#include <ResidueScoresFeatures.hh>

Inheritance diagram for protocols::features::ResidueScoresFeatures:

Public Member Functions
	ResidueScoresFeatures ()

	ResidueScoresFeatures (core::scoring::ScoreFunctionOP scfxn)

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 &data) override

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

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_residue_scores_1b_table_schema (utility::sql_database::sessionOP db_session) const
	generate the residue_scores_1b table schema More...

void	write_residue_scores_2b_table_schema_helper (std::string name, utility::sql_database::sessionOP db_session) const
	2b schema helper More...

void	write_residue_scores_2b_table_schema (utility::sql_database::sessionOP db_session) const
	generate the residue_scores_2b table schema More...

void	write_residue_scores_lr_2b_table_schema (utility::sql_database::sessionOP db_session) const
	generate the residue_scores_2b table schema More...

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

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

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

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

Private Attributes
core::scoring::ScoreFunctionOP	scfxn_

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

◆ ResidueScoresFeatures() [1/2]

protocols::features::ResidueScoresFeatures::ResidueScoresFeatures ( )

◆ ResidueScoresFeatures() [2/2]

protocols::features::ResidueScoresFeatures::ResidueScoresFeatures ( core::scoring::ScoreFunctionOP scfxn )

Member Function Documentation

◆ class_name()

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

static

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

◆ features_reporter_dependencies()

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

◆ insert_one_body_residue_score_rows()

void protocols::features::ResidueScoresFeatures::insert_one_body_residue_score_rows	(	core::pose::Pose const &	pose,
		utility::vector1< bool > const &	relevant_residues,
		core::Size const	batch_id,
		StructureID const	struct_id,
		utility::sql_database::sessionOP	db_session
	)

private

References core::scoring::methods::cd_1b, protocols::features::FeaturesReporter::check_relevant_residues(), core::scoring::methods::ci_1b, core::scoring::EMapVector::clear(), core::pose::Pose::residue(), scfxn_, and core::pose::Pose::size().

Referenced by insert_residue_scores_rows().

◆ insert_residue_scores_rows()

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

private

Score types are either one body, two body, or whole structure and can either dependend on the context or not.
Whole structure terms are reported in the structure_scores table along with the totals from the remaining terms.
The one and two body terms are broken up into two different tables because they are parametrized differently (one residue vs two residues).
Residues are identified by Rosetta's residue numbering scheme. To convert to the PDB residue numbering scheme, join with the residues_pdb table.
Although two body terms can be with in the same residue, these 'intrares' score terms are reported with the two body terms where resNum == otherResNum.
Two body terms always are reported so that resNum1 <= resNum2.
Values for score terms are only reported if they are non-zero.
Values of two body energies are only reported when both residues are true in the relevant_residues vector.

References core::conformation::Residue::aa(), core::chemical::aa_vrt, protocols::features::get_batch_id(), insert_one_body_residue_score_rows(), insert_two_body_long_range_residue_score_rows(), insert_two_body_residue_score_rows(), core::pose::Pose::residue(), scfxn_, and core::pose::Pose::size().

Referenced by report_features().

◆ insert_two_body_long_range_residue_score_rows()

void protocols::features::ResidueScoresFeatures::insert_two_body_long_range_residue_score_rows	(	core::pose::Pose const &	pose,
		utility::vector1< bool > const &	relevant_residues,
		core::Size const	batch_id,
		StructureID const	struct_id,
		utility::sql_database::sessionOP	db_session
	)

private

References core::scoring::methods::cd_lr_2b, protocols::features::FeaturesReporter::check_relevant_residues(), core::scoring::methods::ci_lr_2b, core::pose::Pose::energies(), core::scoring::Energies::long_range_container(), scfxn_, core::pose::Pose::size(), and core::scoring::EMapVector::zero().

Referenced by insert_residue_scores_rows().

◆ insert_two_body_residue_score_rows()

void protocols::features::ResidueScoresFeatures::insert_two_body_residue_score_rows	(	core::pose::Pose const &	pose,
		utility::vector1< bool > const &	relevant_residues,
		core::Size const	batch_id,
		StructureID const	struct_id,
		utility::sql_database::sessionOP	db_session
	)

private

References core::scoring::methods::cd_2b, protocols::features::FeaturesReporter::check_relevant_residues(), core::scoring::methods::ci_2b, core::scoring::EMapVector::clear(), core::pose::Pose::energies(), core::scoring::Energies::energies_updated(), core::scoring::Energies::energy_graph(), core::pose::Pose::residue(), scfxn_, and core::pose::Pose::size().

Referenced by insert_residue_scores_rows().

◆ parse_my_tag()

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

overridevirtual

Reimplemented from protocols::features::FeaturesReporter.

References scfxn_.

◆ provide_xml_schema()

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

static

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

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

◆ report_features()

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

overridevirtual

collect all the feature data for the pose

Implements protocols::features::FeaturesReporter.

References insert_residue_scores_rows().

◆ type_name()

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

overridevirtual

Reimplemented from protocols::features::FeaturesReporter.

References class_name().

◆ write_residue_scores_1b_table_schema()

void protocols::features::ResidueScoresFeatures::write_residue_scores_1b_table_schema ( utility::sql_database::sessionOP db_session ) const

private

generate the residue_scores_1b table schema

Referenced by write_schema_to_db().

◆ write_residue_scores_2b_table_schema()

void protocols::features::ResidueScoresFeatures::write_residue_scores_2b_table_schema ( utility::sql_database::sessionOP db_session ) const

private

generate the residue_scores_2b table schema

References write_residue_scores_2b_table_schema_helper().

Referenced by write_schema_to_db().

◆ write_residue_scores_2b_table_schema_helper()

void protocols::features::ResidueScoresFeatures::write_residue_scores_2b_table_schema_helper	(	std::string	name,
		utility::sql_database::sessionOP	db_session
	)		const

private

2b schema helper

Referenced by write_residue_scores_2b_table_schema(), and write_residue_scores_lr_2b_table_schema().

◆ write_residue_scores_lr_2b_table_schema()

void protocols::features::ResidueScoresFeatures::write_residue_scores_lr_2b_table_schema ( utility::sql_database::sessionOP db_session ) const

private

generate the residue_scores_2b table schema

References write_residue_scores_2b_table_schema_helper().

Referenced by write_schema_to_db().

◆ write_schema_to_db()

void protocols::features::ResidueScoresFeatures::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_residue_scores_1b_table_schema(), write_residue_scores_2b_table_schema(), and write_residue_scores_lr_2b_table_schema().

Member Data Documentation

◆ scfxn_

core::scoring::ScoreFunctionOP protocols::features::ResidueScoresFeatures::scfxn_

private

Referenced by insert_one_body_residue_score_rows(), insert_residue_scores_rows(), insert_two_body_long_range_residue_score_rows(), insert_two_body_residue_score_rows(), and parse_my_tag().

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

src/protocols/features/ResidueScoresFeatures.hh
src/protocols/features/ResidueScoresFeatures.cc

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ ResidueScoresFeatures() [1/2]

◆ ResidueScoresFeatures() [2/2]

Member Function Documentation

◆ class_name()

◆ features_reporter_dependencies()

◆ insert_one_body_residue_score_rows()

◆ insert_residue_scores_rows()

◆ insert_two_body_long_range_residue_score_rows()

◆ insert_two_body_residue_score_rows()

◆ parse_my_tag()

◆ provide_xml_schema()

◆ report_features()

◆ type_name()

◆ write_residue_scores_1b_table_schema()

◆ write_residue_scores_2b_table_schema()

◆ write_residue_scores_2b_table_schema_helper()

◆ write_residue_scores_lr_2b_table_schema()

◆ write_schema_to_db()

Member Data Documentation

◆ scfxn_