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Rosetta Protocols
2014.35
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Rosetta Protocols
2014.35
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base for class used by secondary matcher to determine whether a given residue to be matched interacts satisfactorily with a target residue More...
#include <SecMatchResiduePairEvaluator.hh>
Public Types | |
| typedef core::Size | Size |
| typedef core::Real | Real |
Public Member Functions | |
| SecMatchResiduePairEvaluator () | |
| virtual | ~SecMatchResiduePairEvaluator () |
| virtual bool | evaluate_residues (core::conformation::Residue const &candidate_res, core::conformation::Residue const &target_res) const =0 |
| Returns true if the interaction between the two residues satisifies the secondary match requirement. candidate_res: the rotamer of the residue trying to be placed target_res: the previously placed residue. More... | |
| virtual bool | require_all_target_residue_atom_coordinates () const =0 |
| Returns true if all coordinates of the target residue are required in order to evaluate the interaction between the candidate and the target residues. More... | |
| virtual bool | require_target_atom_coordinate (Size target_atom_id) const =0 |
| If require_all_target_residue_atom_coordinates() returns false, then this method should return true for the atoms on the target residue that the evaluator requires. More... | |
| virtual bool | require_candidate_residue_atoms_to_lie_near_target_atom (Size target_atom_id) const |
| Are there atoms of the candidate residue that must be within some cutoff distance of a given atom on the target residue? Base class implementation returns false. More... | |
| virtual utility::vector1< Size > | candidate_res_atoms_reqd_near_target_atom (Size target_atom_id) const |
| Return a list of atom indices on the candidate residue; if all atoms in this list are further than max_separation_dist_to_target_atom() away from the target_atom_id atom for a given pair of conformations of the target_residue and the candidate_residue, then this evaluator will return false in the call to evaluate( candidate_residue, target_residue ). This list will allow the SecondaryMatcher to (conservatively!) prune conformations of the candidate_residue from consideration. The base class implements a noop – it returns an empty list. More... | |
| virtual Real | max_separation_dist_to_target_atom (Size target_atom_id) const |
| Return the maximum separation distance that any of the match-residue atoms identified by the function match_atoms_reqd_near_target_atom may be from a particular atom on the target residue. Returns a negative value if there is no requirement that any atom be within a certain radius of the target atom. The base class implementation returns -1.0. More... | |
base for class used by secondary matcher to determine whether a given residue to be matched interacts satisfactorily with a target residue
| protocols::match::downstream::SecMatchResiduePairEvaluator::SecMatchResiduePairEvaluator | ( | ) |
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virtual |
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virtual |
Return a list of atom indices on the candidate residue; if all atoms in this list are further than max_separation_dist_to_target_atom() away from the target_atom_id atom for a given pair of conformations of the target_residue and the candidate_residue, then this evaluator will return false in the call to evaluate( candidate_residue, target_residue ). This list will allow the SecondaryMatcher to (conservatively!) prune conformations of the candidate_residue from consideration. The base class implements a noop – it returns an empty list.
Reimplemented in protocols::match::downstream::GeometrySecMatchRPE, and protocols::match::downstream::AtomDistanceSecMatchRPE.
References empty.
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pure virtual |
Returns true if the interaction between the two residues satisifies the secondary match requirement. candidate_res: the rotamer of the residue trying to be placed target_res: the previously placed residue.
Implemented in protocols::match::downstream::GeometrySecMatchRPE, protocols::match::downstream::AtomDihedralSecMatchRPE, protocols::match::downstream::AtomAngleSecMatchRPE, protocols::match::downstream::AtomDistanceSecMatchRPE, protocols::match::downstream::ScoringSecMatchRPE, and protocols::match::downstream::AtomGeometrySecMatchRPE.
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virtual |
Return the maximum separation distance that any of the match-residue atoms identified by the function match_atoms_reqd_near_target_atom may be from a particular atom on the target residue. Returns a negative value if there is no requirement that any atom be within a certain radius of the target atom. The base class implementation returns -1.0.
Reimplemented in protocols::match::downstream::GeometrySecMatchRPE, and protocols::match::downstream::AtomDistanceSecMatchRPE.
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pure virtual |
Returns true if all coordinates of the target residue are required in order to evaluate the interaction between the candidate and the target residues.
Implemented in protocols::match::downstream::GeometrySecMatchRPE, protocols::match::downstream::ScoringSecMatchRPE, and protocols::match::downstream::AtomGeometrySecMatchRPE.
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virtual |
Are there atoms of the candidate residue that must be within some cutoff distance of a given atom on the target residue? Base class implementation returns false.
Reimplemented in protocols::match::downstream::GeometrySecMatchRPE, and protocols::match::downstream::AtomDistanceSecMatchRPE.
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pure virtual |
If require_all_target_residue_atom_coordinates() returns false, then this method should return true for the atoms on the target residue that the evaluator requires.
Implemented in protocols::match::downstream::GeometrySecMatchRPE, protocols::match::downstream::ScoringSecMatchRPE, and protocols::match::downstream::AtomGeometrySecMatchRPE.
1.8.7