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protocols::match::downstream::SecMatchResiduePairEvaluator Class Referenceabstract

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>

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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< Sizecandidate_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...
 

Detailed Description

base for class used by secondary matcher to determine whether a given residue to be matched interacts satisfactorily with a target residue

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::match::downstream::SecMatchResiduePairEvaluator::SecMatchResiduePairEvaluator ( )
protocols::match::downstream::SecMatchResiduePairEvaluator::~SecMatchResiduePairEvaluator ( )
virtual

Member Function Documentation

utility::vector1< SecMatchResiduePairEvaluator::Size > protocols::match::downstream::SecMatchResiduePairEvaluator::candidate_res_atoms_reqd_near_target_atom ( Size  target_atom_id) const
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.

virtual bool protocols::match::downstream::SecMatchResiduePairEvaluator::evaluate_residues ( core::conformation::Residue const &  candidate_res,
core::conformation::Residue const &  target_res 
) const
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.

SecMatchResiduePairEvaluator::Real protocols::match::downstream::SecMatchResiduePairEvaluator::max_separation_dist_to_target_atom ( Size  target_atom_id) const
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.

virtual bool protocols::match::downstream::SecMatchResiduePairEvaluator::require_all_target_residue_atom_coordinates ( ) const
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.

bool protocols::match::downstream::SecMatchResiduePairEvaluator::require_candidate_residue_atoms_to_lie_near_target_atom ( Size  target_atom_id) const
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.

virtual bool protocols::match::downstream::SecMatchResiduePairEvaluator::require_target_atom_coordinate ( Size  target_atom_id) const
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.


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