#include <AtomPairConstraint.hh>

Public Member Functions
	AtomPairConstraint ()

	AtomPairConstraint (AtomID const &a1, AtomID const &a2, core::scoring::func::FuncOP func, ScoreType scoretype=atom_pair_constraint)
	c-tor More...

virtual ConstraintOP	clone () const
	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 (core::scoring::func::FuncOP func) const

virtual ConstraintOP	remapped_clone (pose::Pose const &src, pose::Pose const &dest, 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...

bool	operator== (Constraint const &other) const
	possibility to compare constraint according to data and not just pointers More...

Real	score (Vector const &xyz1, Vector const &xyz2) const

void	score (core::scoring::func::XYZ_Func const &xyz, EnergyMap const &, EnergyMap &emap) const
	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...

Real	score (pose::Pose const &pose) const

virtual void	fill_f1_f2 (AtomID const &atom, core::scoring::func::XYZ_Func const &xyz, Vector &F1, Vector &F2, EnergyMap const &weights) const
	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...

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

Size	natoms () const
	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 ConstraintOP	remap_resid (core::id::SequenceMapping const &seqmap) 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...

AtomID const &	atom (Size const n) const
	Returns the AtomID referred to by index. More...

void	show (std::ostream &out) 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...

void	show_def (std::ostream &out, pose::Pose const &pose) const
	Prints the definition of a Constraint to the given std::ostream, using the given Pose, and the given func::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...

void	read_def (std::istream &in, pose::Pose const &pose, func::FuncFactory const &func_factory)

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

Real	dist (core::conformation::Conformation const &conformation) const

virtual Real	dist (core::scoring::func::XYZ_Func const &xyz) const

virtual Size	show_violations (std::ostream &out, pose::Pose const &pose, Size verbose_level, 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::Func const &	get_func () const
	Returns the func::Func object associated with this Constraint object. More...

virtual core::Size	effective_sequence_separation (core::kinematics::ShortestPathInFoldTree const &sp) const

Public Member Functions inherited from core::scoring::constraints::Constraint
	Constraint (ScoreType const &t)
	Constructor for Constraint class. More...

virtual	~Constraint ()
	Virtual destructor. 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 void	setup_for_scoring (core::scoring::func::XYZ_Func const &, ScoreFunction const &) const

virtual void	setup_for_derivatives (core::scoring::func::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	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...

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 &)

Protected Attributes
AtomID	atom1_

AtomID	atom2_

core::scoring::func::FuncOP	func_

Private Member Functions
Real	func (Real const theta) const

Real	dfunc (Real const theta) const

Additional Inherited Members
Public Types inherited from core::scoring::constraints::Constraint
typedef id::AtomID	AtomID

Constructor & Destructor Documentation

core::scoring::constraints::AtomPairConstraint::AtomPairConstraint ( )

inline

Referenced by clone(), remap_resid(), and remapped_clone().

core::scoring::constraints::AtomPairConstraint::AtomPairConstraint	(	AtomID const &	a1,
		AtomID const &	a2,
		core::scoring::func::FuncOP	func,
		ScoreType	scoretype = `atom_pair_constraint`
	)

inline

c-tor

Member Function Documentation

AtomID const& core::scoring::constraints::AtomPairConstraint::atom ( Size const index ) const

inlinevirtual

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.

Implements core::scoring::constraints::Constraint.

References atom1_, atom2_, and utility_exit_with_message.

Referenced by core::pose::ncbb::add_oop_constraint(), and remapped_clone().

virtual ConstraintOP core::scoring::constraints::AtomPairConstraint::clone ( ) const

inlinevirtual

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.

Implements core::scoring::constraints::Constraint.

Reimplemented in core::scoring::constraints::NamedAtomPairConstraint.

References atom1_, atom2_, AtomPairConstraint(), func_, and core::scoring::constraints::Constraint::score_type().

virtual ConstraintOP core::scoring::constraints::AtomPairConstraint::clone ( core::scoring::func::FuncOP func ) const

inlinevirtual

Reimplemented from core::scoring::constraints::Constraint.

References atom1_, atom2_, AtomPairConstraint(), and core::scoring::constraints::Constraint::score_type().

Real core::scoring::constraints::AtomPairConstraint::dfunc ( Real const theta ) const

inlineprivate

References func_.

Referenced by fill_f1_f2().

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

virtual

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

Reimplemented from core::scoring::constraints::Constraint.

References core::pose::Pose::conformation().

Referenced by dist(), fill_f1_f2(), score(), and show_violations().

Real core::scoring::constraints::AtomPairConstraint::dist ( core::conformation::Conformation const & conformation ) const

References atom1_, atom2_, core::conformation::Conformation::atom_tree(), core::id::AtomID::atomno(), dist(), core::kinematics::AtomTree::has(), core::conformation::Residue::natoms(), core::conformation::Conformation::residue(), core::id::AtomID::rsd(), and core::conformation::Conformation::xyz().

Real core::scoring::constraints::AtomPairConstraint::dist ( core::scoring::func::XYZ_Func const & xyz ) const

virtual

Reimplemented from core::scoring::constraints::Constraint.

References atom1_, atom2_, and core::id::AtomID::atomno().

core::Size core::scoring::constraints::AtomPairConstraint::effective_sequence_separation ( core::kinematics::ShortestPathInFoldTree const & sp ) const

virtual

Reimplemented from core::scoring::constraints::Constraint.

References atom1_, atom2_, core::kinematics::ShortestPathInFoldTree::dist(), and core::id::AtomID::rsd().

void core::scoring::constraints::AtomPairConstraint::fill_f1_f2	(	AtomID const &	atom,
		core::scoring::func::XYZ_Func const &	xyz_func,
		Vector &	F1,
		Vector &	F2,
		EnergyMap const &	weights
	)		const

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!)

Implements core::scoring::constraints::Constraint.

References atom1_, atom2_, dfunc(), dist(), numeric::deriv::distance_f1_f2_deriv(), and core::scoring::constraints::Constraint::score_type().

Real core::scoring::constraints::AtomPairConstraint::func ( Real const theta ) const

inlineprivate

References func_.

Referenced by score().

virtual func::Func const& core::scoring::constraints::AtomPairConstraint::get_func ( ) const

inlinevirtual

Returns the func::Func object associated with this Constraint object.

Reimplemented from core::scoring::constraints::Constraint.

References func_.

Size core::scoring::constraints::AtomPairConstraint::natoms ( ) const

inlinevirtual

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.

Implements core::scoring::constraints::Constraint.

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

virtual

possibility to compare constraint according to data and not just pointers

Reimplemented from core::scoring::constraints::Constraint.

References atom1_, atom2_, func_, and core::scoring::constraints::Constraint::score_type().

void core::scoring::constraints::AtomPairConstraint::read_def	(	std::istream &	data,
		pose::Pose const &	pose,
		func::FuncFactory const &	func_factory
	)

virtual

one line definition "AtomPairs atom1 res1 atom2 res2 function_type function_definition"

Reimplemented from core::scoring::constraints::Constraint.

Reimplemented in core::scoring::constraints::NamedAtomPairConstraint.

References atom1_, atom2_, core::id::AtomID::atomno(), func_, core::pose::Pose::is_fullatom(), core::conformation::named_atom_id_to_atom_id(), core::scoring::func::FuncFactory::new_func(), core::scoring::constraints::ConstraintIO::parse_residue(), runtime_assert, core::pose::Pose::total_residue(), core::scoring::constraints::tr, type(), and core::id::AtomID::valid().

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

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 from core::scoring::constraints::Constraint.

References atom1_, atom2_, core::id::AtomID::atomno(), AtomPairConstraint(), func_, and core::id::AtomID::rsd().

ConstraintOP core::scoring::constraints::AtomPairConstraint::remapped_clone	(	pose::Pose const &	src,
		pose::Pose const &	dest,
		id::SequenceMappingCOP	map = `NULL`
	)		const

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 from core::scoring::constraints::Constraint.

Reimplemented in core::scoring::constraints::NamedAtomPairConstraint.

References atom(), atom1_, atom2_, core::conformation::atom_id_to_named_atom_id(), AtomPairConstraint(), func_, core::conformation::named_atom_id_to_atom_id(), core::id::AtomID::rsd(), core::id::NamedAtomID::rsd(), core::scoring::constraints::Constraint::score_type(), and core::id::AtomID::valid().

Real core::scoring::constraints::AtomPairConstraint::score	(	Vector const &	xyz1,
		Vector const &	xyz2
	)		const

References numeric::xyzVector< class >::distance(), and func().

Referenced by score().

void core::scoring::constraints::AtomPairConstraint::score	(	core::scoring::func::XYZ_Func const &	xyz_func,
		EnergyMap const &	weights,
		EnergyMap &	emap
	)		const

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.

Implements core::scoring::constraints::Constraint.

References atom1_, atom2_, score(), and core::scoring::constraints::Constraint::score_type().

Real core::scoring::constraints::AtomPairConstraint::score ( pose::Pose const & pose ) const

inlinevirtual

Reimplemented from core::scoring::constraints::Constraint.

References dist(), and func_.

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

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 from core::scoring::constraints::Constraint.

References atom1_, atom2_, core::id::AtomID::atomno(), func_, and core::id::AtomID::rsd().

void core::scoring::constraints::AtomPairConstraint::show_def	(	std::ostream &	,
		pose::Pose const &
	)		const

virtual

Prints the definition of a Constraint to the given std::ostream, using the given Pose, and the given func::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 from core::scoring::constraints::Constraint.

Reimplemented in core::scoring::constraints::NamedAtomPairConstraint.

References atom1_, atom2_, core::conformation::atom_id_to_named_atom_id(), func_, and type().

Size core::scoring::constraints::AtomPairConstraint::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 ...

Reimplemented from core::scoring::constraints::Constraint.

References atom1_, atom2_, core::id::AtomID::atomno(), core::pose::Pose::conformation(), dist(), func_, core::pose::Pose::residue_type(), and core::id::AtomID::rsd().