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Rosetta 3.5
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Rosetta 3.5
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#include <ProteinBackboneAtomAtomPairFeatures.hh>
Public Member Functions | |
| ProteinBackboneAtomAtomPairFeatures () | |
| ProteinBackboneAtomAtomPairFeatures (ProteinBackboneAtomAtomPairFeatures const &src) | |
| virtual | ~ProteinBackboneAtomAtomPairFeatures () |
| 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... | |
 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_protein_backbone_atom_atom_pairs_table_schema (utility::sql_database::sessionOP db_session) const |
| generate the protein_backbone_atom_atom_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 ProteinBackboneAtomAtomPairFeatures.hh.
| protocols::features::ProteinBackboneAtomAtomPairFeatures::ProteinBackboneAtomAtomPairFeatures | ( | ) |
Definition at line 58 of file ProteinBackboneAtomAtomPairFeatures.cc.
| protocols::features::ProteinBackboneAtomAtomPairFeatures::ProteinBackboneAtomAtomPairFeatures | ( | ProteinBackboneAtomAtomPairFeatures const & | src) |
Definition at line 60 of file ProteinBackboneAtomAtomPairFeatures.cc.
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virtual |
Definition at line 64 of file ProteinBackboneAtomAtomPairFeatures.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 166 of file ProteinBackboneAtomAtomPairFeatures.cc.
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collect all the feature data for the pose
These atom-atom pairs follow the analysis done in:
Song Y, Tyka M, Leaver-Fay A, Thompson J, Baker D. Structure guided forcefield optimization. Proteins: Structure, Function, and Bioinformatics. 2011:n/a-n/a. Available at: http://doi.wiley.com/10.1002/prot.23013 [Accessed April 4, 2011].
The HBond geometries are recoded in the HBondFeatures reporter
Implements protocols::features::FeaturesReporter.
Definition at line 181 of file ProteinBackboneAtomAtomPairFeatures.cc.
References core::conformation::Residue::aa(), core::chemical::aa_gly, core::graph::Node::const_edge_list_end(), core::pose::Pose::energies(), core::graph::Edge::get_node(), core::conformation::Residue::is_protein(), core::pose::Pose::residue(), core::scoring::Energies::tenA_neighbor_graph(), core::pose::Pose::total_residue(), and core::conformation::Residue::xyz().
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return string with class name
Reimplemented from protocols::features::FeaturesReporter.
Definition at line 67 of file ProteinBackboneAtomAtomPairFeatures.cc.
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generate the protein_backbone_atom_atom_pairs table schema
Definition at line 77 of file ProteinBackboneAtomAtomPairFeatures.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 70 of file ProteinBackboneAtomAtomPairFeatures.cc.
References write_protein_backbone_atom_atom_pairs_table_schema().
1.8.4