#include <UnrecognizedAtomFeatures.hh>

Public Member Functions
	UnrecognizedAtomFeatures ()

	UnrecognizedAtomFeatures (core::Real neighbor_distance_cutoff)

	UnrecognizedAtomFeatures (UnrecognizedAtomFeatures const &src)

virtual	~UnrecognizedAtomFeatures ()

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

virtual 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::TagCOP tag, basic::datacache::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, StructureID struct_id, utility::sql_database::sessionOP db_session)
	collect all the feature data for the pose More...

void	delete_record (StructureID struct_id, utility::sql_database::sessionOP db_sesion)

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 &)

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 Member Functions
virtual void	write_unrecognized_atoms_table_schema (utility::sql_database::sessionOP db_session) const
	generate the unrecognized_atoms table schema More...

virtual void	write_unrecognized_residues_table_schema (utility::sql_database::sessionOP db_session) const
	generate the unrecognized_residues table schema More...

virtual void	write_unrecognized_neighbors_table_schema (utility::sql_database::sessionOP db_session) const
	generate the unrecognized_neighbors table schema More...

void	insert_unrecognized_residues_rows (core::pose::Pose const &pose, StructureID struct_id, utility::sql_database::sessionOP db_session)

void	insert_unrecognized_atoms_rows (core::pose::Pose const &pose, StructureID struct_id, utility::sql_database::sessionOP db_session)

void	insert_unrecognized_neighbors_rows (core::pose::Pose const &pose, utility::vector1< bool > const &relevant_residues, StructureID struct_id, utility::sql_database::sessionOP db_session)

Private Attributes
core::Real	neighbor_distance_cutoff_

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::features::UnrecognizedAtomFeatures::UnrecognizedAtomFeatures ( )

References basic::options::option, basic::options::OptionKeys::in::remember_unrecognized_res, basic::options::OptionKeys::in::remember_unrecognized_water, and protocols::features::TR.

protocols::features::UnrecognizedAtomFeatures::UnrecognizedAtomFeatures ( core::Real neighbor_distance_cutoff )

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

protocols::features::UnrecognizedAtomFeatures::~UnrecognizedAtomFeatures ( )

virtual

Member Function Documentation

void protocols::features::UnrecognizedAtomFeatures::delete_record	(	StructureID	struct_id,
		utility::sql_database::sessionOP	db_sesion
	)

virtual

Reimplemented from protocols::features::FeaturesReporter.

References protocols::features::FeaturesReporter::delete_records_from_table().

utility::vector1< std::string > protocols::features::UnrecognizedAtomFeatures::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::features::UnrecognizedAtomFeatures::insert_unrecognized_atoms_rows	(	core::pose::Pose const &	pose,
		StructureID	struct_id,
		utility::sql_database::sessionOP	db_session
	)

private

References basic::database::insert_statement_generator::InsertGenerator::add_column(), basic::database::insert_statement_generator::InsertGenerator::add_row(), core::pose::UnrecognizedAtomRecord::atom_name(), core::pose::UnrecognizedAtomRecord::coords(), make_vector(), core::pose::Pose::pdb_info(), core::pose::UnrecognizedAtomRecord::res_num(), core::pose::UnrecognizedAtomRecord::temp(), basic::database::insert_statement_generator::InsertGenerator::write_to_database(), numeric::xyzVector< class >::x(), numeric::xyzVector< class >::y(), and numeric::xyzVector< class >::z().

Referenced by report_features().

void protocols::features::UnrecognizedAtomFeatures::insert_unrecognized_neighbors_rows	(	core::pose::Pose const &	pose,
		utility::vector1< bool > const &	relevant_residues,
		StructureID	struct_id,
		utility::sql_database::sessionOP	db_session
	)

private

References basic::database::insert_statement_generator::InsertGenerator::add_column(), basic::database::insert_statement_generator::InsertGenerator::add_row(), protocols::features::FeaturesReporter::check_relevant_residues(), core::pose::UnrecognizedAtomRecord::coords(), make_vector(), neighbor_distance_cutoff_, core::pose::Pose::pdb_info(), core::pose::UnrecognizedAtomRecord::res_num(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), and basic::database::insert_statement_generator::InsertGenerator::write_to_database().

Referenced by report_features().

void protocols::features::UnrecognizedAtomFeatures::insert_unrecognized_residues_rows	(	core::pose::Pose const &	pose,
		StructureID	struct_id,
		utility::sql_database::sessionOP	db_session
	)

private

References basic::database::insert_statement_generator::InsertGenerator::add_column(), basic::database::insert_statement_generator::InsertGenerator::add_row(), make_vector(), core::pose::Pose::pdb_info(), core::pose::UnrecognizedAtomRecord::res_name(), core::pose::UnrecognizedAtomRecord::res_num(), core::pose::UnrecognizedAtomRecord::temp(), and basic::database::insert_statement_generator::InsertGenerator::write_to_database().

Referenced by report_features().

void protocols::features::UnrecognizedAtomFeatures::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

Reimplemented from protocols::features::FeaturesReporter.

References neighbor_distance_cutoff_.

Size protocols::features::UnrecognizedAtomFeatures::report_features	(	core::pose::Pose const &	pose,
		utility::vector1< bool > const &	relevant_residues,
		StructureID	struct_id,
		utility::sql_database::sessionOP	db_session
	)