#include <LoopAnchorFeatures.hh>

Public Member Functions
	LoopAnchorFeatures ()

	LoopAnchorFeatures (LoopAnchorFeatures const &)

virtual	~LoopAnchorFeatures ()

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::TagCOP tag, basic::datacache::DataMap &, 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 &, StructureID struct_id, utility::sql_database::sessionOP db_session)
	collect all the feature data for the pose More...

void	set_use_relevant_residues_as_loop_length (bool const use_relevant_residues_as_loop_length)

void	set_use_single_residue_to_define_anchor_transfrom (bool const use_single_residue_to_define_anchor_transfrom)

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 Member Functions
void	write_loop_anchors_table_schema (utility::sql_database::sessionOP db_session) const
	generate the loop_anchors table schema More...

void	write_loop_anchor_transforms_table_schema (utility::sql_database::sessionOP db_session) const
	generate the loop_anchor_transforms table schema More...

void	write_loop_anchor_transforms_three_res_table_schema (utility::sql_database::sessionOP db_session) const
	generate the loop_anchor_transforms_three_res table schema More...

utility::vector1< Size >	start_residue (Size resNo)

utility::vector1< Size >	end_residue (Size resNo)

utility::vector1< Size >	atoms ()

core::Size	min_loop_length (utility::vector1< bool > const &relevant_residue)

core::Size	max_loop_length (utility::vector1< bool > const &relevant_residue)

core::Size	determine_correct_length (utility::vector1< bool > const &relevant_residue, Size default_length)

numeric::HomogeneousTransform < core::Real >	compute_anchor_transform (core::pose::Pose const &pose, utility::vector1< core::Size > const &residue_begin, utility::vector1< core::Size > const &residue_end, utility::vector1< core::Size > const &atoms)

void	compute_transform_and_write_to_db (StructureID struct_id, core::Size begin, core::Size end, core::pose::Pose const &pose, cppdb::statement &stmt)

core::Real	compute_atom_angles (core::pose::Pose const &pose, utility::vector1< core::Size > const &residues, utility::vector1< core::Size > const &atoms)

Private Attributes
bool	use_relevant_residues_as_loop_length_

bool	use_single_residue_to_define_anchor_transfrom_

core::Size	min_loop_length_

core::Size	max_loop_length_

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::LoopAnchorFeatures::LoopAnchorFeatures ( )

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

protocols::features::LoopAnchorFeatures::~LoopAnchorFeatures ( )

virtual

Member Function Documentation

vector1< Size > protocols::features::LoopAnchorFeatures::atoms ( )

private

References use_single_residue_to_define_anchor_transfrom_.

Referenced by compute_transform_and_write_to_db().

HomogeneousTransform< Real > protocols::features::LoopAnchorFeatures::compute_anchor_transform	(	core::pose::Pose const &	pose,
		utility::vector1< core::Size > const &	residue_begin,
		utility::vector1< core::Size > const &	residue_end,
		utility::vector1< core::Size > const &	atoms
	)

private

References core::pose::Pose::residue(), runtime_assert_string_msg, and core::conformation::Residue::xyz().

Referenced by compute_transform_and_write_to_db().

Real protocols::features::LoopAnchorFeatures::compute_atom_angles	(	core::pose::Pose const &	pose,
		utility::vector1< core::Size > const &	residues,
		utility::vector1< core::Size > const &	atoms
	)

private

References numeric::arccos(), core::pose::Pose::residue(), runtime_assert_string_msg, and core::conformation::Residue::xyz().

Referenced by compute_transform_and_write_to_db().

void protocols::features::LoopAnchorFeatures::compute_transform_and_write_to_db	(	StructureID	struct_id,
		core::Size	begin,
		core::Size	end,
		core::pose::Pose const &	pose,
		cppdb::statement &	stmt
	)

private

References atoms(), compute_anchor_transform(), compute_atom_angles(), end_residue(), numeric::HomogeneousTransform< T >::euler_angles_rad(), protocols::stepwise::sampling::protein::omega(), numeric::HomogeneousTransform< T >::point(), basic::database::safely_write_to_database(), start_residue(), and t.

Referenced by report_features().

Size protocols::features::LoopAnchorFeatures::determine_correct_length	(	utility::vector1< bool > const &	relevant_residue,
		Size	default_length
	)

private

References use_relevant_residues_as_loop_length_.

Referenced by max_loop_length(), and min_loop_length().

vector1< Size > protocols::features::LoopAnchorFeatures::end_residue ( Size resNo )

private

References use_single_residue_to_define_anchor_transfrom_.

Referenced by compute_transform_and_write_to_db().

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

Size protocols::features::LoopAnchorFeatures::max_loop_length ( utility::vector1< bool > const & relevant_residue )

private

References determine_correct_length(), and max_loop_length_.

Referenced by report_features().

Size protocols::features::LoopAnchorFeatures::min_loop_length ( utility::vector1< bool > const & relevant_residue )

private

References determine_correct_length(), and min_loop_length_.

Referenced by report_features().

void protocols::features::LoopAnchorFeatures::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

Reimplemented from protocols::features::FeaturesReporter.

References max_loop_length_, min_loop_length_, and set_use_relevant_residues_as_loop_length().

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

virtual

collect all the feature data for the pose

An anchor is a take off and landing for a loop. Every residue in the loop must be relevant in order for the loop to be stored.

Implements protocols::features::FeaturesReporter.

References begin, core::conformation::Conformation::chain_endings(), compute_transform_and_write_to_db(), core::pose::Pose::conformation(), end, max_loop_length(), min_loop_length(), safely_prepare_statement(), basic::database::safely_write_to_database(), set_use_single_residue_to_define_anchor_transfrom(), and core::pose::Pose::total_residue().

void protocols::features::LoopAnchorFeatures::set_use_relevant_residues_as_loop_length ( bool const use_relevant_residues_as_loop_length )

References use_relevant_residues_as_loop_length_.

Referenced by parse_my_tag().

void protocols::features::LoopAnchorFeatures::set_use_single_residue_to_define_anchor_transfrom ( bool const use_single_residue_to_define_anchor_transfrom )

References use_single_residue_to_define_anchor_transfrom_.

Referenced by report_features().

vector1< Size > protocols::features::LoopAnchorFeatures::start_residue ( Size resNo )

private

References use_single_residue_to_define_anchor_transfrom_.

Referenced by compute_transform_and_write_to_db().

string protocols::features::LoopAnchorFeatures::type_name ( ) const

virtual

return string with class name

Reimplemented from protocols::features::FeaturesReporter.

void protocols::features::LoopAnchorFeatures::write_loop_anchor_transforms_table_schema ( utility::sql_database::sessionOP db_session ) const

private

generate the loop_anchor_transforms table schema

References basic::database::schema_generator::Schema::add_column(), basic::database::schema_generator::Schema::add_foreign_key(), protocols::stepwise::sampling::protein::omega(), protocols::stepwise::sampling::protein::phi(), protocols::stepwise::sampling::protein::psi(), table, and basic::database::schema_generator::Schema::write().

Referenced by write_schema_to_db().

void protocols::features::LoopAnchorFeatures::write_loop_anchor_transforms_three_res_table_schema ( utility::sql_database::sessionOP db_session ) const

private

generate the loop_anchor_transforms_three_res table schema

References basic::database::schema_generator::Schema::add_column(), basic::database::schema_generator::Schema::add_foreign_key(), protocols::stepwise::sampling::protein::omega(), protocols::stepwise::sampling::protein::phi(), protocols::stepwise::sampling::protein::psi(), table, and basic::database::schema_generator::Schema::write().

Referenced by write_schema_to_db().

void protocols::features::LoopAnchorFeatures::write_loop_anchors_table_schema ( utility::sql_database::sessionOP db_session ) const

private

generate the loop_anchors table schema

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

Referenced by write_schema_to_db().

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

virtual

generate the table schemas and write them to the database