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protocols::match::downstream::AtomGeometrySecMatchRPE Class Referenceabstract

helper class for GeometrySec abstract base class for distance, angle, and dihedral derived classes More...

#include <GeometrySecMatchRPE.hh>

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Public Types

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
 

Public Member Functions

 AtomGeometrySecMatchRPE (protocols::toolbox::match_enzdes_util::GeomSampleInfo const &gsi)
 
 ~AtomGeometrySecMatchRPE ()
 
virtual bool evaluate_residues (core::conformation::Residue const &candidate_res, core::conformation::Residue const &target_res) const =0
 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_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
 
virtual std::string print (core::chemical::ResidueTypeCOP candidate_restype, core::chemical::ResidueTypeCOP target_restype) const =0
 
- Public Member Functions inherited from protocols::match::downstream::SecMatchResiduePairEvaluator
 SecMatchResiduePairEvaluator ()
 
virtual ~SecMatchResiduePairEvaluator ()
 
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...
 

Protected Member Functions

void clear_at_inds ()
 
void set_lowval (core::Real lowval)
 
void set_highval (core::Real highval)
 

Private Attributes

Real lowval_
 
Real highval_
 
utility::vector1< SizePairat_inds_
 

Detailed Description

helper class for GeometrySec abstract base class for distance, angle, and dihedral derived classes

Member Typedef Documentation

Constructor & Destructor Documentation

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

References clear_at_inds().

protocols::match::downstream::AtomGeometrySecMatchRPE::~AtomGeometrySecMatchRPE ( )

Member Function Documentation

void protocols::match::downstream::AtomGeometrySecMatchRPE::add_at_ind ( core::Size  which_cst_res,
core::Size  atom_ind_in_res 
)

References at_inds_.

utility::vector1< SizePair > const& protocols::match::downstream::AtomGeometrySecMatchRPE::at_inds ( ) const
inline
bool protocols::match::downstream::AtomGeometrySecMatchRPE::check_value ( core::Real  value) const
void protocols::match::downstream::AtomGeometrySecMatchRPE::clear_at_inds ( )
protected

References at_inds_.

Referenced by AtomGeometrySecMatchRPE().

virtual bool protocols::match::downstream::AtomGeometrySecMatchRPE::evaluate_residues ( core::conformation::Residue const &  candidate_res,
core::conformation::Residue const &  target_res 
) const
pure 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::SecMatchResiduePairEvaluator.

Implemented in protocols::match::downstream::AtomDihedralSecMatchRPE, protocols::match::downstream::AtomAngleSecMatchRPE, and protocols::match::downstream::AtomDistanceSecMatchRPE.

core::Real protocols::match::downstream::AtomGeometrySecMatchRPE::highval ( ) const
inline
core::Real protocols::match::downstream::AtomGeometrySecMatchRPE::lowval ( ) const
inline
virtual std::string protocols::match::downstream::AtomGeometrySecMatchRPE::print ( core::chemical::ResidueTypeCOP  candidate_restype,
core::chemical::ResidueTypeCOP  target_restype 
) const
pure virtual
bool protocols::match::downstream::AtomGeometrySecMatchRPE::require_all_target_residue_atom_coordinates ( ) const
virtual

Returns true if all coordinates of the target residue are required in order to evaluate the interaction between the candidate and the target residues.

Implements protocols::match::downstream::SecMatchResiduePairEvaluator.

bool protocols::match::downstream::AtomGeometrySecMatchRPE::require_target_atom_coordinate ( Size  target_atom_id) const
virtual

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.

Implements protocols::match::downstream::SecMatchResiduePairEvaluator.

References at_inds_.

void protocols::match::downstream::AtomGeometrySecMatchRPE::set_highval ( core::Real  highval)
protected
void protocols::match::downstream::AtomGeometrySecMatchRPE::set_lowval ( core::Real  lowval)
protected

Member Data Documentation

utility::vector1< SizePair > protocols::match::downstream::AtomGeometrySecMatchRPE::at_inds_
private
Real protocols::match::downstream::AtomGeometrySecMatchRPE::highval_
private

Referenced by check_value(), highval(), and set_highval().

Real protocols::match::downstream::AtomGeometrySecMatchRPE::lowval_
private

Referenced by check_value(), lowval(), and set_lowval().


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