#include <StrandBundleFeatures.hh>

Inheritance diagram for protocols::features::strand_assembly::StrandBundleFeatures:

Collaboration diagram for protocols::features::strand_assembly::StrandBundleFeatures:

Public Member Functions
	StrandBundleFeatures ()

void	init_from_options ()

virtual std::string	type_name () const

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...

virtual 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...

utility::vector1< StrandFragment >	get_full_strands (boost::uuids::uuid struct_id, utility::sql_database::sessionOP db_session)

utility::vector1< StrandFragment >	get_i_strand_from_full_strand_pairs (boost::uuids::uuid struct_id, utility::sql_database::sessionOP db_session)

utility::vector1< StrandFragment >	get_j_strand_from_full_strand_pairs (boost::uuids::uuid struct_id, utility::sql_database::sessionOP db_session)

bool	find_antiparallel (core::pose::Pose const &pose, StrandFragment strand_i, StrandFragment strand_j)

bool	find_parallel (core::pose::Pose const &pose, StrandFragment strand_i, StrandFragment strand_j)

core::Real	check_sheet_dis_antiparallel (core::pose::Pose const &pose, StrandFragment strand_i, StrandFragment strand_j)

core::Real	check_sheet_dis_parallel (core::pose::Pose const &pose, StrandFragment strand_i, StrandFragment strand_j)

core::Real	sheet_torsion (core::pose::Pose const &pose, StrandFragment strand_i, StrandFragment strand_j)

core::Real	shortest_dis_sidechain (core::pose::Pose const &pose, StrandFragment strand_i, StrandFragment strand_j)

core::Real	shortest_dis_sidechain (core::Real val_shortest_dis_sidechain_1, core::Real val_shortest_dis_sidechain_2, core::Real val_shortest_dis_sidechain_3, core::Real val_shortest_dis_sidechain_4)

core::Real	shortest_dis_pairs (core::Real return_of_check_sheet_dis_antiparallel_1, core::Real return_of_check_sheet_dis_antiparallel_2, core::Real return_of_check_sheet_dis_antiparallel_3, core::Real return_of_check_sheet_dis_antiparallel_4)

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	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 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 Attributes
core::Size	min_strand_size_

core::Size	max_strand_size_

core::Real	min_O_N_dis_

core::Real	max_O_N_dis_

core::Real	min_sheet_dis_

core::Real	max_sheet_dis_

core::Real	min_sheet_torsion_

core::Real	max_sheet_torsion_

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 StrandBundleFeatures.hh.

Constructor & Destructor Documentation

protocols::features::strand_assembly::StrandBundleFeatures::StrandBundleFeatures ( )

Definition at line 68 of file StrandBundleFeatures.cc.

References init_from_options().

Member Function Documentation

Real protocols::features::strand_assembly::StrandBundleFeatures::check_sheet_dis_antiparallel	(	core::pose::Pose const &	pose,
		StrandFragment	strand_i,
		StrandFragment	strand_j
	)

Definition at line 441 of file StrandBundleFeatures.cc.

References core::conformation::Residue::atom(), protocols::features::strand_assembly::StrandFragment::get_size(), protocols::features::strand_assembly::StrandFragment::get_start(), max_sheet_dis_, min_sheet_dis_, core::pose::Pose::residue(), core::pose::Pose::total_residue(), protocols::features::TR(), and core::conformation::Atom::xyz().

Referenced by report_features().

Real protocols::features::strand_assembly::StrandBundleFeatures::check_sheet_dis_parallel	(	core::pose::Pose const &	pose,
		StrandFragment	strand_i,
		StrandFragment	strand_j
	)

Definition at line 557 of file StrandBundleFeatures.cc.

References core::conformation::Residue::atom(), protocols::features::strand_assembly::StrandFragment::get_size(), protocols::features::strand_assembly::StrandFragment::get_start(), max_sheet_dis_, min_sheet_dis_, core::pose::Pose::residue(), core::pose::Pose::total_residue(), protocols::features::TR(), and core::conformation::Atom::xyz().

Referenced by report_features().

utility::vector1< std::string > protocols::features::strand_assembly::StrandBundleFeatures::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 111 of file StrandBundleFeatures.cc.

bool protocols::features::strand_assembly::StrandBundleFeatures::find_antiparallel	(	core::pose::Pose const &	pose,
		StrandFragment	strand_i,
		StrandFragment	strand_j
	)

Definition at line 360 of file StrandBundleFeatures.cc.

References core::conformation::Residue::atom(), protocols::features::strand_assembly::StrandFragment::get_size(), protocols::features::strand_assembly::StrandFragment::get_start(), max_O_N_dis_, min_O_N_dis_, core::pose::Pose::residue(), and core::conformation::Atom::xyz().

Referenced by report_features().

bool protocols::features::strand_assembly::StrandBundleFeatures::find_parallel	(	core::pose::Pose const &	pose,
		StrandFragment	strand_i,
		StrandFragment	strand_j
	)

Definition at line 402 of file StrandBundleFeatures.cc.

References core::conformation::Residue::atom(), protocols::features::strand_assembly::StrandFragment::get_size(), protocols::features::strand_assembly::StrandFragment::get_start(), max_O_N_dis_, min_O_N_dis_, core::pose::Pose::residue(), and core::conformation::Atom::xyz().

Referenced by report_features().

utility::vector1< StrandFragment > protocols::features::strand_assembly::StrandBundleFeatures::get_full_strands	(	boost::uuids::uuid	struct_id,
		utility::sql_database::sessionOP	db_session
	)

Definition at line 282 of file StrandBundleFeatures.cc.

Referenced by report_features().

utility::vector1< StrandFragment > protocols::features::strand_assembly::StrandBundleFeatures::get_i_strand_from_full_strand_pairs	(	boost::uuids::uuid	struct_id,
		utility::sql_database::sessionOP	db_session
	)

Definition at line 308 of file StrandBundleFeatures.cc.

Referenced by report_features().

utility::vector1< StrandFragment > protocols::features::strand_assembly::StrandBundleFeatures::get_j_strand_from_full_strand_pairs	(	boost::uuids::uuid	struct_id,
		utility::sql_database::sessionOP	db_session
	)

Definition at line 333 of file StrandBundleFeatures.cc.

Referenced by report_features().

void protocols::features::strand_assembly::StrandBundleFeatures::init_from_options ( )

Definition at line 81 of file StrandBundleFeatures.cc.

References max_O_N_dis_, max_sheet_dis_, max_sheet_torsion_, max_strand_size_, min_O_N_dis_, min_sheet_dis_, min_sheet_torsion_, and min_strand_size_.

Referenced by StrandBundleFeatures().

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

virtual

collect all the feature data for the pose

Implements protocols::features::FeaturesReporter.

Definition at line 942 of file StrandBundleFeatures.cc.

References check_sheet_dis_antiparallel(), check_sheet_dis_parallel(), find_antiparallel(), find_parallel(), get_full_strands(), get_i_strand_from_full_strand_pairs(), get_j_strand_from_full_strand_pairs(), max_sheet_torsion_, max_strand_size_, min_sheet_torsion_, min_strand_size_, sheet_torsion(), shortest_dis_pairs(), shortest_dis_sidechain(), and protocols::features::TR().

Real protocols::features::strand_assembly::StrandBundleFeatures::sheet_torsion	(	core::pose::Pose const &	pose,
		StrandFragment	strand_i,
		StrandFragment	strand_j
	)

Definition at line 673 of file StrandBundleFeatures.cc.

References protocols::features::strand_assembly::StrandFragment::get_end(), protocols::features::strand_assembly::StrandFragment::get_start(), core::pose::Pose::residue(), protocols::kinmatch::xyz(), and core::conformation::Residue::xyz().

Referenced by report_features().

Real protocols::features::strand_assembly::StrandBundleFeatures::shortest_dis_pairs	(	core::Real	return_of_check_sheet_dis_antiparallel_1,
		core::Real	return_of_check_sheet_dis_antiparallel_2,
		core::Real	return_of_check_sheet_dis_antiparallel_3,
		core::Real	return_of_check_sheet_dis_antiparallel_4
	)

Definition at line 883 of file StrandBundleFeatures.cc.

Referenced by report_features().

Real protocols::features::strand_assembly::StrandBundleFeatures::shortest_dis_sidechain	(	core::pose::Pose const &	pose,
		StrandFragment	strand_i,
		StrandFragment	strand_j
	)

Definition at line 734 of file StrandBundleFeatures.cc.

References protocols::features::strand_assembly::StrandFragment::get_size(), protocols::features::strand_assembly::StrandFragment::get_start(), core::conformation::Residue::natoms(), core::pose::Pose::residue(), and core::conformation::Residue::xyz().

Referenced by report_features().

Real protocols::features::strand_assembly::StrandBundleFeatures::shortest_dis_sidechain	(	core::Real	val_shortest_dis_sidechain_1,
		core::Real	val_shortest_dis_sidechain_2,
		core::Real	val_shortest_dis_sidechain_3,
		core::Real	val_shortest_dis_sidechain_4
	)

Definition at line 824 of file StrandBundleFeatures.cc.

virtual std::string protocols::features::strand_assembly::StrandBundleFeatures::type_name ( ) const

inlinevirtual

Reimplemented from protocols::features::FeaturesReporter.

Definition at line 50 of file StrandBundleFeatures.hh.

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

virtual

generate the table schemas and write them to the database

Implements protocols::features::FeaturesReporter.

Definition at line 120 of file StrandBundleFeatures.cc.

Member Data Documentation

core::Real protocols::features::strand_assembly::StrandBundleFeatures::max_O_N_dis_

private

Definition at line 99 of file StrandBundleFeatures.hh.

Referenced by find_antiparallel(), find_parallel(), and init_from_options().

core::Real protocols::features::strand_assembly::StrandBundleFeatures::max_sheet_dis_

private

Definition at line 101 of file StrandBundleFeatures.hh.

Referenced by check_sheet_dis_antiparallel(), check_sheet_dis_parallel(), and init_from_options().

core::Real protocols::features::strand_assembly::StrandBundleFeatures::max_sheet_torsion_

private

Definition at line 103 of file StrandBundleFeatures.hh.

Referenced by init_from_options(), and report_features().

core::Size protocols::features::strand_assembly::StrandBundleFeatures::max_strand_size_

private

Definition at line 97 of file StrandBundleFeatures.hh.

Referenced by init_from_options(), and report_features().

core::Real protocols::features::strand_assembly::StrandBundleFeatures::min_O_N_dis_

private

Definition at line 98 of file StrandBundleFeatures.hh.

Referenced by find_antiparallel(), find_parallel(), and init_from_options().

core::Real protocols::features::strand_assembly::StrandBundleFeatures::min_sheet_dis_

private

Definition at line 100 of file StrandBundleFeatures.hh.

Referenced by check_sheet_dis_antiparallel(), check_sheet_dis_parallel(), and init_from_options().

core::Real protocols::features::strand_assembly::StrandBundleFeatures::min_sheet_torsion_

private

Definition at line 102 of file StrandBundleFeatures.hh.

Referenced by init_from_options(), and report_features().

core::Size protocols::features::strand_assembly::StrandBundleFeatures::min_strand_size_

private

Definition at line 96 of file StrandBundleFeatures.hh.

Referenced by init_from_options(), and report_features().

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

src/protocols/features/strand_assembly/StrandBundleFeatures.hh
src/protocols/features/strand_assembly/StrandBundleFeatures.cc

Public Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation