#include <LoopAnchorFeatures.hh>

Inheritance diagram for protocols::features::LoopAnchorFeatures:

Collaboration diagram for protocols::features::LoopAnchorFeatures:

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::TagPtr const tag, protocols::moves::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 &, boost::uuids::uuid 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
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_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 (boost::uuids::uuid 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, 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 31 of file LoopAnchorFeatures.hh.

Constructor & Destructor Documentation

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

Definition at line 69 of file LoopAnchorFeatures.cc.

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

Definition at line 76 of file LoopAnchorFeatures.cc.

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

virtual

Definition at line 83 of file LoopAnchorFeatures.cc.

Member Function Documentation

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

private

Definition at line 397 of file LoopAnchorFeatures.cc.

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

Definition at line 415 of file LoopAnchorFeatures.cc.

References core::pose::Pose::residue(), 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

Definition at line 476 of file LoopAnchorFeatures.cc.

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

Referenced by compute_transform_and_write_to_db().

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

private

Definition at line 441 of file LoopAnchorFeatures.cc.

References atoms(), compute_anchor_transform(), compute_atom_angles(), end_residue(), core::scoring::omega, start_residue(), and core::scoring::hbonds::t().

Referenced by report_features().

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

private

Definition at line 352 of file LoopAnchorFeatures.cc.

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

Definition at line 382 of file LoopAnchorFeatures.cc.

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.

Definition at line 233 of file LoopAnchorFeatures.cc.

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

private

Definition at line 347 of file LoopAnchorFeatures.cc.

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

Definition at line 342 of file LoopAnchorFeatures.cc.

References determine_correct_length(), and min_loop_length_.

Referenced by report_features().

void protocols::features::LoopAnchorFeatures::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

Reimplemented from protocols::features::FeaturesReporter.

Definition at line 240 of file LoopAnchorFeatures.cc.

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 &	,
		boost::uuids::uuid	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.

Definition at line 265 of file LoopAnchorFeatures.cc.

References core::conformation::Conformation::chain_endings(), compute_transform_and_write_to_db(), core::pose::Pose::conformation(), core::sequence::end, max_loop_length(), min_loop_length(), 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)

Definition at line 332 of file LoopAnchorFeatures.cc.

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)

Definition at line 337 of file LoopAnchorFeatures.cc.

References use_single_residue_to_define_anchor_transfrom_.

Referenced by report_features().

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

private

Definition at line 367 of file LoopAnchorFeatures.cc.

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.

Definition at line 86 of file LoopAnchorFeatures.cc.

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

Definition at line 137 of file LoopAnchorFeatures.cc.

References core::scoring::omega, protocols::swa::phi(), and protocols::swa::psi().

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

Definition at line 185 of file LoopAnchorFeatures.cc.

References core::scoring::omega, protocols::swa::phi(), and protocols::swa::psi().

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

Definition at line 98 of file LoopAnchorFeatures.cc.

Referenced by write_schema_to_db().

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

virtual