#include <CoordinateConstraint.hh>

Inheritance diagram for core::scoring::constraints::CoordinateConstraint:

Public Member Functions
	CoordinateConstraint ()

	CoordinateConstraint (CoordinateConstraint const &src)
	Constructor as a deep copy of the src CoordinateConstraint. More...

	CoordinateConstraint (AtomID const &a1, AtomID const &fixed_atom_in, Vector const &xyz_target_in, core::scoring::func::FuncOP func, ScoreType scotype=coordinate_constraint)
	c-tor More...

	~CoordinateConstraint () override

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

ConstraintOP	clone () const override

ConstraintOP	clone (core::scoring::func::FuncOP) const override
	Clone the constraint, but where a new Func object is to be used instead. 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...

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	read_def (std::istream &, pose::Pose const &, func::FuncFactory const &) override

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

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

Real	non_virtual_score (Vector const &xyz) const

void	score (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...

core::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, 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...

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...

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...

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

Vector const &	xyz_target () const

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) const
	Returns the unweighted score of this constraint computed over the given pose. 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 Real	dist (core::pose::Pose const &) const
	return the raw "distance" before that distance is handed to the FUNC object 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

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 &)

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

Private Member Functions
Real	func (Real const theta) const

Real	dfunc (Real const theta) const

Private Attributes
AtomID	atom_

AtomID	fixed_atom_

Vector	xyz_target_

core::scoring::func::FuncOP	func_

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

Detailed Description

CoordinateConstraint compares the coordinates of a given atom (AtomID atom_) to a fixed coordinate triplet (Vector xyz_target_). Its other argument, fixed_atom_, is somewhat nonobvious. CoordinateConstraints are meant to be used with a Pose that has a nonmoving virtual root residue. An AtomID in this virtual root residue should be passed as fixed_atom_. CoordinateConstraint does not use fixed_atom_, but the ScoreFunction code detects when fixed_atom_ and atom_ move relative to one another, and trigger re-scoring at that time. In other words, CoordinateConstraints are really context-independent one body energies, but we wish them to be evaluated as context-independent two-body energies. (Ideally, ScoreFunction would detect when atom_ moves relative to xyz_target_, but since ScoreFunction functions on atoms and not floating coordinate triplets, this is a good workaround.) – SML

Would be good to have something like StubCoordinateConstraint that allows definition of (x,y,z) of moving atom to be defined in coordinate system defined by three "stub" atoms. Shows up when treating the effects of missing loops. Working out a sketch of this as a 'standalone' in rna::StubCoordinateHack, but should ideally integrate into Constraint machinery.

Constructor & Destructor Documentation

core::scoring::constraints::CoordinateConstraint::CoordinateConstraint ( )

Referenced by clone().

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

Constructor as a deep copy of the src CoordinateConstraint.

core::scoring::constraints::CoordinateConstraint::CoordinateConstraint	(	AtomID const &	a1,
		AtomID const &	fixed_atom_in,
		Vector const &	xyz_target_in,
		core::scoring::func::FuncOP	func,
		ScoreType	scotype = `coordinate_constraint`
	)

c-tor

core::scoring::constraints::CoordinateConstraint::~CoordinateConstraint ( )

overridedefault

Member Function Documentation

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

overridevirtual

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 atom_, and fixed_atom_.

Referenced by remapped_clone().

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

overridevirtual

Invoke the copy constructor, which will perform a deep copy by cloning the func object

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

References CoordinateConstraint().

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

overridevirtual

Clone the constraint, but where a new Func object is to be used instead.

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

References atom_, CoordinateConstraint(), fixed_atom_, core::scoring::constraints::Constraint::score_type(), and xyz_target_.

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

private

References func_.

Referenced by fill_f1_f2().

core::Real core::scoring::constraints::CoordinateConstraint::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 atom_, protocols::kinmatch::xyz(), and xyz_target_.

Referenced by fill_f1_f2(), and show_violations().

void core::scoring::constraints::CoordinateConstraint::fill_f1_f2	(	AtomID const &	atom,
		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 atom_, dfunc(), dist(), core::scoring::constraints::Constraint::score_type(), protocols::kinmatch::xyz(), and xyz_target_.

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

private

References func_.

Referenced by non_virtual_score().

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

overridevirtual

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

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

References func_.

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

overridevirtual

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.

Real core::scoring::constraints::CoordinateConstraint::non_virtual_score ( Vector const & xyz ) const

References func(), and xyz_target_.

Referenced by score().

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

overridevirtual

possibility to do object comparison instead of pointer comparison

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

References atom_, fixed_atom_, func_, same_type_as_me(), core::scoring::constraints::Constraint::same_type_as_me(), core::scoring::constraints::Constraint::score_type(), and xyz_target_.

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

overridevirtual

one line definition "CoordinateConstraint Atom1_Name Atom1_ResNum Atom2_Name Atom2_ResNum Atom1_target_X_coordinate Atom1_target_Y_coordinate Atom1_target_Z_coordinate func::Func_Type func::Func_Def"

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

References atom_, core::id::AtomID::atomno(), fixed_atom_, func_, 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 xyz_target_.

ConstraintOP core::scoring::constraints::CoordinateConstraint::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.

References atom_, core::id::AtomID::atomno(), fixed_atom_, func_, core::id::AtomID::rsd(), core::scoring::constraints::Constraint::score_type(), and xyz_target_.

ConstraintOP core::scoring::constraints::CoordinateConstraint::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.

References atom(), 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(), core::id::AtomID::valid(), and xyz_target_.

bool core::scoring::constraints::CoordinateConstraint::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.

Referenced by operator==().

void core::scoring::constraints::CoordinateConstraint::score	(	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 atom_, non_virtual_score(), core::scoring::constraints::Constraint::score_type(), and protocols::kinmatch::xyz().

void core::scoring::constraints::CoordinateConstraint::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 atom_, core::id::AtomID::atomno(), fixed_atom_, func_, and core::id::AtomID::rsd().

void core::scoring::constraints::CoordinateConstraint::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.

References atom_, core::pose::atom_id_to_named_atom_id(), fixed_atom_, func_, type(), and xyz_target_.

Size core::scoring::constraints::CoordinateConstraint::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 atom_, core::id::AtomID::atomno(), dist(), func_, core::pose::Pose::residue_type(), and core::id::AtomID::rsd().