protocols::features::ResidueConformationFeatures Class Reference

#include <ResidueConformationFeatures.hh>

Public Member Functions
	ResidueConformationFeatures ()
	ResidueConformationFeatures (ResidueConformationFeatures const &)
virtual	~ResidueConformationFeatures ()
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...
std::string	type_name () const
	return string with class name More...
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...
void	delete_record (StructureID struct_id, utility::sql_database::sessionOP)
void	load_into_pose (utility::sql_database::sessionOP db_session, StructureID struct_id, core::pose::Pose &pose)
void	load_conformation (utility::sql_database::sessionOP db_session, StructureID struct_id, core::pose::Pose &pose)
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 &)
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	set_coords_for_residue (utility::sql_database::sessionOP db_session, StructureID struct_id, core::Size seqpos, core::pose::Pose &pose)
void	set_coords_for_residue_from_compact_schema (utility::sql_database::sessionOP db_session, StructureID struct_id, core::Size seqpos, core::pose::Pose &pose)

Private Attributes
bool	compact_residue_schema_

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::ResidueConformationFeatures::ResidueConformationFeatures

(

)

References compact_residue_schema_, basic::options::option, and basic::options::OptionKeys::inout::dbms::use_compact_residue_schema.

protocols::features::ResidueConformationFeatures::ResidueConformationFeatures

(

ResidueConformationFeatures const &

)

References compact_residue_schema_, basic::options::option, and basic::options::OptionKeys::inout::dbms::use_compact_residue_schema.

virtual protocols::features::ResidueConformationFeatures::~ResidueConformationFeatures ( )

inlinevirtual

Member Function Documentation

void protocols::features::ResidueConformationFeatures::delete_record ( StructureID  struct_id, utility::sql_database::sessionOP    )

virtual

Reimplemented from protocols::features::FeaturesReporter.

References compact_residue_schema_, basic::database::safely_prepare_statement(), and basic::database::safely_write_to_database().

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

void protocols::features::ResidueConformationFeatures::load_conformation	(	utility::sql_database::sessionOP	db_session,
		StructureID	struct_id,
		core::pose::Pose &	pose
	)

References compact_residue_schema_, core::pose::Pose::is_fullatom(), core::chemical::ResidueType::is_protein(), protocols::stepwise::sampling::protein::omega(), protocols::stepwise::sampling::protein::phi(), protocols::stepwise::sampling::protein::psi(), core::pose::Pose::residue_type(), basic::database::safely_prepare_statement(), basic::database::safely_read_from_database(), core::pose::Pose::set_chi(), set_coords_for_residue(), set_coords_for_residue_from_compact_schema(), core::pose::Pose::set_omega(), core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), and table_exists().

Referenced by load_into_pose().

void protocols::features::ResidueConformationFeatures::load_into_pose ( utility::sql_database::sessionOP  db_session, StructureID  struct_id, core::pose::Pose &  pose  )

virtual

Reimplemented from protocols::features::FeaturesReporter.

References load_conformation().

Size protocols::features::ResidueConformationFeatures::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.

References core::conformation::Residue::aa(), basic::database::insert_statement_generator::InsertGenerator::add_column(), basic::database::insert_statement_generator::InsertGenerator::add_row(), protocols::features::FeaturesReporter::check_relevant_residues(), core::conformation::Residue::chi(), compact_residue_schema_, core::pose::Pose::conformation(), basic::options::OptionKeys::out::file::force_nonideal_structure, core::conformation::is_ideal_position(), core::conformation::Residue::is_ligand(), core::conformation::Residue::mainchain_torsion(), utility::tools::make_vector(), core::pose::Pose::n_residue(), core::conformation::Residue::natoms(), core::conformation::Residue::nchi(), num_canonical_aas, protocols::stepwise::sampling::protein::omega(), basic::options::option, protocols::stepwise::sampling::protein::phi(), protocols::stepwise::sampling::protein::psi(), resi, core::pose::Pose::residue(), protocols::features::serialize_residue_xyz_coords(), core::pose::Pose::total_residue(), basic::database::insert_statement_generator::InsertGenerator::write_to_database(), numeric::xyzVector< class >::x(), core::conformation::Residue::xyz(), numeric::xyzVector< class >::y(), and numeric::xyzVector< class >::z().

void protocols::features::ResidueConformationFeatures::set_coords_for_residue ( utility::sql_database::sessionOP  db_session, StructureID  struct_id, core::Size  seqpos, core::pose::Pose &  pose  )

private

References basic::database::safely_prepare_statement(), basic::database::safely_read_from_database(), and core::pose::Pose::set_xyz().

Referenced by load_conformation().

void protocols::features::ResidueConformationFeatures::set_coords_for_residue_from_compact_schema ( utility::sql_database::sessionOP  db_session, StructureID  struct_id, core::Size  seqpos, core::pose::Pose &  pose  )

private

References protocols::features::deserialize_xyz_coords(), basic::database::safely_prepare_statement(), basic::database::safely_read_from_database(), and core::pose::Pose::set_xyz().

Referenced by load_conformation().

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

virtual

return string with class name

Reimplemented from protocols::features::FeaturesReporter.

void protocols::features::ResidueConformationFeatures::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(), compact_residue_schema_, protocols::stepwise::sampling::protein::omega(), protocols::stepwise::sampling::protein::phi(), protocols::stepwise::sampling::protein::psi(), and basic::database::schema_generator::Schema::write().

Member Data Documentation

bool protocols::features::ResidueConformationFeatures::compact_residue_schema_

private

Referenced by delete_record(), load_conformation(), report_features(), ResidueConformationFeatures(), and write_schema_to_db().

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

• symlinks/rosetta/src/protocols/features/ResidueConformationFeatures.hh
• symlinks/rosetta/src/protocols/features/ResidueConformationFeatures.cc