody/clusters/CDRClusterFeatures.cc

Public Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation