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

#include <GeometrySecMatchRPE.hh>

Inheritance diagram for protocols::match::downstream::AtomGeometrySecMatchRPE:

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 () override

bool	evaluate_residues (core::conformation::Residue const &candidate_res, core::conformation::Residue const &target_res) const override=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...

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 (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

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 ()

	~SecMatchResiduePairEvaluator () override

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...

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< SizePair >	at_inds_

Detailed Description

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

Member Typedef Documentation

typedef core::Real protocols::match::downstream::AtomGeometrySecMatchRPE::Real

typedef std::pair< core::Size, core::Size > protocols::match::downstream::AtomGeometrySecMatchRPE::SizePair

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 ( )

overridedefault

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

References at_inds_.

Referenced by protocols::match::downstream::AtomDistanceSecMatchRPE::candidate_res_atoms_reqd_near_target_atom(), protocols::match::downstream::AtomDistanceSecMatchRPE::evaluate_residues(), protocols::match::downstream::AtomAngleSecMatchRPE::evaluate_residues(), protocols::match::downstream::AtomDihedralSecMatchRPE::evaluate_residues(), protocols::match::downstream::AtomDistanceSecMatchRPE::max_separation_dist_to_target_atom(), protocols::match::downstream::AtomDistanceSecMatchRPE::print(), protocols::match::downstream::AtomAngleSecMatchRPE::print(), protocols::match::downstream::AtomDihedralSecMatchRPE::print(), and protocols::match::downstream::AtomDistanceSecMatchRPE::require_candidate_residue_atoms_to_lie_near_target_atom().

bool protocols::match::downstream::AtomGeometrySecMatchRPE::check_value ( core::Real value ) const

determines if the passed in value is between lowval and highval

References highval_, and lowval_.

Referenced by protocols::match::downstream::AtomDistanceSecMatchRPE::evaluate_residues(), protocols::match::downstream::AtomAngleSecMatchRPE::evaluate_residues(), and protocols::match::downstream::AtomDihedralSecMatchRPE::evaluate_residues().

void protocols::match::downstream::AtomGeometrySecMatchRPE::clear_at_inds ( )

protected

References at_inds_.

Referenced by AtomGeometrySecMatchRPE().

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

overridepure 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

References highval_.

Referenced by protocols::match::downstream::AtomAngleSecMatchRPE::AtomAngleSecMatchRPE(), protocols::match::downstream::AtomDistanceSecMatchRPE::AtomDistanceSecMatchRPE(), protocols::match::downstream::AtomDistanceSecMatchRPE::max_separation_dist_to_target_atom(), protocols::match::downstream::AtomDistanceSecMatchRPE::print(), protocols::match::downstream::AtomAngleSecMatchRPE::print(), protocols::match::downstream::AtomDihedralSecMatchRPE::print(), and set_highval().

core::Real protocols::match::downstream::AtomGeometrySecMatchRPE::lowval ( ) const

inline

References lowval_.

Referenced by protocols::match::downstream::AtomAngleSecMatchRPE::AtomAngleSecMatchRPE(), protocols::match::downstream::AtomDistanceSecMatchRPE::AtomDistanceSecMatchRPE(), protocols::match::downstream::AtomDistanceSecMatchRPE::print(), protocols::match::downstream::AtomAngleSecMatchRPE::print(), protocols::match::downstream::AtomDihedralSecMatchRPE::print(), and set_lowval().

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

pure virtual

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

bool protocols::match::downstream::AtomGeometrySecMatchRPE::require_all_target_residue_atom_coordinates ( ) const

overridevirtual

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

overridevirtual

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

References highval(), and highval_.

Referenced by protocols::match::downstream::AtomAngleSecMatchRPE::AtomAngleSecMatchRPE(), protocols::match::downstream::AtomDihedralSecMatchRPE::AtomDihedralSecMatchRPE(), and protocols::match::downstream::AtomDistanceSecMatchRPE::AtomDistanceSecMatchRPE().

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

protected

References lowval(), and lowval_.

Referenced by protocols::match::downstream::AtomAngleSecMatchRPE::AtomAngleSecMatchRPE(), protocols::match::downstream::AtomDihedralSecMatchRPE::AtomDihedralSecMatchRPE(), and protocols::match::downstream::AtomDistanceSecMatchRPE::AtomDistanceSecMatchRPE().