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Rosetta 3.5
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Rosetta 3.5
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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... | |
| 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. 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... | |
| virtual std::string | print (core::chemical::ResidueTypeCOP candidate_restype, core::chemical::ResidueTypeCOP target_restype) const |
 Public Member Functions inherited from protocols::match::downstream::AtomGeometrySecMatchRPE | |
| AtomGeometrySecMatchRPE (protocols::toolbox::match_enzdes_util::GeomSampleInfo const &gsi) | |
| ~AtomGeometrySecMatchRPE () | |
| virtual bool | require_all_target_residue_atom_coordinates () const |
| 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 |
| 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 () | |
| virtual | ~SecMatchResiduePairEvaluator () |
Additional Inherited Members | |
| Public Types inherited from protocols::match::downstream::AtomGeometrySecMatchRPE | |
| typedef std::pair< core::Size, core::Size > | SizePair |
| 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.
Definition at line 133 of file GeometrySecMatchRPE.hh.
| 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
Definition at line 115 of file GeometrySecMatchRPE.cc.
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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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.
Definition at line 174 of file GeometrySecMatchRPE.cc.
References protocols::match::downstream::AtomGeometrySecMatchRPE::at_inds().
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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.
Definition at line 126 of file GeometrySecMatchRPE.cc.
References protocols::match::downstream::AtomGeometrySecMatchRPE::at_inds(), protocols::match::downstream::AtomGeometrySecMatchRPE::check_value(), core::kinematics::tree::distance_squared(), core::io::serialization::size(), and core::conformation::Residue::xyz().
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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.
Definition at line 188 of file GeometrySecMatchRPE.cc.
References protocols::match::downstream::AtomGeometrySecMatchRPE::at_inds(), and protocols::match::downstream::AtomGeometrySecMatchRPE::highval().
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Implements protocols::match::downstream::AtomGeometrySecMatchRPE.
Definition at line 144 of file GeometrySecMatchRPE.cc.
References protocols::match::downstream::AtomGeometrySecMatchRPE::at_inds(), protocols::match::downstream::AtomGeometrySecMatchRPE::highval(), and protocols::match::downstream::AtomGeometrySecMatchRPE::lowval().
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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.
Definition at line 163 of file GeometrySecMatchRPE.cc.
References protocols::match::downstream::AtomGeometrySecMatchRPE::at_inds(), and core::io::serialization::size().
1.8.4