protocols::features::ProteinResidueConformationFeatures Class Reference

#include <ProteinResidueConformationFeatures.hh>

Public Member Functions
	ProteinResidueConformationFeatures ()
	ProteinResidueConformationFeatures (ProteinResidueConformationFeatures const &)
virtual	~ProteinResidueConformationFeatures ()
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 db_session)
void	load_into_pose (utility::sql_database::sessionOP db_session, StructureID struct_id, core::pose::Pose &pose, bool ideal)
void	load_conformation (utility::sql_database::sessionOP db_session, StructureID struct_id, core::pose::Pose &pose, bool ideal)
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 &)
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	check_num_requested_atoms (core::Size num_requested_atoms, core::Size pose_resNum, core::pose::Pose &pose, core::Size resNum, StructureID struct_id, utility::sql_database::sessionOP db_session) const
void	set_coords_for_residues (utility::sql_database::sessionOP db_session, StructureID struct_id, core::pose::Pose &pose)
void	set_coords_for_residue_from_compact_schema (utility::sql_database::sessionOP db_session, StructureID struct_id, 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::ProteinResidueConformationFeatures::ProteinResidueConformationFeatures

(

)

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

protocols::features::ProteinResidueConformationFeatures::ProteinResidueConformationFeatures

(

ProteinResidueConformationFeatures const &

)

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

virtual protocols::features::ProteinResidueConformationFeatures::~ProteinResidueConformationFeatures ( )

inlinevirtual

Member Function Documentation

void protocols::features::ProteinResidueConformationFeatures::check_num_requested_atoms ( core::Size  num_requested_atoms, core::Size  pose_resNum, core::pose::Pose &  pose, core::Size  resNum, StructureID  struct_id, utility::sql_database::sessionOP  db_session  ) const

private

References core::conformation::change_cys_state(), core::pose::Pose::conformation(), core::chemical::ResidueType::name(), core::chemical::ResidueType::natoms(), core::pose::Pose::residue_type(), basic::database::safely_prepare_statement(), basic::database::safely_read_from_database(), and utility_exit_with_message.

Referenced by set_coords_for_residues().

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

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::ProteinResidueConformationFeatures::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::ProteinResidueConformationFeatures::load_conformation	(	utility::sql_database::sessionOP	db_session,
		StructureID	struct_id,
		core::pose::Pose &	pose,
		bool	ideal
	)

Parameters

[in]

ideal

- Is the input structure ideal? If so, load backbone torsions into pose

References compact_residue_schema_, core::pose::Pose::is_fullatom(), core::chemical::ResidueType::is_protein(), core::chemical::ResidueType::nchi(), omega, core::pose::Pose::residue_type(), basic::database::safely_prepare_statement(), basic::database::safely_read_from_database(), secstruct, core::pose::Pose::set_chi(), set_coords_for_residue_from_compact_schema(), set_coords_for_residues(), core::pose::Pose::set_omega(), core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), core::pose::Pose::set_secstruct(), basic::database::table_exists(), and protocols::features::TR.

Referenced by load_into_pose().

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

Parameters

[in]

ideal

- Is the input structure ideal?

References load_conformation().

Size protocols::features::ProteinResidueConformationFeatures::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(), protocols::simple_filters::coords(), basic::options::OptionKeys::out::file::force_nonideal_structure, fullatom, core::pose::Pose::is_fullatom(), core::conformation::is_ideal_position(), 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, omega, basic::options::option, resi, core::pose::Pose::residue(), core::pose::Pose::secstruct(), secstruct, 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::ProteinResidueConformationFeatures::set_coords_for_residue_from_compact_schema ( utility::sql_database::sessionOP  db_session, StructureID  struct_id, core::pose::Pose &  pose  )

private

References protocols::simple_filters::coords(), 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().

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

private

This is a little complicated: PoseConformationFeatures: renumbers the pose then reports the relevant residues ResidueFeatures: doesn't renumber the pose and reports the relevant residues ProteinResidueConformationFeatures: don't renumber the pose but also only report features for (canonical) protein residues

This means that to reconstruct the pose conformation, first the conformations stored in residue_atom_coords must be aligned with residues table to get the appropriate gaps for non-canonical residues, then these need to be renumbered to align with the renumbered pose reported in PoseConformationFEatures

pose_resNum -> the numbering in the pose to be filled resNum -> the numbering in the residues table

References core::pose::Pose::batch_set_xyz(), check_num_requested_atoms(), protocols::simple_filters::coords(), basic::database::safely_prepare_statement(), basic::database::safely_read_from_database(), and protocols::features::TR.

Referenced by load_conformation().

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

virtual

return string with class name

Reimplemented from protocols::features::FeaturesReporter.

void protocols::features::ProteinResidueConformationFeatures::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_, omega, secstruct, and basic::database::schema_generator::Schema::write().

Member Data Documentation

bool protocols::features::ProteinResidueConformationFeatures::compact_residue_schema_

private

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

---

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

• src/protocols/features/ProteinResidueConformationFeatures.hh
• src/protocols/features/ProteinResidueConformationFeatures.cc