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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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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< 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...
 
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)
 

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(), core::io::serialization::size(), 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::ResidueTypeCOP  candidate_restype,
core::chemical::ResidueTypeCOP  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(), and core::io::serialization::size().


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