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protocols::match::downstream::AtomDihedralSecMatchRPE Class Reference

RPE to figure out if four atoms are within a given dihedral angle atoms need to be set through the parent class add_at_ind function also checks whether a dihedral is periodic, i.e. multiple minima. More...

#include <GeometrySecMatchRPE.hh>

Inheritance diagram for protocols::match::downstream::AtomDihedralSecMatchRPE:
Inheritance graph
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Public Member Functions

 AtomDihedralSecMatchRPE (protocols::toolbox::match_enzdes_util::GeomSampleInfo const &gsi)
 
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...
 
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
 
virtual bool require_candidate_residue_atoms_to_lie_near_target_atom (core::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
< core::Size
candidate_res_atoms_reqd_near_target_atom (core::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 (core::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...
 

Private Attributes

bool check_periodicity_
 
Real periodicity_
 
Real offset_
 

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)
 

Detailed Description

RPE to figure out if four atoms are within a given dihedral angle atoms need to be set through the parent class add_at_ind function also checks whether a dihedral is periodic, i.e. multiple minima.

Constructor & Destructor Documentation

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

Member Function Documentation

bool protocols::match::downstream::AtomDihedralSecMatchRPE::evaluate_residues ( core::conformation::Residue const &  candidate_res,
core::conformation::Residue const &  target_res 
) const
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(), offset_, periodicity_, and core::conformation::Residue::xyz().

std::string protocols::match::downstream::AtomDihedralSecMatchRPE::print ( core::chemical::ResidueTypeCOP  candidate_restype,
core::chemical::ResidueTypeCOP  target_restype 
) const
overridevirtual

Member Data Documentation

bool protocols::match::downstream::AtomDihedralSecMatchRPE::check_periodicity_
private
Real protocols::match::downstream::AtomDihedralSecMatchRPE::offset_
private

Referenced by evaluate_residues(), and print().

Real protocols::match::downstream::AtomDihedralSecMatchRPE::periodicity_
private

Referenced by evaluate_residues(), and print().


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