core::scoring::constraints::Constraint Class Reference

Actually a *restraint*, like a virtual rubber band between a pair of atoms. More...

#include <Constraint.hh>

Inheritance diagram for core::scoring::constraints::Constraint:

Collaboration diagram for core::scoring::constraints::Constraint:

List of all members.

Public Types
typedef id::AtomID	AtomID
Public Member Functions
	Constraint (ScoreType const &t)
	Constructor for Constraint class.
virtual	~Constraint ()
	Virtual destructor.
virtual ConstraintOP	clone () const =0
	Copies the data from this Constraint into a new object and returns an OP to the new object. Intended to be implemented by derived classes and used by pose.add_constraint.
virtual ConstraintOP	clone (FuncOP) const
virtual ConstraintOP	remapped_clone (pose::Pose const &, pose::Pose const &, id::SequenceMappingCOP map=NULL) const
	Copies the data from this Constraint into a new object and returns an OP atoms are mapped to atoms with the same name in dest pose ( e.g. for switch from centroid to fullatom ) if a sequence_mapping is present it is used to map residue numbers .. NULL = identity mapping to the new object. Intended to be implemented by derived classes.
virtual Size	natoms () const =0
	Returns the number of atoms involved in defining this constraint. If the constraint doesn't depend on particular atoms (e.g. a residue type constraint) this function can return zero.
virtual AtomID const &	atom (Size const index) const =0
	Returns the AtomID referred to by index.
virtual utility::vector1 < core::Size >	residues () const
	Returns the pose numbers of the residues involved in this constraint, in no particular order.
virtual void	read_constraint (std::istream &, core::pose::Pose const &)
	This method is totally redundant with read_def YAY.
ScoreType const &	score_type () const
	Returns the ScoreType that this Constraint object will use.
virtual void	read_data (std::istream &)
	initialize this Constraint from the given std::istream. It's amazing that there are three functions for doing this inside of Constraint.hh. SO WHAT IS THIS SUPPOSED TO DO ? not overloaded by e.g., AtomPairConstraint or CoordinateConstraint,
virtual ConstraintOP	remap_resid (core::id::SequenceMapping const &) const
	apply a resid remapping to this constraint, returns the remapped constraint Does this return an owning pointer to this constraint or a copy? Documentation would be nice.
virtual core::Real	dist (core::pose::Pose const &) const
	return the "raw" distance before handed to the FUNC object
virtual core::Real	dist (XYZ_Func const &) const
virtual void	score (XYZ_Func const &xyz_func, EnergyMap const &weights, EnergyMap &emap) const =0
	Calculates a score for this constraint using XYZ_Func, and puts the UNWEIGHTED score into emap. Although the current set of weights currently is provided, Constraint objects should put unweighted scores into emap because the ScoreFunction will do the weighting itself.
virtual std::string	type () const
	Returns a unique string identified for this constraint. Used in several places, including the ConstraintIO class.
virtual void	setup_for_scoring (XYZ_Func const &, ScoreFunction const &) const
virtual void	setup_for_derivatives (XYZ_Func const &, ScoreFunction const &) const
virtual Real	score (conformation::Conformation const &) const
	Returns the score of this constraint computed over the given conformation. Not necessarily implemented in all derived classes, as it's redundant with the score( XYZ_Func, EnergyMap, EnergyMap ) method defined above. Returns 0.0 if not implemented.
virtual void	fill_f1_f2 (AtomID const &atom, XYZ_Func const &xyz_func, Vector &F1, Vector &F2, EnergyMap const &weights) const =0
	Fill the f1 and f2 vectors, necessary for considering the derivative this constraint during minimization. (someone please reference Bill Wedermeyer's paper here, as I'm in an airport and can't fill it in myself!)
virtual void	show (std::ostream &) const
	This method is intended to show the value of the Constraint function evaluated over some reasonable range of values. For example, a constraint between pairs of atoms might show the values of the Constraint function between 4 and 12 angstroms.
virtual void	show_def (std::ostream &, pose::Pose const &) const
	Prints the definition of a Constraint to the given std::ostream, using the given Pose, and the given FuncFactory. This method is intended to be overridden by derived classes if they'd like to use the ConstraintIO machinery. It's also not clear why this method takes a Pose, other than to be symmetric with read_def.
virtual void	read_def (std::istream &, pose::Pose const &, FuncFactory const &)
virtual void	steal_def (pose::Pose const &)
std::string	to_string () const
	Convenience function, returns the results of show() as a string. Not to be overriden by derived classes.
virtual Size	show_violations (std::ostream &out, pose::Pose const &, Size, Real threshold=1) const
	Prints the violations of this constraint to the given std::ostream. What are violations? It's not defined, and it depends on the constraint and the function! also - wtf is threshold? it was defined as a Size in CoordinateConstraint, I don't know which definition is the right one. Documentation would be nice ...
virtual Func const &	get_func () const
	Returns the Func object associated with this Constraint object.
virtual bool	operator== (Constraint const &) const
	possibility to do object comparison instead of pointer comparison
bool	operator!= (Constraint const &other) const
	possibility to do object comparison instead of pointer comparison
virtual core::Size	choose_effective_sequence_separation (core::kinematics::ShortestPathInFoldTree const &sp, numeric::random::RandomGenerator &)
virtual core::Size	effective_sequence_separation (core::kinematics::ShortestPathInFoldTree const &) const

---

Detailed Description

Actually a *restraint*, like a virtual rubber band between a pair of atoms.

All Constraints are expected to be immutable once created, meaning their internal data (state) should not change over their lifetime. This allows Constraints to be shared between copies of Poses (e.g. in Monte Carlo), and is important for both speed (with thousands of contraints) and correctness.

To "change" a constraint, remove the old one and add a new and different one. The steal() methods have been removed because it is incompatible with the idea of immutable constraints.

---

Member Typedef Documentation

typedef id::AtomID core::scoring::constraints::Constraint::AtomID

---

Constructor & Destructor Documentation

core::scoring::constraints::Constraint::Constraint

(

ScoreType const &

t

)

[inline]

Constructor for Constraint class.

virtual core::scoring::constraints::Constraint::~Constraint

(

)

[inline, virtual]

Virtual destructor.

---

Member Function Documentation

virtual AtomID const& core::scoring::constraints::Constraint::atom

(

Size const

index

)

const [pure virtual]

Returns the AtomID referred to by index.

Note that this function isn't actually used by the constraint scoring machenery. If you're calling it on a generic Constraint (as opposed to specifically on a derived class) you're probably doing something wrong.

Implemented in core::pack::dunbrack::DunbrackConstraint, core::pack::dunbrack::RotamerConstraint, core::scoring::constraints::AmbiguousNMRDistanceConstraint, core::scoring::constraints::AngleConstraint, core::scoring::constraints::AtomPairConstraint, core::scoring::constraints::BackboneStubConstraint, core::scoring::constraints::BigBinConstraint, core::scoring::constraints::ConstantConstraint, core::scoring::constraints::CoordinateConstraint, core::scoring::constraints::DihedralConstraint, core::scoring::constraints::DihedralPairConstraint, core::scoring::constraints::LocalCoordinateConstraint, core::scoring::constraints::MultiConstraint, core::scoring::constraints::NonResidueTypeConstraint, core::scoring::constraints::ResidueTypeConstraint, core::scoring::constraints::ResidueTypeLinkingConstraint, core::scoring::constraints::SequenceProfileConstraint, protocols::constraints_additional::BindingSiteConstraint, protocols::constraints_additional::SequenceCouplingConstraint, and protocols::pockets::PocketConstraint.

Referenced by residues().

virtual core::Size core::scoring::constraints::Constraint::choose_effective_sequence_separation	(	core::kinematics::ShortestPathInFoldTree const &	sp,
		numeric::random::RandomGenerator &
	)		[inline, virtual]

Reimplemented in core::scoring::constraints::MultiConstraint.

References effective_sequence_separation().

Referenced by core::scoring::constraints::MultiConstraint::choose_effective_sequence_separation(), and core::scoring::constraints::choose_effective_sequence_separation().

virtual ConstraintOP core::scoring::constraints::Constraint::clone

(

)

const [pure virtual]

Copies the data from this Constraint into a new object and returns an OP to the new object. Intended to be implemented by derived classes and used by pose.add_constraint.

Implemented in core::pack::dunbrack::DunbrackConstraint, core::pack::dunbrack::RotamerConstraint, core::scoring::constraints::AmbiguousConstraint, core::scoring::constraints::AmbiguousNMRConstraint, core::scoring::constraints::AmbiguousNMRDistanceConstraint, core::scoring::constraints::AngleConstraint, core::scoring::constraints::AtomPairConstraint, core::scoring::constraints::BackboneStubConstraint, core::scoring::constraints::BigBinConstraint, core::scoring::constraints::CoordinateConstraint, core::scoring::constraints::DihedralConstraint, core::scoring::constraints::DihedralPairConstraint, core::scoring::constraints::KofNConstraint, core::scoring::constraints::LocalCoordinateConstraint, core::scoring::constraints::MultiConstraint, core::scoring::constraints::NamedAtomPairConstraint, core::scoring::constraints::NonResidueTypeConstraint, core::scoring::constraints::ResidueTypeConstraint, core::scoring::constraints::ResidueTypeLinkingConstraint, core::scoring::constraints::SequenceProfileConstraint, core::scoring::constraints::SiteConstraint, protocols::constraints_additional::AmbiguousMultiConstraint, protocols::constraints_additional::BindingSiteConstraint, protocols::constraints_additional::SequenceCoupling1BDConstraint, protocols::constraints_additional::SequenceCouplingConstraint, and protocols::pockets::PocketConstraint.

virtual ConstraintOP core::scoring::constraints::Constraint::clone

(

FuncOP

)

const [inline, virtual]

Reimplemented in core::scoring::constraints::AmbiguousNMRConstraint, core::scoring::constraints::AmbiguousNMRDistanceConstraint, and core::scoring::constraints::AtomPairConstraint.

virtual core::Real core::scoring::constraints::Constraint::dist

(

core::pose::Pose const &

)

const [inline, virtual]

return the "raw" distance before handed to the FUNC object

Reimplemented in core::scoring::constraints::AmbiguousNMRConstraint, core::scoring::constraints::AmbiguousNMRDistanceConstraint, core::scoring::constraints::AtomPairConstraint, core::scoring::constraints::CoordinateConstraint, and core::scoring::constraints::LocalCoordinateConstraint.

virtual core::Real core::scoring::constraints::Constraint::dist

(

XYZ_Func const &

)

const [inline, virtual]

Reimplemented in core::scoring::constraints::AmbiguousNMRConstraint, core::scoring::constraints::AmbiguousNMRDistanceConstraint, and core::scoring::constraints::AtomPairConstraint.

virtual core::Size core::scoring::constraints::Constraint::effective_sequence_separation

(

core::kinematics::ShortestPathInFoldTree const &

)

const [inline, virtual]

Reimplemented in core::scoring::constraints::AmbiguousNMRDistanceConstraint, core::scoring::constraints::AtomPairConstraint, and core::scoring::constraints::MultiConstraint.

Referenced by choose_effective_sequence_separation(), and protocols::constraints_additional::MaxSeqSepConstraintSet::eval_non_residue_pair_energy().

virtual void core::scoring::constraints::Constraint::fill_f1_f2	(	AtomID const &	atom,
		XYZ_Func const &	xyz_func,
		Vector &	F1,
		Vector &	F2,
		EnergyMap const &	weights
	)		const [pure virtual]

Fill the f1 and f2 vectors, necessary for considering the derivative this constraint during minimization. (someone please reference Bill Wedermeyer's paper here, as I'm in an airport and can't fill it in myself!)

Implemented in core::pack::dunbrack::DunbrackConstraint, core::pack::dunbrack::RotamerConstraint, core::scoring::constraints::AmbiguousConstraint, core::scoring::constraints::AmbiguousNMRConstraint, core::scoring::constraints::AmbiguousNMRDistanceConstraint, core::scoring::constraints::BigBinConstraint, core::scoring::constraints::ConstantConstraint, core::scoring::constraints::KofNConstraint, core::scoring::constraints::LocalCoordinateConstraint, core::scoring::constraints::MultiConstraint, core::scoring::constraints::NonResidueTypeConstraint, core::scoring::constraints::ResidueTypeConstraint, core::scoring::constraints::ResidueTypeLinkingConstraint, core::scoring::constraints::SequenceProfileConstraint, protocols::constraints_additional::AmbiguousMultiConstraint, protocols::constraints_additional::SequenceCoupling1BDConstraint, protocols::constraints_additional::SequenceCouplingConstraint, and protocols::pockets::PocketConstraint.

Referenced by core::scoring::constraints::Constraints::eval_intrares_atom_derivative(), core::scoring::constraints::Constraints::eval_respair_atom_derivative(), and core::scoring::constraints::Constraints::eval_ws_atom_derivative().

virtual Func const& core::scoring::constraints::Constraint::get_func

(

)

const [inline, virtual]

Returns the Func object associated with this Constraint object.

Reimplemented in core::scoring::constraints::AmbiguousNMRConstraint, core::scoring::constraints::AmbiguousNMRDistanceConstraint, and core::scoring::constraints::AtomPairConstraint.

virtual Size core::scoring::constraints::Constraint::natoms

(

)

const [pure virtual]

Returns the number of atoms involved in defining this constraint. If the constraint doesn't depend on particular atoms (e.g. a residue type constraint) this function can return zero.

Note that this function isn't actually used by the constraint scoring machenery. If you're calling it on a generic Constraint (as opposed to specifically on a derived class) you're probably doing something wrong.

Implemented in core::pack::dunbrack::DunbrackConstraint, core::pack::dunbrack::RotamerConstraint, core::scoring::constraints::AmbiguousNMRDistanceConstraint, core::scoring::constraints::AngleConstraint, core::scoring::constraints::AtomPairConstraint, core::scoring::constraints::BackboneStubConstraint, core::scoring::constraints::BigBinConstraint, core::scoring::constraints::ConstantConstraint, core::scoring::constraints::CoordinateConstraint, core::scoring::constraints::DihedralConstraint, core::scoring::constraints::DihedralPairConstraint, core::scoring::constraints::LocalCoordinateConstraint, core::scoring::constraints::MultiConstraint, core::scoring::constraints::NonResidueTypeConstraint, core::scoring::constraints::ResidueTypeConstraint, core::scoring::constraints::ResidueTypeLinkingConstraint, core::scoring::constraints::SequenceProfileConstraint, protocols::constraints_additional::BindingSiteConstraint, protocols::constraints_additional::SequenceCouplingConstraint, and protocols::pockets::PocketConstraint.

Referenced by residues().

bool core::scoring::constraints::Constraint::operator!=

(

Constraint const &

other

)

const [inline]

possibility to do object comparison instead of pointer comparison

virtual bool core::scoring::constraints::Constraint::operator==

(

Constraint const &

)

const [inline, virtual]

possibility to do object comparison instead of pointer comparison

Reimplemented in core::scoring::constraints::AmbiguousConstraint, core::scoring::constraints::AngleConstraint, core::scoring::constraints::AtomPairConstraint, core::scoring::constraints::BackboneStubConstraint, core::scoring::constraints::CoordinateConstraint, core::scoring::constraints::DihedralConstraint, core::scoring::constraints::DihedralPairConstraint, core::scoring::constraints::MultiConstraint, core::scoring::constraints::ResidueTypeConstraint, and core::scoring::constraints::ResidueTypeLinkingConstraint.

virtual void core::scoring::constraints::Constraint::read_constraint	(	std::istream &	,
		core::pose::Pose const &
	)		[inline, virtual]

This method is totally redundant with read_def YAY.

virtual void core::scoring::constraints::Constraint::read_data

(

std::istream &

)

[inline, virtual]

initialize this Constraint from the given std::istream. It's amazing that there are three functions for doing this inside of Constraint.hh. SO WHAT IS THIS SUPPOSED TO DO ? not overloaded by e.g., AtomPairConstraint or CoordinateConstraint,

virtual void core::scoring::constraints::Constraint::read_def	(	std::istream &	,
		pose::Pose const &	,
		FuncFactory const &
	)		[inline, virtual]

Reimplemented in core::pack::dunbrack::DunbrackConstraint, core::scoring::constraints::AmbiguousConstraint, core::scoring::constraints::AmbiguousNMRConstraint, core::scoring::constraints::AmbiguousNMRDistanceConstraint, core::scoring::constraints::AngleConstraint, core::scoring::constraints::AtomPairConstraint, core::scoring::constraints::BigBinConstraint, core::scoring::constraints::CoordinateConstraint, core::scoring::constraints::DihedralConstraint, core::scoring::constraints::DihedralPairConstraint, core::scoring::constraints::KofNConstraint, core::scoring::constraints::LocalCoordinateConstraint, core::scoring::constraints::MultiConstraint, core::scoring::constraints::NamedAtomPairConstraint, core::scoring::constraints::SequenceProfileConstraint, core::scoring::constraints::SiteConstraint, protocols::constraints_additional::BindingSiteConstraint, protocols::constraints_additional::SequenceCoupling1BDConstraint, protocols::constraints_additional::SequenceCouplingConstraint, and protocols::pockets::PocketConstraint.

virtual ConstraintOP core::scoring::constraints::Constraint::remap_resid

(

core::id::SequenceMapping const &

)

const [inline, virtual]

apply a resid remapping to this constraint, returns the remapped constraint Does this return an owning pointer to this constraint or a copy? Documentation would be nice.

Reimplemented in core::scoring::constraints::AmbiguousConstraint, core::scoring::constraints::AmbiguousNMRConstraint, core::scoring::constraints::AmbiguousNMRDistanceConstraint, core::scoring::constraints::AngleConstraint, core::scoring::constraints::AtomPairConstraint, core::scoring::constraints::CoordinateConstraint, core::scoring::constraints::DihedralConstraint, core::scoring::constraints::DihedralPairConstraint, core::scoring::constraints::KofNConstraint, core::scoring::constraints::LocalCoordinateConstraint, core::scoring::constraints::MultiConstraint, core::scoring::constraints::NonResidueTypeConstraint, core::scoring::constraints::ResidueTypeConstraint, core::scoring::constraints::SequenceProfileConstraint, protocols::constraints_additional::AmbiguousMultiConstraint, and protocols::constraints_additional::BindingSiteConstraint.

virtual ConstraintOP core::scoring::constraints::Constraint::remapped_clone	(	pose::Pose const &	,
		pose::Pose const &	,
		id::SequenceMappingCOP	map = NULL
	)		const [inline, virtual]

Copies the data from this Constraint into a new object and returns an OP atoms are mapped to atoms with the same name in dest pose ( e.g. for switch from centroid to fullatom ) if a sequence_mapping is present it is used to map residue numbers .. NULL = identity mapping to the new object. Intended to be implemented by derived classes.

Reimplemented in core::scoring::constraints::AmbiguousNMRDistanceConstraint, core::scoring::constraints::AngleConstraint, core::scoring::constraints::AtomPairConstraint, core::scoring::constraints::BackboneStubConstraint, core::scoring::constraints::CoordinateConstraint, core::scoring::constraints::DihedralConstraint, core::scoring::constraints::DihedralPairConstraint, core::scoring::constraints::LocalCoordinateConstraint, core::scoring::constraints::MultiConstraint, core::scoring::constraints::NamedAtomPairConstraint, core::scoring::constraints::ResidueTypeConstraint, and core::scoring::constraints::SequenceProfileConstraint.

utility::vector1< core::Size > core::scoring::constraints::Constraint::residues

(

)

const [virtual]

Returns the pose numbers of the residues involved in this constraint, in no particular order.

Used in determining one-body/two-body/multi-body status. For historical reasons, the default uses a simple protocol based on natoms()/atom() - feel free to reimplement more efficiently.

Reimplemented in core::scoring::constraints::MultiConstraint, core::scoring::constraints::NonResidueTypeConstraint, core::scoring::constraints::ResidueTypeConstraint, core::scoring::constraints::ResidueTypeLinkingConstraint, core::scoring::constraints::SequenceProfileConstraint, and protocols::constraints_additional::SequenceCouplingConstraint.

References atom(), and natoms().

Referenced by core::scoring::constraints::combinable().

virtual Real core::scoring::constraints::Constraint::score

(

conformation::Conformation const &

)

const [inline, virtual]

Returns the score of this constraint computed over the given conformation. Not necessarily implemented in all derived classes, as it's redundant with the score( XYZ_Func, EnergyMap, EnergyMap ) method defined above. Returns 0.0 if not implemented.

Reimplemented in core::scoring::constraints::DihedralConstraint, and core::scoring::constraints::DihedralPairConstraint.

virtual void core::scoring::constraints::Constraint::score	(	XYZ_Func const &	xyz_func,
		EnergyMap const &	weights,
		EnergyMap &	emap
	)		const [pure virtual]

Calculates a score for this constraint using XYZ_Func, and puts the UNWEIGHTED score into emap. Although the current set of weights currently is provided, Constraint objects should put unweighted scores into emap because the ScoreFunction will do the weighting itself.

Implemented in core::pack::dunbrack::DunbrackConstraint, core::pack::dunbrack::RotamerConstraint, core::scoring::constraints::AmbiguousConstraint, core::scoring::constraints::AmbiguousNMRConstraint, core::scoring::constraints::AmbiguousNMRDistanceConstraint, core::scoring::constraints::AngleConstraint, core::scoring::constraints::AtomPairConstraint, core::scoring::constraints::BackboneStubConstraint, core::scoring::constraints::BigBinConstraint, core::scoring::constraints::ConstantConstraint, core::scoring::constraints::CoordinateConstraint, core::scoring::constraints::DihedralConstraint, core::scoring::constraints::DihedralPairConstraint, core::scoring::constraints::KofNConstraint, core::scoring::constraints::LocalCoordinateConstraint, core::scoring::constraints::MultiConstraint, core::scoring::constraints::NonResidueTypeConstraint, core::scoring::constraints::ResidueTypeConstraint, core::scoring::constraints::ResidueTypeLinkingConstraint, core::scoring::constraints::SequenceProfileConstraint, protocols::constraints_additional::AmbiguousMultiConstraint, protocols::constraints_additional::BindingSiteConstraint, protocols::constraints_additional::SequenceCoupling1BDConstraint, protocols::constraints_additional::SequenceCouplingConstraint, and protocols::pockets::PocketConstraint.

Referenced by protocols::constraints_additional::MaxSeqSepConstraintSet::eval_non_residue_pair_energy().

ScoreType const& core::scoring::constraints::Constraint::score_type

(

)

const [inline]

Returns the ScoreType that this Constraint object will use.

Referenced by core::scoring::constraints::NamedAtomPairConstraint::clone(), core::scoring::constraints::DihedralPairConstraint::clone(), core::scoring::constraints::DihedralConstraint::clone(), core::scoring::constraints::AtomPairConstraint::clone(), core::scoring::constraints::AngleConstraint::clone(), core::scoring::constraints::AmbiguousNMRDistanceConstraint::clone(), protocols::pockets::PocketConstraint::fill_f1_f2(), protocols::constraints_additional::BindingSiteConstraint::fill_f1_f2(), core::scoring::constraints::LocalCoordinateConstraint::fill_f1_f2(), core::scoring::constraints::DihedralPairConstraint::fill_f1_f2(), core::scoring::constraints::DihedralConstraint::fill_f1_f2(), core::scoring::constraints::CoordinateConstraint::fill_f1_f2(), core::scoring::constraints::BackboneStubConstraint::fill_f1_f2(), core::scoring::constraints::AtomPairConstraint::fill_f1_f2(), core::scoring::constraints::AngleConstraint::fill_f1_f2(), core::scoring::constraints::AmbiguousNMRDistanceConstraint::fill_f1_f2(), core::scoring::constraints::AmbiguousNMRConstraint::fill_f1_f2(), core::scoring::constraints::AmbiguousNMRDistanceConstraint::map_to_CB(), core::scoring::constraints::ResidueTypeLinkingConstraint::operator==(), core::scoring::constraints::ResidueTypeConstraint::operator==(), core::scoring::constraints::MultiConstraint::operator==(), core::scoring::constraints::DihedralPairConstraint::operator==(), core::scoring::constraints::DihedralConstraint::operator==(), core::scoring::constraints::CoordinateConstraint::operator==(), core::scoring::constraints::AtomPairConstraint::operator==(), core::scoring::constraints::AngleConstraint::operator==(), core::scoring::constraints::LocalCoordinateConstraint::remap_resid(), core::scoring::constraints::CoordinateConstraint::remap_resid(), core::scoring::constraints::AmbiguousNMRDistanceConstraint::remap_resid(), core::scoring::constraints::NamedAtomPairConstraint::remapped_clone(), core::scoring::constraints::LocalCoordinateConstraint::remapped_clone(), core::scoring::constraints::DihedralPairConstraint::remapped_clone(), core::scoring::constraints::DihedralConstraint::remapped_clone(), core::scoring::constraints::CoordinateConstraint::remapped_clone(), core::scoring::constraints::AtomPairConstraint::remapped_clone(), core::scoring::constraints::AngleConstraint::remapped_clone(), core::scoring::constraints::AmbiguousNMRDistanceConstraint::remapped_clone(), protocols::pockets::PocketConstraint::score(), protocols::constraints_additional::SequenceCouplingConstraint::score(), protocols::constraints_additional::SequenceCoupling1BDConstraint::score(), protocols::constraints_additional::BindingSiteConstraint::score(), core::scoring::constraints::SequenceProfileConstraint::score(), core::scoring::constraints::ResidueTypeLinkingConstraint::score(), core::scoring::constraints::ResidueTypeConstraint::score(), core::scoring::constraints::NonResidueTypeConstraint::score(), core::scoring::constraints::LocalCoordinateConstraint::score(), core::scoring::constraints::DihedralPairConstraint::score(), core::scoring::constraints::DihedralConstraint::score(), core::scoring::constraints::CoordinateConstraint::score(), core::scoring::constraints::ConstantConstraint::score(), core::scoring::constraints::BackboneStubConstraint::score(), core::scoring::constraints::AtomPairConstraint::score(), core::scoring::constraints::AngleConstraint::score(), core::scoring::constraints::AmbiguousNMRDistanceConstraint::score(), core::scoring::constraints::AmbiguousNMRConstraint::score(), core::pack::dunbrack::RotamerConstraint::score(), and core::pack::dunbrack::DunbrackConstraint::score().

virtual void core::scoring::constraints::Constraint::setup_for_derivatives	(	XYZ_Func const &	,
		ScoreFunction const &
	)		const [inline, virtual]

Reimplemented in protocols::constraints_additional::BindingSiteConstraint.

virtual void core::scoring::constraints::Constraint::setup_for_scoring	(	XYZ_Func const &	,
		ScoreFunction const &
	)		const [inline, virtual]

Reimplemented in core::scoring::constraints::MultiConstraint, core::scoring::constraints::NamedAtomPairConstraint, and protocols::constraints_additional::BindingSiteConstraint.

virtual void core::scoring::constraints::Constraint::show

(

std::ostream &

)

const [inline, virtual]

This method is intended to show the value of the Constraint function evaluated over some reasonable range of values. For example, a constraint between pairs of atoms might show the values of the Constraint function between 4 and 12 angstroms.

Reimplemented in core::pack::dunbrack::DunbrackConstraint, core::pack::dunbrack::RotamerConstraint, core::scoring::constraints::AmbiguousConstraint, core::scoring::constraints::AmbiguousNMRDistanceConstraint, core::scoring::constraints::AngleConstraint, core::scoring::constraints::AtomPairConstraint, core::scoring::constraints::BackboneStubConstraint, core::scoring::constraints::BigBinConstraint, core::scoring::constraints::ConstantConstraint, core::scoring::constraints::CoordinateConstraint, core::scoring::constraints::DihedralConstraint, core::scoring::constraints::DihedralPairConstraint, core::scoring::constraints::KofNConstraint, core::scoring::constraints::LocalCoordinateConstraint, core::scoring::constraints::MultiConstraint, core::scoring::constraints::NonResidueTypeConstraint, core::scoring::constraints::ResidueTypeConstraint, core::scoring::constraints::ResidueTypeLinkingConstraint, core::scoring::constraints::SequenceProfileConstraint, core::scoring::constraints::SiteConstraint, protocols::constraints_additional::AmbiguousMultiConstraint, protocols::constraints_additional::BindingSiteConstraint, protocols::constraints_additional::SequenceCoupling1BDConstraint, and protocols::constraints_additional::SequenceCouplingConstraint.

Referenced by core::scoring::constraints::operator<<(), core::scoring::constraints::Constraints::show(), and to_string().

virtual void core::scoring::constraints::Constraint::show_def	(	std::ostream &	,
		pose::Pose const &
	)		const [inline, virtual]

Prints the definition of a Constraint to the given std::ostream, using the given Pose, and the given FuncFactory. This method is intended to be overridden by derived classes if they'd like to use the ConstraintIO machinery. It's also not clear why this method takes a Pose, other than to be symmetric with read_def.

Reimplemented in core::scoring::constraints::AmbiguousNMRConstraint, core::scoring::constraints::AmbiguousNMRDistanceConstraint, core::scoring::constraints::AngleConstraint, core::scoring::constraints::AtomPairConstraint, core::scoring::constraints::CoordinateConstraint, core::scoring::constraints::DihedralConstraint, core::scoring::constraints::LocalCoordinateConstraint, core::scoring::constraints::MultiConstraint, core::scoring::constraints::NamedAtomPairConstraint, core::scoring::constraints::SequenceProfileConstraint, protocols::constraints_additional::BindingSiteConstraint, protocols::constraints_additional::SequenceCouplingConstraint, and protocols::pockets::PocketConstraint.

Referenced by core::scoring::constraints::Constraints::show_definition().

virtual Size core::scoring::constraints::Constraint::show_violations	(	std::ostream &	out,
		pose::Pose const &	,
		Size	,
		Real	threshold = 1
	)		const [inline, virtual]

Prints the violations of this constraint to the given std::ostream. What are violations? It's not defined, and it depends on the constraint and the function! also - wtf is threshold? it was defined as a Size in CoordinateConstraint, I don't know which definition is the right one. Documentation would be nice ...

Reimplemented in core::scoring::constraints::AmbiguousConstraint, core::scoring::constraints::AmbiguousNMRConstraint, core::scoring::constraints::AmbiguousNMRDistanceConstraint, core::scoring::constraints::AngleConstraint, core::scoring::constraints::AtomPairConstraint, core::scoring::constraints::ConstantConstraint, core::scoring::constraints::CoordinateConstraint, core::scoring::constraints::DihedralConstraint, core::scoring::constraints::DihedralPairConstraint, core::scoring::constraints::KofNConstraint, core::scoring::constraints::LocalCoordinateConstraint, core::scoring::constraints::MultiConstraint, protocols::constraints_additional::AmbiguousMultiConstraint, and protocols::constraints_additional::BindingSiteConstraint.

Referenced by core::scoring::constraints::Constraints::show_violations().

virtual void core::scoring::constraints::Constraint::steal_def

(

pose::Pose const &

)

[inline, virtual]

Reimplemented in core::scoring::constraints::CoordinateConstraint, and core::scoring::constraints::LocalCoordinateConstraint.

std::string core::scoring::constraints::Constraint::to_string

(

)

const [inline]

Convenience function, returns the results of show() as a string. Not to be overriden by derived classes.

References show().

virtual std::string core::scoring::constraints::Constraint::type

(

)

const [inline, virtual]

Returns a unique string identified for this constraint. Used in several places, including the ConstraintIO class.

Reimplemented in core::pack::dunbrack::DunbrackConstraint, core::pack::dunbrack::RotamerConstraint, core::scoring::constraints::AmbiguousConstraint, core::scoring::constraints::AmbiguousNMRConstraint, core::scoring::constraints::AmbiguousNMRDistanceConstraint, core::scoring::constraints::AngleConstraint, core::scoring::constraints::AtomPairConstraint, core::scoring::constraints::BackboneStubConstraint, core::scoring::constraints::BigBinConstraint, core::scoring::constraints::ConstantConstraint, core::scoring::constraints::CoordinateConstraint, core::scoring::constraints::DihedralConstraint, core::scoring::constraints::DihedralPairConstraint, core::scoring::constraints::KofNConstraint, core::scoring::constraints::LocalCoordinateConstraint, core::scoring::constraints::MultiConstraint, core::scoring::constraints::SequenceProfileConstraint, core::scoring::constraints::SiteConstraint, protocols::constraints_additional::AmbiguousMultiConstraint, protocols::constraints_additional::BindingSiteConstraint, protocols::constraints_additional::SequenceCoupling1BDConstraint, protocols::constraints_additional::SequenceCouplingConstraint, and protocols::pockets::PocketConstraint.

---

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

• src/core/scoring/constraints/Constraint.hh
• src/core/scoring/constraints/Constraint.cc