#include <LocalCoordinateConstraint.hh>

Inheritance diagram for core::scoring::constraints::LocalCoordinateConstraint:

Public Member Functions
	LocalCoordinateConstraint ()

	LocalCoordinateConstraint (id::AtomID const &a1, id::StubID const &fixed_stub_in, Vector const &xyz_target_in, func::FuncOP func, ScoreType scotype=coordinate_constraint)
	c-tor More...

	~LocalCoordinateConstraint ()

virtual std::string	type () const
	Returns a unique string identified for this constraint. Used in several places, including the ConstraintIO class. 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. This function must return a deep copy of itself – meaning that if this Constraint holds pointers to other Constraints that it must invoke clone on those Constraints as well. If the Constraint holds a FuncOP, then the Func should also be cloned. More...

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...

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...

virtual bool	operator== (Constraint const &rhs) const
	Equality operator to test whether two constraints are functionally identical. More...

virtual bool	same_type_as_me (Constraint const &other) const
	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 (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...

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

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...

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

Real	score (Vector const &xyz, Vector const &s1, Vector const &s2, Vector const &s3) const

void	score (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...

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

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

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...

void	set_fixed_stub (id::StubID new_stub)

Vector	xyz_target (core::pose::Pose const &local_frame_pose) const

void	set_xyz_target (Vector const &xyz_in, core::pose::Pose const &local_frame_pose)

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

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

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

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

Protected Member Functions
	LocalCoordinateConstraint (LocalCoordinateConstraint 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
id::AtomID	atom_

id::StubID	fixed_stub_

Vector	xyz_target_

func::FuncOP	func_

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

Constructor & Destructor Documentation

core::scoring::constraints::LocalCoordinateConstraint::LocalCoordinateConstraint ( )

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

core::scoring::constraints::LocalCoordinateConstraint::LocalCoordinateConstraint	(	id::AtomID const &	a1,
		id::StubID const &	fixed_stub_in,
		Vector const &	xyz_target_in,
		func::FuncOP	func,
		ScoreType	scotype = `coordinate_constraint`
	)

c-tor

References core::id::StubID::atom(), core::id::StubID::center(), fixed_stub_, and core::id::AtomID::valid().

core::scoring::constraints::LocalCoordinateConstraint::~LocalCoordinateConstraint ( )

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

protected

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

Member Function Documentation

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

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.

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

References core::id::StubID::atom(), atom_, and fixed_stub_.

Referenced by remapped_clone().

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

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. This function must return a deep copy of itself – meaning that if this Constraint holds pointers to other Constraints that it must invoke clone on those Constraints as well. If the Constraint holds a FuncOP, then the Func should also be cloned.

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

References LocalCoordinateConstraint().

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

private

References func_.

Referenced by fill_f1_f2().

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

virtual

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 core::id::StubID::atom(), atom_, fixed_stub_, core::kinematics::Stub::global2local(), protocols::kinmatch::xyz(), and xyz_target_.

Referenced by fill_f1_f2(), and show_violations().

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

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

private

References func_.

Referenced by score().

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

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.

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

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

virtual

Equality operator to test whether two constraints are functionally identical.

This operator should use floating point comparison and should not decide that two floats are identical if they are within some epsilon > 0. This method allows developes to remove specific constraints from Poses, even if the constraints have been cloned. Remapped constraints should not be considered identical – i.e., if cst1 is between residues i and j and cst2 is between residues i+1 and j+1. All subclasses of Constraint must implement this method.

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

References atom_, fixed_stub_, 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::LocalCoordinateConstraint::read_def	(	std::istream &	data,
		pose::Pose const &	pose,
		func::FuncFactory const &	func_factory
	)

virtual

one line definition "LocalCoordinateConstraint Atom1_Name Atom1_ResNum Atom2_Name Atom3_Name Atom4_Name Atom234_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_, fixed_stub_, func_, core::pose::named_atom_id_to_atom_id(), core::pose::named_stub_id_to_stub_id(), core::scoring::func::FuncFactory::new_func(), core::scoring::constraints::ConstraintIO::parse_residue(), core::pose::Pose::size(), core::scoring::constraints::tr(), core::id::AtomID::valid(), core::id::StubID::valid(), and xyz_target_.

ConstraintOP core::scoring::constraints::LocalCoordinateConstraint::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 core::id::StubID::atom(), atom_, core::id::AtomID::atomno(), fixed_stub_, func_, LocalCoordinateConstraint(), core::id::AtomID::rsd(), core::scoring::constraints::Constraint::score_type(), and xyz_target_.

ConstraintOP core::scoring::constraints::LocalCoordinateConstraint::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.

References atom(), core::pose::atom_id_to_named_atom_id(), func_, LocalCoordinateConstraint(), core::pose::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::LocalCoordinateConstraint::same_type_as_me ( Constraint const & other ) const

virtual

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==().

Real core::scoring::constraints::LocalCoordinateConstraint::score	(	Vector const &	xyz,
		Vector const &	s1,
		Vector const &	s2,
		Vector const &	s3
	)		const

References func(), core::kinematics::Stub::global2local(), and xyz_target_.

Referenced by score().

void core::scoring::constraints::LocalCoordinateConstraint::score	(	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 core::id::StubID::atom(), atom_, fixed_stub_, score(), core::scoring::constraints::Constraint::score_type(), and protocols::kinmatch::xyz().

void core::scoring::constraints::LocalCoordinateConstraint::set_fixed_stub ( id::StubID new_stub )

References fixed_stub_.

void core::scoring::constraints::LocalCoordinateConstraint::set_xyz_target	(	Vector const &	xyz_in,
		core::pose::Pose const &	local_frame_pose
	)

References core::pose::Pose::conformation(), fixed_stub_, and xyz_target_.

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

void core::scoring::constraints::LocalCoordinateConstraint::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.

References core::id::NamedStubID::atom(), core::id::NamedAtomID::atom(), atom_, core::pose::atom_id_to_named_atom_id(), fixed_stub_, func_, core::id::NamedAtomID::rsd(), core::pose::stub_id_to_named_stub_id(), type(), and xyz_target_.

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