#include <StrandBundleFeatures.hh>

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, StructureID struct_id, utility::sql_database::sessionOP db_session)
	collect all the feature data for the pose More...

utility::vector1< StrandFragment >	get_full_strands (StructureID struct_id, utility::sql_database::sessionOP db_session)

utility::vector1< StrandFragment >	get_selected_strands (StructureID struct_id, utility::sql_database::sessionOP db_session)

utility::vector1< StrandFragment >	get_strand_pairs (StructureID struct_id, utility::sql_database::sessionOP db_session)

utility::vector1< StrandFragment >	get_strand_from_bss_id (StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size bss_id)

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)

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

core::Real	get_avg_dis_CA_CA (core::pose::Pose const &pose, core::Size i_resnum, core::Size i_resnum_1, core::Size i_resnum_2, core::Size i_resnum_3, core::Size j_resnum, core::Size j_resnum_1, core::Size j_resnum_2, core::Size j_resnum_3)

core::Real	check_sw_by_dis (core::pose::Pose const &pose, StrandFragment strand_i, StrandFragment strand_j, bool antiparalell)

bool	final_check_sw_by_dis (core::pose::Pose const &pose, StrandFragment temp_strand_ii_i, StrandFragment temp_strand_ii_j, StrandFragment temp_strand_jj_i, StrandFragment temp_strand_jj_j, bool antiparalell)

bool	judge_sw_dis_too_close (core::pose::Pose const &pose, StrandFragment temp_strand_ii_i, StrandFragment temp_strand_ii_j, StrandFragment temp_strand_jj_i, StrandFragment temp_strand_jj_j)

bool	judge_sw_torsion (core::pose::Pose const &pose, StrandFragment temp_strand_ii_i, StrandFragment temp_strand_ii_j, StrandFragment temp_strand_jj_i, StrandFragment temp_strand_jj_j)

core::Real	judge_sw_inter_dis (core::pose::Pose const &pose, StrandFragment temp_strand_ii_i, StrandFragment temp_strand_ii_j, StrandFragment temp_strand_jj_i, StrandFragment temp_strand_jj_j)

core::Size	round (core::Real x)

core::Size	get_nearest_res_from_strand (core::pose::Pose const &pose, StrandFragment strand_to_be_searched, core::Size rounded_resnum)

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

bool	judge_facing (core::pose::Pose const &pose, StrandFragment strand_ii_i, StrandFragment strand_ii_j, StrandFragment strand_jj_i, StrandFragment strand_jj_j)

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

core::Real	get_shortest_among_4 (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	sheet_dis_by_terminals (core::pose::Pose const &pose, StrandFragment strand_i, StrandFragment strand_j)

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	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 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

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::strand_assembly::StrandBundleFeatures::StrandBundleFeatures ( )

References init_from_options().

Member Function Documentation

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

References core::conformation::Residue::atom(), numeric::xyzVector< class >::distance(), protocols::features::strand_assembly::StrandFragment::get_size(), protocols::features::strand_assembly::StrandFragment::get_start(), core::pose::Pose::residue(), and core::conformation::Atom::xyz().

Referenced by judge_sw_dis_too_close().

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

References get_avg_dis_CA_CA(), protocols::features::strand_assembly::StrandFragment::get_size(), protocols::features::strand_assembly::StrandFragment::get_start(), and core::pose::Pose::total_residue().

Referenced by final_check_sw_by_dis().

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.

bool protocols::features::strand_assembly::StrandBundleFeatures::final_check_sw_by_dis	(	core::pose::Pose const &	pose,
		StrandFragment	temp_strand_ii_i,
		StrandFragment	temp_strand_ii_j,
		StrandFragment	temp_strand_jj_i,
		StrandFragment	temp_strand_jj_j,
		bool	antiparalell
	)

References check_sw_by_dis().

Referenced by report_features().

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

References core::conformation::Residue::atom(), numeric::xyzVector< class >::distance(), protocols::features::strand_assembly::StrandFragment::get_end(), 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
	)

References core::conformation::Residue::atom(), numeric::xyzVector< class >::distance(), protocols::features::strand_assembly::StrandFragment::get_end(), 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().

Real protocols::features::strand_assembly::StrandBundleFeatures::get_avg_dis_CA_CA	(	core::pose::Pose const &	pose,
		core::Size	i_resnum,
		core::Size	i_resnum_1,
		core::Size	i_resnum_2,
		core::Size	i_resnum_3,
		core::Size	j_resnum,
		core::Size	j_resnum_1,
		core::Size	j_resnum_2,
		core::Size	j_resnum_3
	)

References core::conformation::Residue::atom(), numeric::xyzVector< class >::distance(), max_sheet_dis_, core::pose::Pose::residue(), and core::conformation::Atom::xyz().

Referenced by check_sw_by_dis().

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

References basic::database::safely_prepare_statement(), and basic::database::safely_read_from_database().

Referenced by report_features().

Size protocols::features::strand_assembly::StrandBundleFeatures::get_nearest_res_from_strand	(	core::pose::Pose const &	pose,
		StrandFragment	strand_to_be_searched,
		core::Size	rounded_resnum
	)

References core::conformation::Residue::atom(), numeric::xyzVector< class >::distance(), protocols::features::strand_assembly::StrandFragment::get_size(), protocols::features::strand_assembly::StrandFragment::get_start(), core::pose::Pose::residue(), and core::conformation::Atom::xyz().

Referenced by judge_facing().

utility::vector1< StrandFragment > protocols::features::strand_assembly::StrandBundleFeatures::get_selected_strands	(	StructureID	struct_id,
		utility::sql_database::sessionOP	db_session
	)

References basic::database::safely_prepare_statement(), and basic::database::safely_read_from_database().

Referenced by report_features().

Real protocols::features::strand_assembly::StrandBundleFeatures::get_shortest_among_4	(	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
	)

Referenced by judge_facing(), and judge_sw_inter_dis().

utility::vector1< StrandFragment > protocols::features::strand_assembly::StrandBundleFeatures::get_strand_from_bss_id	(	StructureID	struct_id,
		utility::sql_database::sessionOP	db_session,
		core::Size	bss_id
	)

References basic::database::safely_prepare_statement(), and basic::database::safely_read_from_database().

Referenced by report_features().

utility::vector1< StrandFragment > protocols::features::strand_assembly::StrandBundleFeatures::get_strand_pairs	(	StructureID	struct_id,
		utility::sql_database::sessionOP	db_session
	)

References basic::database::safely_prepare_statement(), and basic::database::safely_read_from_database().

Referenced by report_features().

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

References extract_native_only_, max_num_strands_to_deal_, max_O_N_dis_, max_res_in_strand_, max_sheet_angle_, max_sheet_dis_, max_sheet_torsion_, min_num_strands_to_deal_, min_O_N_dis_, min_res_in_strand_, min_sheet_angle_, min_sheet_dis_, min_sheet_torsion_, min_shortest_dis_sidechain_inter_sheet_, option, and user.

Referenced by StrandBundleFeatures().

bool protocols::features::strand_assembly::StrandBundleFeatures::judge_facing	(	core::pose::Pose const &	pose,
		StrandFragment	strand_ii_i,
		StrandFragment	strand_ii_j,
		StrandFragment	strand_jj_i,
		StrandFragment	strand_jj_j
	)

References numeric::angle_degrees(), core::conformation::Residue::atom(), numeric::xyzVector< class >::distance(), protocols::features::strand_assembly::StrandFragment::get_end(), get_nearest_res_from_strand(), get_shortest_among_4(), protocols::features::strand_assembly::StrandFragment::get_start(), max_sheet_angle_, min_sheet_angle_, core::pose::Pose::residue(), round(), core::conformation::Residue::xyz(), and core::conformation::Atom::xyz().

Referenced by report_features().

bool protocols::features::strand_assembly::StrandBundleFeatures::judge_sw_dis_too_close	(	core::pose::Pose const &	pose,
		StrandFragment	temp_strand_ii_i,
		StrandFragment	temp_strand_ii_j,
		StrandFragment	temp_strand_jj_i,
		StrandFragment	temp_strand_jj_j
	)

References check_strand_too_closeness().

Referenced by report_features().

Real protocols::features::strand_assembly::StrandBundleFeatures::judge_sw_inter_dis	(	core::pose::Pose const &	pose,
		StrandFragment	temp_strand_ii_i,
		StrandFragment	temp_strand_ii_j,
		StrandFragment	temp_strand_jj_i,
		StrandFragment	temp_strand_jj_j
	)

References get_shortest_among_4(), min_shortest_dis_sidechain_inter_sheet_, and shortest_dis_sidechain().

Referenced by report_features().

bool protocols::features::strand_assembly::StrandBundleFeatures::judge_sw_torsion	(	core::pose::Pose const &	pose,
		StrandFragment	temp_strand_ii_i,
		StrandFragment	temp_strand_ii_j,
		StrandFragment	temp_strand_jj_i,
		StrandFragment	temp_strand_jj_j
	)

References max_sheet_torsion_, min_sheet_torsion_, and sheet_torsion().

Referenced by report_features().

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

virtual

Size protocols::features::strand_assembly::StrandBundleFeatures::round ( core::Real x )

Referenced by judge_facing().

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

References numeric::xyzVector< class >::distance(), protocols::features::strand_assembly::StrandFragment::get_end(), protocols::features::strand_assembly::StrandFragment::get_start(), core::pose::Pose::residue(), and core::conformation::Residue::xyz().

Referenced by report_features().

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

References numeric::dihedral_degrees(), numeric::xyzVector< class >::distance(), protocols::features::strand_assembly::StrandFragment::get_end(), protocols::features::strand_assembly::StrandFragment::get_start(), core::pose::Pose::residue(), core::conformation::Residue::xyz(), and protocols::kinmatch::xyz().

Referenced by judge_sw_torsion().

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

References numeric::xyzVector< class >::distance(), 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 judge_sw_inter_dis().

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

inlinevirtual

Reimplemented from protocols::features::FeaturesReporter.

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.

References basic::database::schema_generator::Schema::add_column(), basic::database::schema_generator::Schema::add_foreign_key(), and basic::database::schema_generator::Schema::write().

Member Data Documentation

bool protocols::features::strand_assembly::StrandBundleFeatures::extract_native_only_

private

Referenced by init_from_options(), and report_features().

core::Size protocols::features::strand_assembly::StrandBundleFeatures::max_num_strands_to_deal_

private

Referenced by init_from_options(), and report_features().

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

private

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

core::Size protocols::features::strand_assembly::StrandBundleFeatures::max_res_in_strand_

private

Referenced by init_from_options(), and report_features().

core::Real protocols::features::strand_assembly::StrandBundleFeatures::max_sheet_angle_

private

Referenced by init_from_options(), and judge_facing().

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

private

Referenced by get_avg_dis_CA_CA(), and init_from_options().

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

private

Referenced by init_from_options(), and judge_sw_torsion().

core::Size protocols::features::strand_assembly::StrandBundleFeatures::min_num_strands_to_deal_

private

Referenced by init_from_options(), and report_features().

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

private

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

core::Size protocols::features::strand_assembly::StrandBundleFeatures::min_res_in_strand_

private

Referenced by init_from_options(), and report_features().

core::Real protocols::features::strand_assembly::StrandBundleFeatures::min_sheet_angle_

private

Referenced by init_from_options(), and judge_facing().

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

private

Referenced by init_from_options().

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

private

Referenced by init_from_options(), and judge_sw_torsion().

core::Real protocols::features::strand_assembly::StrandBundleFeatures::min_shortest_dis_sidechain_inter_sheet_

private

Referenced by init_from_options(), and judge_sw_inter_dis().

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

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

Private Attributes
core::Size	min_num_strands_to_deal_

core::Size	max_num_strands_to_deal_

bool	extract_native_only_

core::Size	min_res_in_strand_

core::Size	max_res_in_strand_

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_

core::Real	min_sheet_angle_

core::Real	max_sheet_angle_

core::Real	min_shortest_dis_sidechain_inter_sheet_

Public Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation