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Rosetta 3.4
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Rosetta 3.4
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RPE to figure out if two atoms are within a given distance atoms need to be set through the parent class add_at_ind function. More...
#include <GeometrySecMatchRPE.hh>
Public Member Functions | |
| AtomDistanceSecMatchRPE (protocols::toolbox::match_enzdes_util::GeomSampleInfo const &gsi) | |
| the constructor for this rpe sets the lowval and highval to the squared values of the initial values, that should make distance evaluation faster | |
| virtual bool | evaluate_residues (core::conformation::Residue const &candidate_res, core::conformation::Residue const &target_res) const |
| 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. | |
| 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. | |
| 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. | |
| 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. | |
| virtual std::string | print (core::chemical::ResidueTypeCAP candidate_restype, core::chemical::ResidueTypeCAP target_restype) const |
RPE to figure out if two atoms are within a given distance atoms need to be set through the parent class add_at_ind function.
| protocols::match::downstream::AtomDistanceSecMatchRPE::AtomDistanceSecMatchRPE | ( | protocols::toolbox::match_enzdes_util::GeomSampleInfo const & | gsi | ) |
the constructor for this rpe sets the lowval and highval to the squared values of the initial values, that should make distance evaluation faster
References protocols::match::downstream::AtomGeometrySecMatchRPE::highval(), protocols::match::downstream::AtomGeometrySecMatchRPE::lowval(), protocols::match::downstream::AtomGeometrySecMatchRPE::set_highval(), and protocols::match::downstream::AtomGeometrySecMatchRPE::set_lowval().
| utility::vector1< AtomDistanceSecMatchRPE::Size > protocols::match::downstream::AtomDistanceSecMatchRPE::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 from protocols::match::downstream::SecMatchResiduePairEvaluator.
References protocols::match::downstream::AtomGeometrySecMatchRPE::at_inds().
| bool protocols::match::downstream::AtomDistanceSecMatchRPE::evaluate_residues | ( | core::conformation::Residue const & | candidate_res, |
| core::conformation::Residue const & | target_res | ||
| ) | const [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.
Implements protocols::match::downstream::AtomGeometrySecMatchRPE.
References protocols::match::downstream::AtomGeometrySecMatchRPE::at_inds(), protocols::match::downstream::AtomGeometrySecMatchRPE::check_value(), core::kinematics::tree::distance_squared(), and core::conformation::Residue::xyz().
| AtomDistanceSecMatchRPE::Real protocols::match::downstream::AtomDistanceSecMatchRPE::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 from protocols::match::downstream::SecMatchResiduePairEvaluator.
References protocols::match::downstream::AtomGeometrySecMatchRPE::at_inds(), and protocols::match::downstream::AtomGeometrySecMatchRPE::highval().
| std::string protocols::match::downstream::AtomDistanceSecMatchRPE::print | ( | core::chemical::ResidueTypeCAP | candidate_restype, |
| core::chemical::ResidueTypeCAP | target_restype | ||
| ) | const [virtual] |
| bool protocols::match::downstream::AtomDistanceSecMatchRPE::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 from protocols::match::downstream::SecMatchResiduePairEvaluator.
References protocols::match::downstream::AtomGeometrySecMatchRPE::at_inds().
1.7.4
