#include <ResidueScoresFeatures.hh>

Inheritance diagram for protocols::features::ResidueScoresFeatures:

Collaboration diagram for protocols::features::ResidueScoresFeatures:

Public Member Functions
	ResidueScoresFeatures ()

	ResidueScoresFeatures (core::scoring::ScoreFunctionOP scfxn)

	ResidueScoresFeatures (ResidueScoresFeatures const &src)

virtual	~ResidueScoresFeatures ()

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 &data, 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...

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_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 (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, boost::uuids::uuid 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, Size const batch_id, boost::uuids::uuid 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, Size const batch_id, boost::uuids::uuid 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, Size const batch_id, boost::uuids::uuid 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, 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 43 of file ResidueScoresFeatures.hh.

Constructor & Destructor Documentation

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

Definition at line 93 of file ResidueScoresFeatures.cc.

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

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

Definition at line 102 of file ResidueScoresFeatures.cc.

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

virtual

Definition at line 107 of file ResidueScoresFeatures.cc.

Member Function Documentation

utility::vector1< std::string > protocols::features::ResidueScoresFeatures::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 284 of file ResidueScoresFeatures.cc.

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

private

Definition at line 395 of file ResidueScoresFeatures.cc.

References core::scoring::methods::cd_1b, core::scoring::methods::ci_1b, core::pose::Pose::residue(), scfxn_, and core::pose::Pose::total_residue().

Referenced by insert_residue_scores_rows().

void protocols::features::ResidueScoresFeatures::insert_residue_scores_rows	(	core::pose::Pose const &	pose,
		utility::vector1< bool > const &	relevant_residues,
		boost::uuids::uuid 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.

Definition at line 354 of file ResidueScoresFeatures.cc.

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::total_residue().

Referenced by report_features().

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

private

Definition at line 584 of file ResidueScoresFeatures.cc.

References core::scoring::methods::cd_lr_2b, core::scoring::methods::ci_lr_2b, core::pose::Pose::energies(), core::scoring::Energies::long_range_container(), scfxn_, and core::pose::Pose::total_residue().

Referenced by insert_residue_scores_rows().

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

private

Definition at line 475 of file ResidueScoresFeatures.cc.

References core::scoring::methods::cd_2b, core::scoring::methods::ci_2b, core::graph::Node::const_upper_edge_list_end(), core::pose::Pose::energies(), core::graph::Edge::get_node(), core::graph::Edge::get_second_node_ind(), core::pose::Pose::residue(), scfxn_, and core::pose::Pose::total_residue().

Referenced by insert_residue_scores_rows().

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

virtual

Reimplemented from protocols::features::FeaturesReporter.

Definition at line 292 of file ResidueScoresFeatures.cc.

References protocols::moves::DataMap::get(), scfxn_, and type_name().

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