Rosetta 3.4
Public Member Functions
protocols::match::downstream::AtomDistanceSecMatchRPE Class Reference

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>

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List of all members.

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< 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.
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

Detailed Description

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.


Constructor & Destructor Documentation

protocols::match::downstream::AtomDistanceSecMatchRPE::AtomDistanceSecMatchRPE ( protocols::toolbox::match_enzdes_util::GeomSampleInfo const &  gsi)

Member Function Documentation

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().


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