#include <AtomPairConstraint.hh>

Inheritance diagram for core::scoring::constraints::AtomPairConstraint:

Public Member Functions
	AtomPairConstraint ()

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

ConstraintOP	clone () const override
	Create a deep copy of this AtomPairConstraint, cloning its Func. More...

ConstraintOP	clone (func::FuncOP func) const override
	Create a deep copy of this AtomPairConstraint except that the copy should use the input Func instead of its existing one. More...

ConstraintOP	remapped_clone (pose::Pose const &src, pose::Pose const &dest, id::SequenceMappingCOP map=nullptr) const override
	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 .. nullptr = identity mapping to the new object. Intended to be implemented by derived classes. More...

bool	operator== (Constraint const &other) const override
	Compare a) the class types (w/ same_type_as_me), b) the atoms being constrained, c) the score_type being used, and d) the Func objects (the FuncOPs may point at different objects, but as long as those objects are equal, that counts) More...

bool	same_type_as_me (Constraint const &other) const override
	Determine if the calling class has the same type as the input class, using dynamic casts. This is important in ensuring that two constraints are equal: both this and other must check that the other is the same as it. This is not an optional method and every class should implement it, regaurdless of whether a parent class implements it. More...

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

void	score (core::scoring::func::XYZ_Func const &xyz, EnergyMap const &, EnergyMap &emap) const override
	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 override
	Returns the unweighted score of this constraint computed over the given pose. More...

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

Real	dist (core::scoring::func::XYZ_Func const &xyz) const override
	return the raw "distance" before that distance is handed to the FUNC object More...

void	fill_f1_f2 (AtomID const &atom, core::scoring::func::XYZ_Func const &xyz, Vector &F1, Vector &F2, EnergyMap const &weights) const override
	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 override
	Returns a unique string identified for this constraint. Used in several places, including the ConstraintIO class. More...

Size	natoms () const override
	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...

ConstraintOP	remap_resid (core::id::SequenceMapping const &seqmap) const override
	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 override
	Returns the AtomID referred to by index. More...

AtomID const &	atom1 () const

AtomID const &	atom2 () const

void	show (std::ostream &out) const override
	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 override
	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) override

Size	show_violations (std::ostream &out, pose::Pose const &pose, Size verbose_level, Real threshold=1) const override
	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...

func::Func const &	get_func () const override
	Returns the func::Func object associated with this Constraint object. More...

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

void	setup_for_scoring (func::XYZ_Func const &, ScoreFunction const &) const override

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

	~Constraint () override
	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 DON'T USE THIS ONE.. Most Constraint classes have not overloaded this one, but read_def ! OL. 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 Real	score (pose::Pose const &pose, EnergyMap const &weights) const
	Returns the weighted score of this constraint computed over the given pose. More...

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

virtual void	steal_def (pose::Pose const &)
	take coordinates, distances, angles, etc from given pose More...

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
	Inequality operator to test whether two constraints are not functionally identical. More...

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

Protected Member Functions
void	set_func (func::FuncOP setting)
	Setter for the derived class. More...

void	atom1 (AtomID newid) const
	Setter for the mutable atom1_ data member to be used by derived classes. Remember: data must never be protected, only private. Instead, protected mutators can be added if derived classes ought to have the ability to change the base class data that other classes/functions should not. More...

void	atom2 (AtomID newid) const
	Setter for the mutable atom2_ data member to be used by derived classes. Remember: data must never be protected, only private. Instead, protected mutators can be added if derived classes ought to have the ability to change the base class data that other classes/functions should not. More...

	AtomPairConstraint (AtomPairConstraint const &src)
	Explicit copy constructor so that derived classes will recieve a deep copy of the Func this class contains. More...

Private Member Functions
Real	func (Real const theta) const

Real	dfunc (Real const theta) const

Private Attributes
AtomID	atom1_

AtomID	atom2_

core::scoring::func::FuncOP	func_

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

Constructor & Destructor Documentation

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

Referenced by clone().

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

c-tor

core::scoring::constraints::AtomPairConstraint::AtomPairConstraint ( AtomPairConstraint const & src )

protected

Explicit copy constructor so that derived classes will recieve a deep copy of the Func this class contains.

Member Function Documentation

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

inlineoverridevirtual

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_, and atom2_.

Referenced by remapped_clone().

AtomID const& core::scoring::constraints::AtomPairConstraint::atom1 ( ) const

inline

References atom1_.

Referenced by core::scoring::constraints::NamedAtomPairConstraint::read_def(), remapped_clone(), core::scoring::constraints::NamedAtomPairConstraint::remapped_clone(), and core::scoring::constraints::NamedAtomPairConstraint::setup_for_scoring().

void core::scoring::constraints::AtomPairConstraint::atom1 ( AtomID newid ) const

protected

Setter for the mutable atom1_ data member to be used by derived classes. Remember: data must never be protected, only private. Instead, protected mutators can be added if derived classes ought to have the ability to change the base class data that other classes/functions should not.

References atom1_.

AtomID const& core::scoring::constraints::AtomPairConstraint::atom2 ( ) const

inline

References atom2_.

Referenced by core::scoring::constraints::NamedAtomPairConstraint::read_def(), remapped_clone(), core::scoring::constraints::NamedAtomPairConstraint::remapped_clone(), and core::scoring::constraints::NamedAtomPairConstraint::setup_for_scoring().

void core::scoring::constraints::AtomPairConstraint::atom2 ( AtomID newid ) const

protected

Setter for the mutable atom2_ data member to be used by derived classes. Remember: data must never be protected, only private. Instead, protected mutators can be added if derived classes ought to have the ability to change the base class data that other classes/functions should not.

References atom2_.

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

overridevirtual

Create a deep copy of this AtomPairConstraint, cloning its Func.

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

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

References AtomPairConstraint().

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

overridevirtual

Create a deep copy of this AtomPairConstraint except that the copy should use the input Func instead of its existing one.

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

private

References func_.

Referenced by fill_f1_f2().

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

overridevirtual

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

If such a distance doesn't make sense for this constraint, just return 0

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

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

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

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

overridevirtual

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

If such a distance doesn't make sense for this constraint, just return 0

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

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

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

overridevirtual

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

overridevirtual

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(), core::scoring::constraints::Constraint::score_type(), and protocols::kinmatch::xyz().

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

private

References func_.

Referenced by score().

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

overridevirtual

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

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

References func_.

Referenced by core::scoring::constraints::NamedAtomPairConstraint::read_def(), core::scoring::constraints::NamedAtomPairConstraint::remap_resid(), core::scoring::constraints::NamedAtomPairConstraint::remapped_clone(), and core::scoring::constraints::NamedAtomPairConstraint::show_def_nopose().

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

inlineoverridevirtual

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

overridevirtual

Compare a) the class types (w/ same_type_as_me), b) the atoms being constrained, c) the score_type being used, and d) the Func objects (the FuncOPs may point at different objects, but as long as those objects are equal, that counts)

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

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

References atom1_, atom2_, func_, same_type_as_me(), core::scoring::constraints::Constraint::same_type_as_me(), 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
	)

overridevirtual

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(), core::pose::Pose::size(), core::scoring::constraints::tr(), and core::id::AtomID::valid().

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

overridevirtual

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.

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

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

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

overridevirtual

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 .. nullptr = identity mapping to the new object. Intended to be implemented by derived classes.

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(), atom1_, atom2(), atom2_, core::conformation::atom_id_to_named_atom_id(), 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().

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

overridevirtual

Determine if the calling class has the same type as the input class, using dynamic casts. This is important in ensuring that two constraints are equal: both this and other must check that the other is the same as it. This is not an optional method and every class should implement it, regaurdless of whether a parent class implements it.

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

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

Referenced by operator==().

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

References func().

Referenced by score().

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

overridevirtual

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(), core::scoring::constraints::Constraint::score_type(), and protocols::kinmatch::xyz().

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

overridevirtual

Returns the unweighted score of this constraint computed over the given pose.

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

References dist(), and func_.

void core::scoring::constraints::AtomPairConstraint::set_func ( func::FuncOP setting )

protected

Setter for the derived class.

References func_.

Referenced by core::scoring::constraints::NamedAtomPairConstraint::read_def().

void core::scoring::constraints::AtomPairConstraint::setup_for_scoring	(	func::XYZ_Func const &	,
		ScoreFunction const &
	)		const

overridevirtual

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

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

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

overridevirtual

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

overridevirtual

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

overridevirtual

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().