#include <MultiConstraint.hh>

Public Member Functions
	MultiConstraint (ScoreType const &t=dof_constraint)
	default Constructor More...

	MultiConstraint (const ConstraintCOPs &cst_in, ScoreType const &t=dof_constraint)
	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 MultiConstraintOP	empty_clone () const

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

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

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

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

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

virtual void	score (func::XYZ_Func const &xyz_func, EnergyMap const &weights, EnergyMap &emap) const
	compute score 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	add_individual_constraint (ConstraintCOP cst_in)
	add individual constraint into MultiConstraint 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 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	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...

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 ConstraintOP	clone (core::scoring::func::FuncOP) const

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 Real	score (pose::Pose const &) const

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

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

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...

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
	possibility to do object comparison instead of pointer comparison More...

Protected Attributes
ConstraintCOPs	member_constraints_

Private Attributes
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_

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

Constructor & Destructor Documentation

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

inline

default Constructor

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

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

Constructor.

References add_individual_constraint().

Member Function Documentation

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::SiteConstraint::setup_csts(), core::scoring::constraints::SiteConstraintResidues::setup_csts(), and core::scoring::constraints::FabConstraint::setup_csts().

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

inlinevirtual

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_.

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

virtual

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

References core::scoring::constraints::Constraint::choose_effective_sequence_separation(), cst, member_constraints(), report_this_as_effective_sequence_separation_, and numeric::random::RandomGenerator::uniform().

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

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

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

References member_constraints_, and MultiConstraint().

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

inlinevirtual

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

References report_this_as_effective_sequence_separation_.

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

inlinevirtual

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

References MultiConstraint().

Referenced by remapped_clone().

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

virtual

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.

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

References AtomID_to_Csts_.

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

inline

References member_constraints_.

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

inlinevirtual

number of atoms involved in this MultiConstraint container

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

References member_atoms_.

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

virtual

possibility to compare constraint according to data and not just pointers

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

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

Reimplemented in core::scoring::constraints::AmbiguousConstraint.

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

Referenced by core::scoring::constraints::AmbiguousConstraint::operator==().

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

virtual

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::AmbiguousNMRConstraint, core::scoring::constraints::KofNConstraint, core::scoring::constraints::AmbiguousConstraint, core::scoring::constraints::FabConstraint, core::scoring::constraints::SiteConstraint, and core::scoring::constraints::SiteConstraintResidues.

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

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

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

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

References member_constraints_, and MultiConstraint().

ConstraintOP core::scoring::constraints::MultiConstraint::remapped_clone	(	pose::Pose const &	,
		pose::Pose const &	,
		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 empty_clone(), and member_constraints_.

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

inlinevirtual

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_.

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

virtual

compute score

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

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

References member_constraints_.

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

inline

References report_this_as_effective_sequence_separation_.

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

virtual

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

References member_constraints_.

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

Reimplemented in core::scoring::constraints::KofNConstraint, core::scoring::constraints::AmbiguousConstraint, core::scoring::constraints::SiteConstraint, core::scoring::constraints::SiteConstraintResidues, and core::scoring::constraints::FabConstraint.

References member_constraints_.

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

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

References begin, member_constraints(), and type().

Referenced by read_def().

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

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

References member_constraints_.

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

inline

number of constraints data

References member_constraints_.

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