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protocols::features::ProteinResidueConformationFeatures Class Reference

#include <ProteinResidueConformationFeatures.hh>

Inheritance diagram for protocols::features::ProteinResidueConformationFeatures:
Inheritance graph
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Public Member Functions

 ProteinResidueConformationFeatures ()
 
void write_schema_to_db (utility::sql_database::sessionOP db_session) const override
 generate the table schemas and write them to the database More...
 
utility::vector1< std::string > features_reporter_dependencies () const override
 return the set of features reporters that are required to also already be extracted by the time this one is used. 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) override
 return string with class name More...
 
void delete_record (StructureID struct_id, utility::sql_database::sessionOP db_session) override
 
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)
 
std::string type_name () const override
 
- Public Member Functions inherited from protocols::features::FeaturesReporter
 FeaturesReporter ()
 
 ~FeaturesReporter () override
 Automatically generated virtual destructor for class deriving directly from VirtualBase. 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 &)
 
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
 

Static Public Member Functions

static std::string class_name ()
 
static void provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
 

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 ( )

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
std::string protocols::features::ProteinResidueConformationFeatures::class_name ( )
static
void protocols::features::ProteinResidueConformationFeatures::delete_record ( StructureID  struct_id,
utility::sql_database::sessionOP  db_session 
)
overridevirtual
utility::vector1< std::string > protocols::features::ProteinResidueConformationFeatures::features_reporter_dependencies ( ) const
overridevirtual

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 
)
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().

void protocols::features::ProteinResidueConformationFeatures::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
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 
)
overridevirtual
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
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(), and protocols::features::TR().

Referenced by load_conformation().

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

Reimplemented from protocols::features::FeaturesReporter.

References class_name().

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

generate the table schemas and write them to the database

Implements protocols::features::FeaturesReporter.

References compact_residue_schema_, and core::scoring::omega.

Member Data Documentation

bool protocols::features::ProteinResidueConformationFeatures::compact_residue_schema_
private

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