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:

Public Types
typedef id::AtomID	AtomID

Public Member Functions
	Constraint (ScoreType const &t)
	Constructor for Constraint class. More...

virtual	~Constraint ()
	Virtual destructor. More...

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. More...

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. More...

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. More...

virtual AtomID const &	atom (Size const index) const =0
	Returns the AtomID referred to by index. More...

virtual utility::vector1 < core::Size >	residues () const
	Returns the pose numbers of the residues involved in this constraint, in no particular order. More...

virtual void	read_constraint (std::istream &, core::pose::Pose const &)
	This method is totally redundant with read_def YAY. More...

ScoreType const &	score_type () const
	Returns the ScoreType that this Constraint object will use. More...

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, More...

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. More...

virtual core::Real	dist (core::pose::Pose const &) const
	return the "raw" distance before handed to the FUNC object More...

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. More...

virtual std::string	type () const
	Returns a unique string identified for this constraint. Used in several places, including the ConstraintIO class. More...

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. More...

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!) More...

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. More...

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. More...

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. More...

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 ... More...

virtual Func const &	get_func () const
	Returns the Func object associated with this Constraint object. More...

virtual bool	operator== (Constraint const &) const
	possibility to do object comparison instead of pointer comparison More...

bool	operator!= (Constraint const &other) const
	possibility to do object comparison instead of pointer comparison More...

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

Private Member Functions
void	unimplemented_method_error (std::string const &method_name) const
	Utility method for producing useful error messages and exiting from program. Declared const which is funny, because exiting the program certainly changes the state of this object! This might be replaced with exception handling if we ever start using those inside of mini. More...

Private Attributes
ScoreType const	score_type_

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.

Definition at line 69 of file Constraint.hh.

Member Typedef Documentation

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

Definition at line 72 of file Constraint.hh.

Constructor & Destructor Documentation

core::scoring::constraints::Constraint::Constraint ( ScoreType const & t)

inline

Constructor for Constraint class.

Definition at line 76 of file Constraint.hh.

core::scoring::constraints::Constraint::~Constraint ( )

virtual

Virtual destructor.

Auto-generated virtual destructor

Definition at line 32 of file Constraint.cc.

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.

Referenced by residues().

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

inlinevirtual

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

Definition at line 298 of file Constraint.hh.

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.

virtual ConstraintOP core::scoring::constraints::Constraint::clone ( FuncOP ) const

inlinevirtual

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

Definition at line 87 of file Constraint.hh.

References unimplemented_method_error().

virtual core::Real core::scoring::constraints::Constraint::dist ( core::pose::Pose const & ) const

inlinevirtual

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

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

Definition at line 168 of file Constraint.hh.

References unimplemented_method_error().

Referenced by core::scoring::constraints::DistancePairConstraint::fill_f1_f2().

virtual core::Real core::scoring::constraints::Constraint::dist ( XYZ_Func const & ) const

inlinevirtual

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

Definition at line 175 of file Constraint.hh.

References unimplemented_method_error().

virtual core::Size core::scoring::constraints::Constraint::effective_sequence_separation ( core::kinematics::ShortestPathInFoldTree const & ) const

inlinevirtual

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

Definition at line 307 of file Constraint.hh.

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!)

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

inlinevirtual

Returns the Func object associated with this Constraint object.

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

Definition at line 276 of file Constraint.hh.

References unimplemented_method_error().

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.

Referenced by residues().

bool core::scoring::constraints::Constraint::operator!= ( Constraint const & other) const

inline

possibility to do object comparison instead of pointer comparison

Definition at line 293 of file Constraint.hh.

virtual bool core::scoring::constraints::Constraint::operator== ( Constraint const & ) const

inlinevirtual

possibility to do object comparison instead of pointer comparison

Definition at line 286 of file Constraint.hh.

References unimplemented_method_error().

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

inlinevirtual

This method is totally redundant with read_def YAY.

Definition at line 136 of file Constraint.hh.

References unimplemented_method_error().

virtual void core::scoring::constraints::Constraint::read_data ( std::istream & )

inlinevirtual

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,

Definition at line 151 of file Constraint.hh.

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

inlinevirtual

Definition at line 244 of file Constraint.hh.

References unimplemented_method_error().

virtual ConstraintOP core::scoring::constraints::Constraint::remap_resid ( core::id::SequenceMapping const & ) const

inlinevirtual

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.

Definition at line 158 of file Constraint.hh.

References unimplemented_method_error().

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

inlinevirtual

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.

Definition at line 98 of file Constraint.hh.

References unimplemented_method_error().

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

Definition at line 47 of file Constraint.cc.

References atom(), and natoms().

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

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.

Referenced by core::scoring::constraints::Constraints::energy(), and protocols::constraints_additional::MaxSeqSepConstraintSet::eval_non_residue_pair_energy().

virtual Real core::scoring::constraints::Constraint::score ( conformation::Conformation const & ) const

inlinevirtual

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, core::scoring::constraints::DihedralPairConstraint, and core::scoring::constraints::DistancePairConstraint.

Definition at line 207 of file Constraint.hh.

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

inline

Returns the ScoreType that this Constraint object will use.

Definition at line 142 of file Constraint.hh.

References score_type_.

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

inlinevirtual

Reimplemented in protocols::constraints_additional::BindingSiteConstraint.

Definition at line 199 of file Constraint.hh.

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

inlinevirtual

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

Definition at line 196 of file Constraint.hh.

virtual void core::scoring::constraints::Constraint::show ( std::ostream & ) const

inlinevirtual

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.

Definition at line 227 of file Constraint.hh.

References unimplemented_method_error().

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

inlinevirtual

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.

Definition at line 236 of file Constraint.hh.

References unimplemented_method_error().

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

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

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 ...

Definition at line 35 of file Constraint.cc.

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

virtual void core::scoring::constraints::Constraint::steal_def ( pose::Pose const & )

inlinevirtual

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

Definition at line 250 of file Constraint.hh.

References unimplemented_method_error().

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.

Definition at line 256 of file Constraint.hh.

References show().

virtual std::string core::scoring::constraints::Constraint::type ( ) const

inlinevirtual

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

Definition at line 191 of file Constraint.hh.

Referenced by unimplemented_method_error().

void core::scoring::constraints::Constraint::unimplemented_method_error ( std::string const & method_name) const

inlineprivate

Utility method for producing useful error messages and exiting from program. Declared const which is funny, because exiting the program certainly changes the state of this object! This might be replaced with exception handling if we ever start using those inside of mini.

Definition at line 318 of file Constraint.hh.

References type().

Referenced by clone(), dist(), get_func(), operator==(), read_constraint(), read_def(), remap_resid(), remapped_clone(), show(), show_def(), and steal_def().

Member Data Documentation

ScoreType const core::scoring::constraints::Constraint::score_type_

private

Definition at line 312 of file Constraint.hh.

Referenced by score_type().

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

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

Public Types

Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation