#include <LoopAnchorFeatures.hh>

Inheritance diagram for protocols::features::LoopAnchorFeatures:

Public Member Functions
	LoopAnchorFeatures ()

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

utility::vector1< std::string >	features_reporter_dependencies () const override
	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 &) override

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

void	set_use_relevant_residues_as_loop_length (bool const use_relevant_residues_as_loop_length)

void	set_use_single_residue_to_define_anchor_transfrom (bool const use_single_residue_to_define_anchor_transfrom)

std::string	type_name () const override

Public Member Functions inherited from protocols::features::FeaturesReporter
	FeaturesReporter ()

	~FeaturesReporter () override
	Automatically generated virtual destructor for class deriving directly from VirtualBase. 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

Static Public Member Functions
static std::string	class_name ()

static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)

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

void	write_loop_anchor_transforms_table_schema (utility::sql_database::sessionOP db_session) const
	generate the loop_anchor_transforms table schema More...

void	write_loop_anchor_transforms_three_res_table_schema (utility::sql_database::sessionOP db_session) const
	generate the loop_anchor_transforms_three_res table schema More...

core::Size	min_loop_length (utility::vector1< bool > const &relevant_residue) const

core::Size	max_loop_length (utility::vector1< bool > const &relevant_residue) const

core::Size	determine_correct_length (utility::vector1< bool > const &relevant_residue, core::Size default_length) const

numeric::HomogeneousTransform < core::Real > const	frame_for_residue (core::conformation::Residue const &residue) const

numeric::HomogeneousTransform < core::Real > const	compute_anchor_transform (core::pose::Pose const &pose, core::Size const residue_begin, core::Size const residue_end) const

void	compute_transform_and_write_to_db (StructureID struct_id, core::Size begin, core::Size end, core::pose::Pose const &pose, cppdb::statement &stmt) const

Private Attributes
bool	use_relevant_residues_as_loop_length_

bool	use_single_residue_to_define_anchor_transfrom_

core::Size	min_loop_length_

core::Size	max_loop_length_

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::LoopAnchorFeatures::LoopAnchorFeatures ( )

Member Function Documentation

std::string protocols::features::LoopAnchorFeatures::class_name ( )

static

Referenced by provide_xml_schema(), protocols::features::LoopAnchorFeaturesCreator::type_name(), and type_name().

HomogeneousTransform< Real > const protocols::features::LoopAnchorFeatures::compute_anchor_transform	(	core::pose::Pose const &	pose,
		core::Size const	residue_begin,
		core::Size const	residue_end
	)		const

private

References frame_for_residue(), and core::pose::Pose::residue().

Referenced by compute_transform_and_write_to_db().

void protocols::features::LoopAnchorFeatures::compute_transform_and_write_to_db	(	StructureID	struct_id,
		core::Size	begin,
		core::Size	end,
		core::pose::Pose const &	pose,
		cppdb::statement &	stmt
	)		const

private

References compute_anchor_transform(), core::pose::Pose::residue(), protocols::hybridization::t, and core::conformation::Residue::xyz().

Referenced by report_features().

Size protocols::features::LoopAnchorFeatures::determine_correct_length	(	utility::vector1< bool > const &	relevant_residue,
		core::Size	default_length
	)		const

private

References use_relevant_residues_as_loop_length_.

Referenced by max_loop_length(), and min_loop_length().

utility::vector1< std::string > protocols::features::LoopAnchorFeatures::features_reporter_dependencies ( ) const

overridevirtual

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.

HomogeneousTransform< Real > const protocols::features::LoopAnchorFeatures::frame_for_residue ( core::conformation::Residue const & residue ) const

private

References core::conformation::Residue::xyz().

Referenced by compute_anchor_transform().

Size protocols::features::LoopAnchorFeatures::max_loop_length ( utility::vector1< bool > const & relevant_residue ) const

private

References determine_correct_length(), and max_loop_length_.

Referenced by report_features().

Size protocols::features::LoopAnchorFeatures::min_loop_length ( utility::vector1< bool > const & relevant_residue ) const

private

References determine_correct_length(), and min_loop_length_.

Referenced by report_features().

void protocols::features::LoopAnchorFeatures::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &
	)

overridevirtual

Reimplemented from protocols::features::FeaturesReporter.

References max_loop_length_, min_loop_length_, and set_use_relevant_residues_as_loop_length().

void protocols::features::LoopAnchorFeatures::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References class_name(), and protocols::features::xsd_type_definition_w_attributes().

Referenced by protocols::features::LoopAnchorFeaturesCreator::provide_xml_schema().

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

overridevirtual

collect all the feature data for the pose

An anchor is a take off and landing for a loop. Every residue in the loop must be relevant in order for the loop to be stored.

Implements protocols::features::FeaturesReporter.

References core::conformation::Conformation::chain_endings(), compute_transform_and_write_to_db(), core::pose::Pose::conformation(), core::sequence::end, max_loop_length(), min_loop_length(), set_use_single_residue_to_define_anchor_transfrom(), and core::pose::Pose::size().

void protocols::features::LoopAnchorFeatures::set_use_relevant_residues_as_loop_length ( bool const use_relevant_residues_as_loop_length )

References use_relevant_residues_as_loop_length_.

Referenced by parse_my_tag().

void protocols::features::LoopAnchorFeatures::set_use_single_residue_to_define_anchor_transfrom ( bool const use_single_residue_to_define_anchor_transfrom )

References use_single_residue_to_define_anchor_transfrom_.

Referenced by report_features().

std::string protocols::features::LoopAnchorFeatures::type_name ( ) const

overridevirtual

Reimplemented from protocols::features::FeaturesReporter.

References class_name().

void protocols::features::LoopAnchorFeatures::write_loop_anchor_transforms_table_schema ( utility::sql_database::sessionOP db_session ) const

private

generate the loop_anchor_transforms table schema

Referenced by write_schema_to_db().

void protocols::features::LoopAnchorFeatures::write_loop_anchor_transforms_three_res_table_schema ( utility::sql_database::sessionOP db_session ) const

private

generate the loop_anchor_transforms_three_res table schema

void protocols::features::LoopAnchorFeatures::write_loop_anchors_table_schema ( utility::sql_database::sessionOP db_session ) const

private

generate the loop_anchors table schema

Referenced by write_schema_to_db().

void protocols::features::LoopAnchorFeatures::write_schema_to_db ( utility::sql_database::sessionOP db_session ) const

overridevirtual

generate the table schemas and write them to the database

Implements protocols::features::FeaturesReporter.

References write_loop_anchor_transforms_table_schema(), and write_loop_anchors_table_schema().