#include <HelixBundleFeatures.hh>

Public Member Functions
	HelixBundleFeatures ()

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...

virtual void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data, protocols::filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &pose)

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...

bool	overlapping (HelicalFragmentOP const &fragment_1, HelicalFragmentOP const &fragment_2)

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 < HelicalFragmentOP >	get_helix_fragments (StructureID struct_id, utility::sql_database::sessionOP db_session)

void	calc_pc_and_com (core::pose::Pose const &pose, HelicalFragmentOP fragment)

void	record_helix_sasas (core::pose::Pose const &pose, std::set< HelicalFragmentOP > const &frag_set)
	create a bundle-pose from the combination of fragments and record the "interface" SASA for each helix against the rest of the bundle More...

PairMap	get_helix_pairs (core::pose::Pose const &pose, utility::vector1< HelicalFragmentOP > helix_fragments)

void	calc_fa_energy (core::pose::Pose const &pose, FragmentPair &fragment_pair)
	calculate the shared fa_attr for each pair of helices in the bundle More...

void	calc_crossing_angles (core::pose::Pose const &pose, FragmentPair &fragment_pair)
	calculate the crossing angles of the helix fragment in the bundle set More...

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	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

Private Attributes
core::Real	helix_cap_dist_cutoff_

core::Size	bundle_size_

core::Size	helix_size_

core::Real	min_per_residue_fa_attr_

core::Real	min_interacting_set_fraction_

core::Real	max_degrees_off_parallel_

protocols::simple_filters::InterfaceSasaFilter	sasa_filter_

core::scoring::ScoreFunctionOP	scorefxn_

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::helixAssembly::HelixBundleFeatures::HelixBundleFeatures ( )

References core::scoring::get_score_function(), and scorefxn_.

Member Function Documentation

void protocols::features::helixAssembly::HelixBundleFeatures::calc_crossing_angles	(	core::pose::Pose const &	pose,
		FragmentPair &	fragment_pair
	)

calculate the crossing angles of the helix fragment in the bundle set

References calc_pc_and_com(), closest_point_on_line(), protocols::features::helixAssembly::FragmentPair::crossing_angle, numeric::dihedral_degrees(), protocols::features::helixAssembly::FragmentPair::fragment_1, protocols::features::helixAssembly::FragmentPair::fragment_2, core::pose::Pose::residue(), and core::conformation::Residue::xyz().

Referenced by get_helix_pairs().

void protocols::features::helixAssembly::HelixBundleFeatures::calc_fa_energy	(	core::pose::Pose const &	pose,
		FragmentPair &	fragment_pair
	)

calculate the shared fa_attr for each pair of helices in the bundle

References core::pose::Pose::energies(), core::scoring::Energies::energy_graph(), core::scoring::fa_atr, protocols::features::helixAssembly::FragmentPair::fa_attr, protocols::features::helixAssembly::FragmentPair::fa_fraction, protocols::features::helixAssembly::FragmentPair::fragment_1, protocols::features::helixAssembly::FragmentPair::fragment_2, and helix_size_.

Referenced by get_helix_pairs().

void protocols::features::helixAssembly::HelixBundleFeatures::calc_pc_and_com	(	core::pose::Pose const &	pose,
		HelicalFragmentOP	fragment
	)

References core::conformation::Residue::atom(), numeric::center_of_mass(), numeric::first_principal_component(), core::pose::Pose::residue(), and core::conformation::Atom::xyz().

Referenced by calc_crossing_angles().

utility::vector1< std::string > protocols::features::helixAssembly::HelixBundleFeatures::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.

utility::vector1< HelicalFragmentOP > protocols::features::helixAssembly::HelixBundleFeatures::get_helix_fragments	(	StructureID	struct_id,
		utility::sql_database::sessionOP	db_session
	)

References helix_size_, basic::database::safely_prepare_statement(), basic::database::safely_read_from_database(), and protocols::features::TR.

Referenced by report_features().

PairMap protocols::features::helixAssembly::HelixBundleFeatures::get_helix_pairs	(	core::pose::Pose const &	pose,
		utility::vector1< HelicalFragmentOP >	helix_fragments
	)

References calc_crossing_angles(), calc_fa_energy(), numeric::xyzVector< class >::distance_squared(), protocols::features::helixAssembly::FragmentPair::end_1_distance, protocols::features::helixAssembly::FragmentPair::end_2_distance, protocols::features::helixAssembly::FragmentPair::fa_attr, protocols::features::helixAssembly::FragmentPair::fa_fraction, protocols::features::helixAssembly::FragmentPair::fragment_1, protocols::features::helixAssembly::FragmentPair::fragment_2, helix_cap_dist_cutoff_, min_interacting_set_fraction_, min_per_residue_fa_attr_, core::pose::Pose::residue(), and core::conformation::Residue::xyz().

Referenced by report_features().

bool protocols::features::helixAssembly::HelixBundleFeatures::overlapping	(	HelicalFragmentOP const &	fragment_1,
		HelicalFragmentOP const &	fragment_2
	)

Referenced by report_features().

void protocols::features::helixAssembly::HelixBundleFeatures::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data,
		protocols::filters::Filters_map const &	,
		protocols::moves::Movers_map const &	,
		core::pose::Pose const &	pose
	)

virtual

Reimplemented from protocols::features::FeaturesReporter.

References bundle_size_, helix_cap_dist_cutoff_, helix_size_, max_degrees_off_parallel_, min_interacting_set_fraction_, min_per_residue_fa_attr_, runtime_assert, and type_name().

void protocols::features::helixAssembly::HelixBundleFeatures::record_helix_sasas	(	core::pose::Pose const &	pose,
		std::set< HelicalFragmentOP > const &	frag_set
	)

create a bundle-pose from the combination of fragments and record the "interface" SASA for each helix against the rest of the bundle

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

virtual

collect all the feature data for the pose

Implements protocols::features::FeaturesReporter.

virtual std::string protocols::features::helixAssembly::HelixBundleFeatures::type_name ( ) const

inlinevirtual

Reimplemented from protocols::features::FeaturesReporter.

Referenced by parse_my_tag().

void protocols::features::helixAssembly::HelixBundleFeatures::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(), sasa, and basic::database::schema_generator::Schema::write().

Member Data Documentation

core::Size protocols::features::helixAssembly::HelixBundleFeatures::bundle_size_

private

Referenced by parse_my_tag(), and report_features().

core::Real protocols::features::helixAssembly::HelixBundleFeatures::helix_cap_dist_cutoff_

private

Referenced by get_helix_pairs(), and parse_my_tag().

core::Size protocols::features::helixAssembly::HelixBundleFeatures::helix_size_

private

Referenced by calc_fa_energy(), get_helix_fragments(), parse_my_tag(), and report_features().

core::Real protocols::features::helixAssembly::HelixBundleFeatures::max_degrees_off_parallel_

private

Referenced by parse_my_tag().

core::Real protocols::features::helixAssembly::HelixBundleFeatures::min_interacting_set_fraction_

private

Referenced by get_helix_pairs(), and parse_my_tag().

core::Real protocols::features::helixAssembly::HelixBundleFeatures::min_per_residue_fa_attr_

private

Referenced by get_helix_pairs(), and parse_my_tag().

protocols::simple_filters::InterfaceSasaFilter protocols::features::helixAssembly::HelixBundleFeatures::sasa_filter_

private

core::scoring::ScoreFunctionOP protocols::features::helixAssembly::HelixBundleFeatures::scorefxn_

private

Referenced by HelixBundleFeatures(), and report_features().

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

src/protocols/features/helixAssembly/HelixBundleFeatures.hh
src/protocols/features/helixAssembly/HelixBundleFeatures.cc

Public Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation