#include <AmbiguousNMRDistanceConstraint.hh>

Inheritance diagram for core::scoring::constraints::AmbiguousNMRDistanceConstraint:

Collaboration diagram for core::scoring::constraints::AmbiguousNMRDistanceConstraint:

Public Types
typedef utility::vector1< AtomID >	Atoms
Public Member Functions
	AmbiguousNMRDistanceConstraint (Atoms const &a1, Atoms const &a2, FuncOP func, ScoreType scoretype=atom_pair_constraint)
	c-tor
	AmbiguousNMRDistanceConstraint (id::NamedAtomID const &a1, id::NamedAtomID const &a2, core::pose::Pose const &, FuncOP func, ScoreType scoretype=atom_pair_constraint)
	AmbiguousNMRDistanceConstraint ()
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.
virtual ConstraintOP	clone (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.
ConstraintOP	map_to_CB (pose::Pose const &src, pose::Pose const &centroid, core::Size &nr_mapped) const
	returns AtomPairConstraint or AmbigousNMRDistanceConstraint (e.g. for GLY HA1-HA2 ... )
void	score (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.
core::Real	inv_dist6 (XYZ_Func const &xyz) const
virtual void	fill_f1_f2 (AtomID const &atom, 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!)
std::string	type () const
	Returns a unique string identified for this constraint. Used in several places, including the ConstraintIO class.
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.
Size	natoms (core::Size i) const
Size	multiplicity () const
Size	resid (core::Size i) const
	return residue number: i=1,2
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.
AtomID const &	atom (Size const n) const
	Returns the AtomID referred to by index.
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.
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 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.
void	read_def (std::istream &in, pose::Pose const &pose, FuncFactory const &func_factory)
Real	dist (pose::Pose const &pose) const
	return the "raw" distance before handed to the FUNC object
Real	dist (XYZ_Func const &xyz) const
Real	score (pose::Pose const &pose) 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 ...
virtual Func const &	get_func () const
	Returns the Func object associated with this Constraint object.
virtual core::Size	effective_sequence_separation (core::kinematics::ShortestPathInFoldTree const &sp) const
Protected Attributes
Atoms	atoms1_
Atoms	atoms2_
FuncOP	func_

Member Typedef Documentation

typedef utility::vector1< AtomID > core::scoring::constraints::AmbiguousNMRDistanceConstraint::Atoms

Constructor & Destructor Documentation

core::scoring::constraints::AmbiguousNMRDistanceConstraint::AmbiguousNMRDistanceConstraint	(	Atoms const &	a1,
		Atoms const &	a2,
		FuncOP	func,
		ScoreType	scoretype = `atom_pair_constraint`
	)		`[inline]`

c-tor

core::scoring::constraints::AmbiguousNMRDistanceConstraint::AmbiguousNMRDistanceConstraint	(	id::NamedAtomID const &	a1,
		id::NamedAtomID const &	a2,
		core::pose::Pose const &	pose,
		FuncOP	func,
		ScoreType	scoretype = `atom_pair_constraint`
	)

References core::id::NamedAtomID::atom(), atoms1_, atoms2_, core::scoring::constraints::parse_NMR_name(), core::id::NamedAtomID::rsd(), and core::scoring::constraints::tr().

core::scoring::constraints::AmbiguousNMRDistanceConstraint::AmbiguousNMRDistanceConstraint ( ) [inline]

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

Member Function Documentation

AtomID const& core::scoring::constraints::AmbiguousNMRDistanceConstraint::atom ( Size const index ) const [inline, 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 atoms1_, atoms2_, and natoms().

Referenced by fill_f1_f2(), remap_resid(), and remapped_clone().

virtual ConstraintOP core::scoring::constraints::AmbiguousNMRDistanceConstraint::clone ( FuncOP func ) const [inline, virtual]

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

References AmbiguousNMRDistanceConstraint(), atoms1_, atoms2_, and core::scoring::constraints::Constraint::score_type().

virtual ConstraintOP core::scoring::constraints::AmbiguousNMRDistanceConstraint::clone ( ) const [inline, 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.

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

References AmbiguousNMRDistanceConstraint(), atoms1_, atoms2_, func_, and core::scoring::constraints::Constraint::score_type().

Real core::scoring::constraints::AmbiguousNMRDistanceConstraint::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 fill_f1_f2(), inv_dist6(), score(), and show_violations().

Real core::scoring::constraints::AmbiguousNMRDistanceConstraint::dist ( XYZ_Func const & xyz ) const [virtual]

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

References inv_dist6().

core::Size core::scoring::constraints::AmbiguousNMRDistanceConstraint::effective_sequence_separation ( core::kinematics::ShortestPathInFoldTree const & sp ) const [virtual]

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

References core::kinematics::ShortestPathInFoldTree::dist(), and resid().

void core::scoring::constraints::AmbiguousNMRDistanceConstraint::fill_f1_f2	(	AtomID const &	atom,
		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(), atoms1_, atoms2_, dist(), core::scoring::constraints::Constraint::score_type(), and protocols::kinmatch::xyz().

virtual Func const& core::scoring::constraints::AmbiguousNMRDistanceConstraint::get_func ( ) const [inline, virtual]

Returns the Func object associated with this Constraint object.

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

References func_.

Real core::scoring::constraints::AmbiguousNMRDistanceConstraint::inv_dist6 ( XYZ_Func const & xyz ) const

References atoms1_, atoms2_, dist(), and protocols::kinmatch::xyz().

Referenced by dist(), core::scoring::constraints::AmbiguousNMRConstraint::dist(), score(), and core::scoring::constraints::AmbiguousNMRConstraint::score().

ConstraintOP core::scoring::constraints::AmbiguousNMRDistanceConstraint::map_to_CB	(	pose::Pose const &	src,
		pose::Pose const &	centroid,
		core::Size &	nr_mapped
	)		const

returns AtomPairConstraint or AmbigousNMRDistanceConstraint (e.g. for GLY HA1-HA2 ... )

References AmbiguousNMRDistanceConstraint(), atoms1_, atoms2_, core::scoring::constraints::combine_NMR_atom_string(), func_, core::conformation::named_atom_id_to_atom_id(), core::scoring::constraints::requires_CB_mapping(), resid(), core::scoring::constraints::Constraint::score_type(), and core::scoring::constraints::tr().

Size core::scoring::constraints::AmbiguousNMRDistanceConstraint::multiplicity ( ) const [inline]

References atoms1_, and atoms2_.

Size core::scoring::constraints::AmbiguousNMRDistanceConstraint::natoms ( ) const [inline, 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.

References atoms1_, and atoms2_.

Referenced by atom().

Size core::scoring::constraints::AmbiguousNMRDistanceConstraint::natoms ( core::Size i ) const [inline]

References atoms1_, and atoms2_.

void core::scoring::constraints::AmbiguousNMRDistanceConstraint::read_def	(	std::istream &	data,
		pose::Pose const &	pose,
		FuncFactory const &	func_factory
	)		`[virtual]`

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

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

References atoms1_, atoms2_, func_, core::scoring::constraints::FuncFactory::new_func(), core::scoring::constraints::parse_NMR_name(), core::scoring::constraints::ConstraintIO::parse_residue(), core::pose::Pose::total_residue(), core::scoring::constraints::tr(), and type().

ConstraintOP core::scoring::constraints::AmbiguousNMRDistanceConstraint::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 AmbiguousNMRDistanceConstraint(), atom(), atoms1_, atoms2_, func_, core::scoring::constraints::Constraint::score_type(), and core::id::AtomID::valid().

ConstraintOP core::scoring::constraints::AmbiguousNMRDistanceConstraint::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 AmbiguousNMRDistanceConstraint(), atom(), core::conformation::atom_id_to_named_atom_id(), core::pose::atom_id_to_named_atom_id(), atoms1_, atoms2_, func_, core::pose::named_atom_id_to_atom_id(), core::id::NamedAtomID::rsd(), core::scoring::constraints::Constraint::score_type(), and core::id::AtomID::valid().

Size core::scoring::constraints::AmbiguousNMRDistanceConstraint::resid ( core::Size i ) const [inline]

return residue number: i=1,2

References atoms1_, and atoms2_.

Referenced by effective_sequence_separation(), and map_to_CB().

Real core::scoring::constraints::AmbiguousNMRDistanceConstraint::score ( pose::Pose const & pose ) const [inline]

References dist(), and func_.

void core::scoring::constraints::AmbiguousNMRDistanceConstraint::score	(	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 inv_dist6(), and core::scoring::constraints::Constraint::score_type().

void core::scoring::constraints::AmbiguousNMRDistanceConstraint::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 atoms1_, atoms2_, and func_.

void core::scoring::constraints::AmbiguousNMRDistanceConstraint::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 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 atoms1_, atoms2_, core::scoring::constraints::combine_NMR_atom_string(), func_, and type().

Size core::scoring::constraints::AmbiguousNMRDistanceConstraint::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 dist(), and func_.

std::string core::scoring::constraints::AmbiguousNMRDistanceConstraint::type ( ) const [inline, virtual]

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

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

Referenced by read_def(), and show_def().