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Rosetta
2021.16
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Rosetta
2021.16
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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 More... | |
| bool | evaluate_residues (core::conformation::Residue const &candidate_res, core::conformation::Residue const &target_res) const override |
| 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... | |
| bool | require_candidate_residue_atoms_to_lie_near_target_atom (core::Size target_atom_id) const override |
| 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... | |
| utility::vector1< core::Size > | candidate_res_atoms_reqd_near_target_atom (core::Size target_atom_id) const override |
| 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... | |
| Real | max_separation_dist_to_target_atom (core::Size target_atom_id) const override |
| 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... | |
| std::string | print (core::chemical::ResidueTypeCOP candidate_restype, core::chemical::ResidueTypeCOP target_restype) const override |
 Public Member Functions inherited from protocols::match::downstream::AtomGeometrySecMatchRPE | |
| AtomGeometrySecMatchRPE (protocols::toolbox::match_enzdes_util::GeomSampleInfo const &gsi) | |
| ~AtomGeometrySecMatchRPE () override | |
| bool | require_all_target_residue_atom_coordinates () const override |
| 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... | |
| bool | require_target_atom_coordinate (core::Size target_atom_id) const override |
| 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... | |
| bool | check_value (core::Real value) const |
| determines if the passed in value is between lowval and highval More... | |
| utility::vector1< SizePair > const & | at_inds () const |
| void | add_at_ind (core::Size which_cst_res, core::Size atom_ind_in_res) |
| core::Real | lowval () const |
| core::Real | highval () const |
| Public Member Functions inherited from protocols::match::downstream::SecMatchResiduePairEvaluator | |
| SecMatchResiduePairEvaluator () | |
| ~SecMatchResiduePairEvaluator () override | |
Additional Inherited Members | |
| Public Types inherited from protocols::match::downstream::AtomGeometrySecMatchRPE | |
| typedef std::pair< core::Size, core::Size > | SizePair |
| typedef core::Real | Real |
| Public Types inherited from protocols::match::downstream::SecMatchResiduePairEvaluator | |
| typedef core::Size | Size |
| typedef core::Real | Real |
| Protected Member Functions inherited from protocols::match::downstream::AtomGeometrySecMatchRPE | |
| void | clear_at_inds () |
| void | set_lowval (core::Real lowval) |
| void | set_highval (core::Real highval) |
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().
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overridevirtual |
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().
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overridevirtual |
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().
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overridevirtual |
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().
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overridevirtual |
Implements protocols::match::downstream::AtomGeometrySecMatchRPE.
References protocols::match::downstream::AtomGeometrySecMatchRPE::at_inds(), protocols::match::downstream::AtomGeometrySecMatchRPE::highval(), protocols::match::downstream::AtomGeometrySecMatchRPE::lowval(), and core::id::to_string().
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overridevirtual |
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().
1.8.7