#include <AmbiguousNMRConstraint.hh>

Inheritance diagram for core::scoring::constraints::AmbiguousNMRConstraint:

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

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

ConstraintOP	clone () const override
	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...

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

MultiConstraintOP	empty_clone () const override

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

bool	operator== (Constraint const &other) const override
	Equality operator to test whether two constraints are functionally identical. 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	score (func::XYZ_Func const &xyz_func, EnergyMap const &weights, EnergyMap &emap) const override
	compute score More...

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

void	add_individual_constraint (ConstraintCOP cst_in) override
	add individual constraint into AmbiguousNMRConstraint 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...

void	fill_f1_f2 (AtomID const &atom, func::XYZ_Func const &xyz, Vector &F1, Vector &F2, EnergyMap const &weights) const override
	compute atom deriv More...

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

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

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...

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

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

	MultiConstraint (ConstraintCOPs const &cst_in, ScoreType const &t=dof_constraint)
	Constructor – performs a shallow copy of the input ConstraintCOPs. More...

ConstraintOP	clone () const override
	Creates a deep copy of this MultiConstaint, cloning all constraints that it holds. More...

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

Size	size () const
	number of constraints that are held by this MultiConstraint More...

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

void	read_def (std::istream &data, pose::Pose const &pose, func::FuncFactory const &func_factory) override
	read in constraint defiinition More...

bool	operator== (Constraint const &other) const override
	possibility to compare constraint according to data and not just pointers 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	score (func::XYZ_Func const &xyz_func, EnergyMap const &weights, EnergyMap &emap) const override
	compute score More...

core::Real	dist (core::scoring::func::XYZ_Func const &) const override

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

utility::vector1< core::Size >	residues () const override
	Returns the pose numbers of the residues involved in this constraint, in no particular order. More...

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

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...

void	fill_f1_f2 (AtomID const &atom, func::XYZ_Func const &xyz, Vector &F1, Vector &F2, EnergyMap const &weights) const override
	compute atom deriv 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	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...

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

ConstraintCOPs const &	member_constraints () const

ConstraintOP	remapped_clone (pose::Pose const &, pose::Pose const &, 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 .. NULL = identity mapping to the new object. Intended to be implemented by derived classes. More...

void	set_effective_sequence_separation (core::Size setting)

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

core::Size	effective_sequence_separation (core::kinematics::ShortestPathInFoldTree 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 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_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...

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

Protected Member Functions inherited from core::scoring::constraints::MultiConstraint
	MultiConstraint (MultiConstraint const &src)
	Explicit copy constructor so that derived classes will recieve a deep copy of the member constraints held in this class. More...

	MultiConstraint (MultiConstraint const &src, dont_copy_constraints const &)
	non-public key for special constructor More...

ConstraintCOPs	cloned_member_constraints () const
	Return a vector of Constraints that are clones of the member constraints. More...

Private Attributes
func::FuncOP	func_

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

Constructor & Destructor Documentation

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

default Constructor

Constructor.

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

Referenced by clone(), and empty_clone().

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

Constructor.

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

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

protected

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

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

Member Function Documentation

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

overridevirtual

add individual constraint into AmbiguousNMRConstraint

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

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

Referenced by AmbiguousNMRConstraint().

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

overridevirtual

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 AmbiguousNMRConstraint().

Referenced by empty_clone().

ConstraintOP core::scoring::constraints::AmbiguousNMRConstraint::clone ( 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 AmbiguousNMRConstraint(), and core::scoring::constraints::MultiConstraint::cloned_member_constraints().

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

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

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

overridevirtual

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

overridevirtual

compute atom deriv

function to minimize lowest scoring member constraint

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

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

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

overridevirtual

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

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

References func_.

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

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

overridevirtual

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 func_, core::scoring::constraints::MultiConstraint::operator==(), and core::scoring::constraints::Constraint::same_type_as_me().

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

overridevirtual

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

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

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

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 core::scoring::func::Func::clone(), get_func(), and core::scoring::constraints::MultiConstraint::member_constraints().

bool core::scoring::constraints::AmbiguousNMRConstraint::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.

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

overridevirtual

compute score

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

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

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

void core::scoring::constraints::AmbiguousNMRConstraint::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 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

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

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

overridevirtual

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

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

Referenced by show_def().