#include <AtomInResidueAtomInResiduePairFeatures.hh>
Public Member Functions | |
| AtomInResidueAtomInResiduePairFeatures () | |
| void | write_schema_to_db (utility::sql_database::sessionOP db_session) const override |
| return string with class name 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 |
| collect all the feature data for the pose More... | |
| void | report_atom_pairs (core::pose::Pose const &pose, utility::vector1< bool > const &relevant_residues, StructureID struct_id, utility::sql_database::sessionOP db_session) |
| Similar to radial density distributions defined in Lu H, Skolnick J. A distance-dependent atomic knowledge-based potential for improved protein structure selection. Proteins. 2001;44(3):223-32. Available at: http://www.ncbi.nlm.nih.gov/pubmed/11455595. More... | |
| 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 &) |
| 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 |
Static Public Member Functions | |
| static std::string | class_name () |
| static void | provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd) |
Private Member Functions | |
| void | write_atom_in_residue_pairs_table_schema (utility::sql_database::sessionOP db_session) const |
| generate the atom_in_residue_pairs table schema More... | |
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
◆ AtomInResidueAtomInResiduePairFeatures()
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default |
Member Function Documentation
◆ class_name()
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static |
◆ features_reporter_dependencies()
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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.
◆ provide_xml_schema()
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static |
◆ report_atom_pairs()
| void protocols::features::AtomInResidueAtomInResiduePairFeatures::report_atom_pairs | ( | core::pose::Pose const & | pose, |
| utility::vector1< bool > const & | relevant_residues, | ||
| StructureID | struct_id, | ||
| utility::sql_database::sessionOP | db_session | ||
| ) |
Similar to radial density distributions defined in Lu H, Skolnick J. A distance-dependent atomic knowledge-based potential for improved protein structure selection. Proteins. 2001;44(3):223-32. Available at: http://www.ncbi.nlm.nih.gov/pubmed/11455595.
@detail This is very similar in spirit to the potential described in
Lu H, Skolnick J. A distance-dependent atomic knowledge-based potential for improved protein structure selection. Proteins. 2001;44(3):223-32. Available at: http://www.ncbi.nlm.nih.gov/pubmed/11455595.
However, they use different distance bins. Here, [0,1), ..., [9,10) are used because they are easy and as they report the the paper, most of the signal comes in the 3.5-6.5 range. To get the molar fraction of atom types–since the types are unique within each residue type, there is exactly one per residue of that type. Therefore this information can be extracted from the Residues table when needed. It may make sense to include it here if it turns to to be too cumbersom to get those quantities.
TODO: Expand for not just canonical residue types
References core::conformation::Residue::aa(), protocols::features::FeaturesReporter::check_relevant_residues(), core::pose::Pose::conformation(), core::pose::Pose::energies(), core::conformation::Residue::natoms(), core::chemical::num_canonical_aas, core::pose::Pose::residue(), core::scoring::Energies::residue_neighbors_updated(), core::pose::Pose::size(), core::conformation::Conformation::structure_moved(), core::scoring::Energies::tenA_neighbor_graph(), and core::conformation::Residue::xyz().
Referenced by report_features().
◆ report_features()
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overridevirtual |
collect all the feature data for the pose
Implements protocols::features::FeaturesReporter.
References report_atom_pairs().
◆ type_name()
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overridevirtual |
Reimplemented from protocols::features::FeaturesReporter.
References class_name().
◆ write_atom_in_residue_pairs_table_schema()
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private |
generate the atom_in_residue_pairs table schema
Referenced by write_schema_to_db().
◆ write_schema_to_db()
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overridevirtual |
return string with class name
generate the table schemas and write them to the database
Implements protocols::features::FeaturesReporter.
References write_atom_in_residue_pairs_table_schema().
The documentation for this class was generated from the following files:
- src/protocols/features/AtomInResidueAtomInResiduePairFeatures.hh
- src/protocols/features/AtomInResidueAtomInResiduePairFeatures.cc
