#include <AtomAtomPairFeatures.hh>

Inheritance diagram for protocols::features::AtomAtomPairFeatures:

Collaboration diagram for protocols::features::AtomAtomPairFeatures:

Public Member Functions
	AtomAtomPairFeatures ()

	AtomAtomPairFeatures (AtomAtomPairFeatures const &src)

virtual	~AtomAtomPairFeatures ()

std::string	type_name () const
	return string with class name More...

void	write_schema_to_db (utility::sql_database::sessionOP db_session) const
	generate the table schemas and write them to the database 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...

void	parse_my_tag (utility::tag::TagPtr const tag, protocols::moves::DataMap &, protocols::filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &)

core::Size	report_features (core::pose::Pose const &pose, utility::vector1< bool > const &relevant_residues, boost::uuids::uuid struct_id, utility::sql_database::sessionOP db_session)
	collect all the feature data for the pose More...

void	report_atom_pairs (core::pose::Pose const &pose, utility::vector1< bool > const &relevant_residues, boost::uuids::uuid struct_id, utility::sql_database::sessionOP db_session)

Public Member Functions inherited from protocols::features::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 &, boost::uuids::uuid, utility::sql_database::sessionOP)
	collect all the feature data for the pose. More...

virtual void	load_into_pose (utility::sql_database::sessionOP, boost::uuids::uuid, core::pose::Pose &)

virtual void	delete_record (boost::uuids::uuid, utility::sql_database::sessionOP)

Private Member Functions
void	write_atom_pairs_table_schema (utility::sql_database::sessionOP db_session) const
	generate the atom_in_residue_pairs table schema More...

Private Attributes
core::Real	min_dist_

core::Real	max_dist_

core::Size	nbins_

utility::vector1< std::string >	relevant_atom_names_

std::map< core::Size, core::Size >	atom_index_to_relevant_atom_index_

std::map< std::string, core::Size >	relevant_elements_

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, boost::uuids::uuid 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...

Detailed Description

Definition at line 40 of file AtomAtomPairFeatures.hh.

Constructor & Destructor Documentation

protocols::features::AtomAtomPairFeatures::AtomAtomPairFeatures ( )

Definition at line 90 of file AtomAtomPairFeatures.cc.

References atom_index_to_relevant_atom_index_, core::chemical::ChemicalManager::get_instance(), relevant_atom_names_, and relevant_elements_.

protocols::features::AtomAtomPairFeatures::AtomAtomPairFeatures ( AtomAtomPairFeatures const & src)

Definition at line 136 of file AtomAtomPairFeatures.cc.

protocols::features::AtomAtomPairFeatures::~AtomAtomPairFeatures ( )

virtual

Definition at line 145 of file AtomAtomPairFeatures.cc.

Member Function Documentation

utility::vector1< std::string > protocols::features::AtomAtomPairFeatures::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.

Definition at line 192 of file AtomAtomPairFeatures.cc.

void protocols::features::AtomAtomPairFeatures::parse_my_tag	(	utility::tag::TagPtr const	tag,
		protocols::moves::DataMap &	,
		protocols::filters::Filters_map const &	,
		protocols::moves::Movers_map const &	,
		core::pose::Pose const &
	)

virtual

Reimplemented from protocols::features::FeaturesReporter.

Definition at line 199 of file AtomAtomPairFeatures.cc.

References max_dist_, min_dist_, and nbins_.

void protocols::features::AtomAtomPairFeatures::report_atom_pairs	(	core::pose::Pose const &	pose,
		utility::vector1< bool > const &	relevant_residues,
		boost::uuids::uuid	struct_id,
		utility::sql_database::sessionOP	db_session
	)

Definition at line 228 of file AtomAtomPairFeatures.cc.

References atom_index_to_relevant_atom_index_, core::chemical::ResidueType::atom_type_set(), core::pose::Pose::conformation(), core::pose::Pose::energies(), max_dist_, min_dist_, core::chemical::AtomTypeSet::name(), nbins_, relevant_atom_names_, relevant_elements_, core::pose::Pose::residue(), core::scoring::Energies::residue_neighbors_updated(), core::conformation::Conformation::structure_moved(), core::pose::Pose::total_residue(), and core::conformation::Residue::type().

Referenced by report_features().

Size protocols::features::AtomAtomPairFeatures::report_features	(	core::pose::Pose const &	pose,
		utility::vector1< bool > const &	relevant_residues,
		boost::uuids::uuid	struct_id,
		utility::sql_database::sessionOP	db_session
	)