#include <MultiConstraint.hh>

Inheritance diagram for core::scoring::constraints::MultiConstraint:

[legend]

Classes
struct	dont_copy_constraints

Public Member Functions
	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...

virtual MultiConstraintOP	empty_clone () const

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

virtual void	add_individual_constraint (ConstraintCOP cst_in)
	add individual constraint into MultiConstraint 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...

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

virtual void	score (core::scoring::func::XYZ_Func const &xyz_func, EnergyMap const &weights, EnergyMap &emap) const=0
	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 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 core::Real	dist (core::scoring::func::XYZ_Func const &) const=0
	return the raw "distance" before that distance is handed to the FUNC object More...

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

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

	~Constraint () override
	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 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...

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...

Protected Member Functions
	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
ConstraintCOPs	member_constraints_

utility::vector1< core::Size >	member_residues_

utility::vector1< AtomID >	member_atoms_

std::map< AtomID, ConstraintCOPs >	atomid_to_csts_

core::Size	report_this_as_effective_sequence_separation_ = 0

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

Constructor & Destructor Documentation

◆ MultiConstraint() [1/4]

core::scoring::constraints::MultiConstraint::MultiConstraint ( ScoreType const & t = dof_constraint )

default Constructor

Referenced by clone().

◆ MultiConstraint() [2/4]

core::scoring::constraints::MultiConstraint::MultiConstraint	(	ConstraintCOPs const &	cst_in,
		ScoreType const &	t = `dof_constraint`
	)

Constructor – performs a shallow copy of the input ConstraintCOPs.

Constructor.

References add_individual_constraint().

◆ MultiConstraint() [3/4]

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

protected

Explicit copy constructor so that derived classes will recieve a deep copy of the member constraints held in this class.

References add_individual_constraint(), and member_constraints_.

◆ MultiConstraint() [4/4]

core::scoring::constraints::MultiConstraint::MultiConstraint	(	MultiConstraint const &	src,
		dont_copy_constraints const &
	)

protected

non-public key for special constructor

a copy constructor where the underlying constraints aren't copied. (For subclasses which handle their own constraint copying.

Member Function Documentation

◆ add_individual_constraint()

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

virtual

add individual constraint into MultiConstraint

Reimplemented in core::scoring::constraints::AmbiguousNMRConstraint.

References atomid_to_csts_, member_atoms_, member_constraints_, member_residues_, and core::id::AtomID::rsd().

Referenced by core::scoring::constraints::AmbiguousNMRConstraint::add_individual_constraint(), MultiConstraint(), core::scoring::constraints::AmbiguousConstraint::read_def(), core::scoring::constraints::KofNConstraint::read_def(), read_def(), core::scoring::constraints::FabConstraint::setup_csts(), core::scoring::constraints::SiteConstraint::setup_csts(), and core::scoring::constraints::SiteConstraintResidues::setup_csts().

◆ atom()

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

inlineoverridevirtual

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 member_atoms_.

Referenced by core::scoring::constraints::AmbiguousConstraint::fill_f1_f2(), core::scoring::constraints::AmbiguousNMRConstraint::fill_f1_f2(), core::scoring::constraints::KofNConstraint::fill_f1_f2(), fill_f1_f2(), and protocols::constraints_additional::AmbiguousMultiConstraint::fill_f1_f2().

◆ choose_effective_sequence_separation()

core::Size core::scoring::constraints::MultiConstraint::choose_effective_sequence_separation	(	core::kinematics::ShortestPathInFoldTree const &	sp,
		numeric::random::RandomGenerator &	RG
	)

overridevirtual

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

References core::scoring::constraints::Constraint::choose_effective_sequence_separation(), member_constraints(), and report_this_as_effective_sequence_separation_.

◆ clone()

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

overridevirtual

Creates a deep copy of this MultiConstaint, cloning all constraints that it holds.

Clone all of the member constraints into a new vector and then invoke the (shallow-copy) constructor that accepts a vector of ConstriantCOPs – if this MultiConstraint doesn't have any member constraints, then return a default-constructed one.

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

Reimplemented in protocols::constraints_additional::AmbiguousMultiConstraint, core::scoring::constraints::SiteConstraintResidues, and core::scoring::constraints::SiteConstraint.

References MultiConstraint().

Referenced by cloned_member_constraints().

◆ cloned_member_constraints()

ConstraintCOPs core::scoring::constraints::MultiConstraint::cloned_member_constraints ( ) const

protected

Return a vector of Constraints that are clones of the member constraints.

References clone(), and member_constraints_.

Referenced by core::scoring::constraints::AmbiguousConstraint::clone(), core::scoring::constraints::KofNConstraint::clone(), and core::scoring::constraints::AmbiguousNMRConstraint::clone().

◆ dist() [1/3]

Real core::scoring::constraints::Constraint::dist

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

◆ dist() [2/3]

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

inlineoverridevirtual

MultiConstraints don't have a single distance

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

◆ dist() [3/3]

virtual core::Real core::scoring::constraints::Constraint::dist

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

◆ effective_sequence_separation()

core::Size core::scoring::constraints::MultiConstraint::effective_sequence_separation ( core::kinematics::ShortestPathInFoldTree const & ) const

inlineoverridevirtual

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

References report_this_as_effective_sequence_separation_.

◆ empty_clone()

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

virtual

Reimplemented in core::scoring::constraints::KofNConstraint, core::scoring::constraints::AmbiguousNMRConstraint, and core::scoring::constraints::AmbiguousConstraint.

Referenced by remapped_clone().

◆ fill_f1_f2()

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

overridevirtual

compute atom deriv

function that figures out what constraints this atom is part of and calculates the derivative for those

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

References atom(), atomid_to_csts_, and protocols::kinmatch::xyz().

◆ member_constraints()

ConstraintCOPs const& core::scoring::constraints::MultiConstraint::member_constraints ( ) const

inline

References member_constraints_.

◆ natoms()

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

overridevirtual

number of atoms involved in this MultiConstraint container

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

References member_atoms_.

◆ operator==()

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

overridevirtual

possibility to compare constraint according to data and not just pointers

@detail this function only checks whether the member_constraints_ are identical. should mean by inference that the member_residues_, member_atoms_ and atomid_to_csts_ are also identical

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

Reimplemented in protocols::constraints_additional::AmbiguousMultiConstraint, core::scoring::constraints::SiteConstraintResidues, and core::scoring::constraints::SiteConstraint.

References member_constraints_, report_this_as_effective_sequence_separation_, core::scoring::constraints::Constraint::same_type_as_me(), same_type_as_me(), and core::scoring::constraints::Constraint::score_type().

Referenced by core::scoring::constraints::AmbiguousConstraint::operator==(), core::scoring::constraints::AmbiguousNMRConstraint::operator==(), and core::scoring::constraints::FabConstraint::operator==().

◆ read_def()

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

overridevirtual

read in constraint defiinition

read definition of a multiconstraint. Since a MultiConstraint is essentially a vector of ?????? (Please someone finish this)

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

Reimplemented in core::scoring::constraints::SiteConstraintResidues, and core::scoring::constraints::SiteConstraint.

References add_individual_constraint(), member_constraints_, show_def(), size(), core::scoring::constraints::tr(), and type().

Referenced by core::scoring::constraints::AmbiguousNMRConstraint::read_def().

◆ remap_resid()

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

Reimplemented in protocols::constraints_additional::AmbiguousMultiConstraint.

References member_constraints_.

◆ remapped_clone()

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

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

References empty_clone(), and member_constraints_.

◆ residues()

utility::vector1< core::Size > core::scoring::constraints::MultiConstraint::residues ( ) const

inlineoverridevirtual

Returns the pose numbers of the residues involved in this constraint, in no particular order.

Used in determining one-body/two-body/multi-body status. For historical reasons, the default uses a simple protocol based on natoms()/atom() - feel free to reimplement more efficiently.

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

References member_residues_.

Referenced by core::scoring::constraints::SiteConstraint::setup_csts().

◆ same_type_as_me()

bool core::scoring::constraints::MultiConstraint::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.

Reimplemented in protocols::constraints_additional::AmbiguousMultiConstraint, core::scoring::constraints::SiteConstraintResidues, and core::scoring::constraints::SiteConstraint.

Referenced by operator==().

◆ score() [1/4]

virtual void core::scoring::constraints::Constraint::score

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.

Referenced by core::scoring::constraints::AmbiguousConstraint::fill_f1_f2().

◆ score() [2/4]

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

overridevirtual

compute score

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

Reimplemented in protocols::constraints_additional::AmbiguousMultiConstraint.

References member_constraints_.

◆ score() [3/4]

Real core::scoring::constraints::Constraint::score

Returns the unweighted score of this constraint computed over the given pose.

◆ score() [4/4]

Real core::scoring::constraints::Constraint::score

Returns the weighted score of this constraint computed over the given pose.

◆ set_effective_sequence_separation()

void core::scoring::constraints::MultiConstraint::set_effective_sequence_separation ( core::Size setting )

inline

References report_this_as_effective_sequence_separation_.

◆ setup_for_scoring()

void core::scoring::constraints::MultiConstraint::setup_for_scoring	(	func::XYZ_Func const &	xyz,
		ScoreFunction const &	scfxn
	)		const

overridevirtual

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

References member_constraints_, and protocols::kinmatch::xyz().

◆ show()

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

Reimplemented in protocols::constraints_additional::AmbiguousMultiConstraint, core::scoring::constraints::SiteConstraintResidues, and core::scoring::constraints::SiteConstraint.

References member_constraints_, and core::conformation::membrane::out.

◆ show_def()

void core::scoring::constraints::MultiConstraint::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 member_constraints(), core::conformation::membrane::out, and type().

Referenced by read_def().

◆ show_violations()

Size core::scoring::constraints::MultiConstraint::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.

Reimplemented in protocols::constraints_additional::AmbiguousMultiConstraint.

References member_constraints_, and core::conformation::membrane::out.

◆ size()

Size core::scoring::constraints::MultiConstraint::size ( ) const

number of constraints that are held by this MultiConstraint

number of constraints data

References member_constraints_.

Referenced by core::scoring::constraints::AmbiguousConstraint::AmbiguousConstraint(), core::scoring::constraints::AmbiguousNMRConstraint::AmbiguousNMRConstraint(), core::scoring::constraints::KofNConstraint::empty_clone(), core::scoring::constraints::AmbiguousConstraint::fill_f1_f2(), core::scoring::constraints::KofNConstraint::KofNConstraint(), read_def(), protocols::constraints_additional::AmbiguousMultiConstraint::score(), and core::scoring::constraints::KofNConstraint::score().

◆ type()

std::string core::scoring::constraints::MultiConstraint::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.

Reimplemented in protocols::constraints_additional::AmbiguousMultiConstraint, core::scoring::constraints::SiteConstraintResidues, and core::scoring::constraints::SiteConstraint.

Referenced by read_def(), and show_def().

Member Data Documentation

◆ atomid_to_csts_

std::map< AtomID, ConstraintCOPs > core::scoring::constraints::MultiConstraint::atomid_to_csts_

private

Referenced by add_individual_constraint(), and fill_f1_f2().

◆ member_atoms_

utility::vector1< AtomID > core::scoring::constraints::MultiConstraint::member_atoms_

private

Referenced by add_individual_constraint(), atom(), and natoms().

◆ member_constraints_

ConstraintCOPs core::scoring::constraints::MultiConstraint::member_constraints_

private

Referenced by add_individual_constraint(), cloned_member_constraints(), member_constraints(), MultiConstraint(), operator==(), read_def(), remap_resid(), remapped_clone(), score(), setup_for_scoring(), show(), show_violations(), and size().

◆ member_residues_

utility::vector1< core::Size > core::scoring::constraints::MultiConstraint::member_residues_

private

Referenced by add_individual_constraint(), and residues().

◆ report_this_as_effective_sequence_separation_

core::Size core::scoring::constraints::MultiConstraint::report_this_as_effective_sequence_separation_ = 0

private

Referenced by choose_effective_sequence_separation(), effective_sequence_separation(), operator==(), and set_effective_sequence_separation().

The documentation for this class was generated from the following files:

src/core/scoring/constraints/MultiConstraint.hh
src/core/scoring/constraints/MultiConstraint.cc

Classes

Public Member Functions

Protected Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ MultiConstraint() [1/4]

◆ MultiConstraint() [2/4]

◆ MultiConstraint() [3/4]

◆ MultiConstraint() [4/4]

Member Function Documentation

◆ add_individual_constraint()

◆ atom()

◆ choose_effective_sequence_separation()

◆ clone()

◆ cloned_member_constraints()

◆ dist() [1/3]

◆ dist() [2/3]

◆ dist() [3/3]

◆ effective_sequence_separation()

◆ empty_clone()

◆ fill_f1_f2()

◆ member_constraints()

◆ natoms()

◆ operator==()

◆ read_def()

◆ remap_resid()

◆ remapped_clone()

◆ residues()

◆ same_type_as_me()

◆ score() [1/4]

◆ score() [2/4]

◆ score() [3/4]

◆ score() [4/4]

◆ set_effective_sequence_separation()

◆ setup_for_scoring()

◆ show()

◆ show_def()

◆ show_violations()

◆ size()

◆ type()

Member Data Documentation

◆ atomid_to_csts_

◆ member_atoms_

◆ member_constraints_

◆ member_residues_

◆ report_this_as_effective_sequence_separation_