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Rosetta 3.5
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Rosetta 3.5
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#include <AtomInResidueAtomInResiduePairFeatures.hh>
Public Member Functions | |
| AtomInResidueAtomInResiduePairFeatures () | |
| AtomInResidueAtomInResiduePairFeatures (AtomInResidueAtomInResiduePairFeatures const &src) | |
| virtual | ~AtomInResidueAtomInResiduePairFeatures () |
| 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... | |
| core::Size | report_features (core::pose::Pose const &pose, utility::vector1< bool > const &relevant_residues, boost::uuids::uuid struct_id, utility::sql_database::sessionOP db_session) |
| collect all the feature data for the pose More... | |
| void | report_atom_pairs (core::pose::Pose const &pose, utility::vector1< bool > const &relevant_residues, boost::uuids::uuid 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... | |
 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 | 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 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_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, 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... | |
Definition at line 39 of file AtomInResidueAtomInResiduePairFeatures.hh.
| protocols::features::AtomInResidueAtomInResiduePairFeatures::AtomInResidueAtomInResiduePairFeatures | ( | ) |
Definition at line 64 of file AtomInResidueAtomInResiduePairFeatures.cc.
| protocols::features::AtomInResidueAtomInResiduePairFeatures::AtomInResidueAtomInResiduePairFeatures | ( | AtomInResidueAtomInResiduePairFeatures const & | src) |
Definition at line 66 of file AtomInResidueAtomInResiduePairFeatures.cc.
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virtual |
Definition at line 70 of file AtomInResidueAtomInResiduePairFeatures.cc.
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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 123 of file AtomInResidueAtomInResiduePairFeatures.cc.
| void protocols::features::AtomInResidueAtomInResiduePairFeatures::report_atom_pairs | ( | core::pose::Pose const & | pose, |
| utility::vector1< bool > const & | relevant_residues, | ||
| boost::uuids::uuid | 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.
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
Definition at line 157 of file AtomInResidueAtomInResiduePairFeatures.cc.
References core::pose::Pose::conformation(), core::graph::Node::const_edge_list_end(), core::pose::Pose::energies(), core::graph::Edge::get_node(), core::chemical::num_canonical_aas, core::pose::Pose::residue(), core::scoring::Energies::residue_neighbors_updated(), core::conformation::Conformation::structure_moved(), core::scoring::Energies::tenA_neighbor_graph(), and core::pose::Pose::total_residue().
Referenced by report_features().
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collect all the feature data for the pose
Implements protocols::features::FeaturesReporter.
Definition at line 130 of file AtomInResidueAtomInResiduePairFeatures.cc.
References report_atom_pairs().
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return string with class name
Reimplemented from protocols::features::FeaturesReporter.
Definition at line 73 of file AtomInResidueAtomInResiduePairFeatures.cc.
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generate the atom_in_residue_pairs table schema
Definition at line 83 of file AtomInResidueAtomInResiduePairFeatures.cc.
Referenced by write_schema_to_db().
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generate the table schemas and write them to the database
Implements protocols::features::FeaturesReporter.
Definition at line 76 of file AtomInResidueAtomInResiduePairFeatures.cc.
References write_atom_in_residue_pairs_table_schema().
1.8.4