#include <AmbiguousNMRConstraint.hh>

Public Member Functions
	AmbiguousNMRConstraint (func::FuncOP func=NULL)
	default Constructor More...

	AmbiguousNMRConstraint (const ConstraintCOPs &cst_in, func::FuncOP func)
	Constructor. 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 (func::FuncOP func) const

virtual MultiConstraintOP	empty_clone () const

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

virtual void	score (func::XYZ_Func const &xyz_func, EnergyMap const &weights, EnergyMap &emap) const
	compute score More...

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

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

virtual void	add_individual_constraint (ConstraintCOP cst_in)
	add individual constraint into AmbiguousNMRConstraint 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 void	fill_f1_f2 (AtomID const &atom, func::XYZ_Func const &xyz, Vector &F1, Vector &F2, EnergyMap const &weights) const
	compute atom deriv More...

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

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

virtual 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 Size	show_violations (std::ostream &out, pose::Pose const &pose, Size verbose_level, Real threshold=1.0) 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...

Public Member Functions inherited from core::scoring::constraints::MultiConstraint
	MultiConstraint (ScoreType const &t=dof_constraint)
	default Constructor More...

	MultiConstraint (const ConstraintCOPs &cst_in, ScoreType const &t=dof_constraint)
	Constructor. More...

Size	natoms () const
	number of atoms involved in this MultiConstraint container More...

Size	size () const
	number of constraints data More...

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

virtual AtomID const &	atom (Size const n) const
	Returns the AtomID referred to by index. 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	setup_for_scoring (func::XYZ_Func const &, ScoreFunction const &) const

virtual 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...

ConstraintCOPs const &	member_constraints () const

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

void	set_effective_sequence_separation (core::Size setting)

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

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

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

Private Attributes
func::FuncOP	func_

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

Protected Attributes inherited from core::scoring::constraints::MultiConstraint
ConstraintCOPs	member_constraints_

Constructor & Destructor Documentation

core::scoring::constraints::AmbiguousNMRConstraint::AmbiguousNMRConstraint ( func::FuncOP func = NULL )

default Constructor

Constructor.

References core::scoring::constraints::MultiConstraint::member_constraints(), and core::scoring::constraints::MultiConstraint::size().

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

core::scoring::constraints::AmbiguousNMRConstraint::AmbiguousNMRConstraint	(	const ConstraintCOPs &	cst_in,
		func::FuncOP	func
	)

Constructor.

References core::scoring::constraints::MultiConstraint::member_constraints(), and core::scoring::constraints::MultiConstraint::size().

Member Function Documentation

void core::scoring::constraints::AmbiguousNMRConstraint::add_individual_constraint ( ConstraintCOP cst_in )

virtual

add individual constraint into AmbiguousNMRConstraint

Reimplemented from core::scoring::constraints::MultiConstraint.

References core::scoring::constraints::MultiConstraint::add_individual_constraint(), and utility::pointer::owning_ptr< T >::get().

virtual ConstraintOP core::scoring::constraints::AmbiguousNMRConstraint::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.

Reimplemented from core::scoring::constraints::MultiConstraint.

References AmbiguousNMRConstraint(), func_, core::scoring::constraints::MultiConstraint::member_constraints_, and core::scoring::constraints::MultiConstraint::size().

Referenced by empty_clone(), and remap_resid().

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

inlinevirtual

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

References AmbiguousNMRConstraint(), core::scoring::constraints::MultiConstraint::member_constraints_, and core::scoring::constraints::MultiConstraint::size().

core::Real core::scoring::constraints::AmbiguousNMRConstraint::dist ( core::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().

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

virtual

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

References begin, dist(), core::scoring::constraints::MultiConstraint::member_constraints(), basic::NOESY_ASSIGN_DIST_CST_CAST, PROF_START, PROF_STOP, and runtime_assert.

virtual MultiConstraintOP core::scoring::constraints::AmbiguousNMRConstraint::empty_clone ( ) const

inlinevirtual

Reimplemented from core::scoring::constraints::MultiConstraint.

References AmbiguousNMRConstraint(), clone(), and get_func().

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

virtual

compute atom deriv

function to minimize lowest scoring member constraint

Reimplemented from core::scoring::constraints::MultiConstraint.

References begin, dist(), get_func(), core::scoring::constraints::MultiConstraint::member_constraints(), and core::scoring::constraints::Constraint::score_type().

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

inlinevirtual

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

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

References func_, and runtime_assert.

Referenced by empty_clone(), fill_f1_f2(), remap_resid(), and score().

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

virtual

read definition of a multiconstraint. Since a MultiConstraint is essentially a vector of

Reimplemented from core::scoring::constraints::MultiConstraint.

References func_, core::scoring::func::FuncFactory::new_func(), and core::scoring::constraints::MultiConstraint::read_def().

ConstraintOP core::scoring::constraints::AmbiguousNMRConstraint::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::MultiConstraint.

References AmbiguousNMRConstraint(), clone(), get_func(), and core::scoring::constraints::MultiConstraint::member_constraints_.

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

virtual

compute score

ScoreFunction, scores all member constraints but only reports the lowest one.

Reimplemented from core::scoring::constraints::MultiConstraint.

References begin, dist(), core::scoring::func::Func::func(), get_func(), core::scoring::constraints::MultiConstraint::member_constraints(), runtime_assert, and core::scoring::constraints::Constraint::score_type().

void core::scoring::constraints::AmbiguousNMRConstraint::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::MultiConstraint.

References begin, func_, core::scoring::constraints::MultiConstraint::member_constraints(), and type().

Size core::scoring::constraints::AmbiguousNMRConstraint::show_violations	(	std::ostream &	out,
		pose::Pose const &	,
		Size	,
		Real	threshold = `1.0`
	)		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::MultiConstraint.

References begin, dist(), func_, core::scoring::constraints::MultiConstraint::member_constraints(), and viol.

virtual std::string core::scoring::constraints::AmbiguousNMRConstraint::type ( ) const

inlinevirtual

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

Reimplemented from core::scoring::constraints::MultiConstraint.

Referenced by show_def().