#include <MultiConstraint.hh>

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

Collaboration diagram for core::scoring::constraints::MultiConstraint:

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

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

virtual void	setup_for_derivatives (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 Func const &	get_func () const
	Returns the 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

Detailed Description

Definition at line 50 of file MultiConstraint.hh.

Constructor & Destructor Documentation

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

inline

default Constructor

Definition at line 54 of file MultiConstraint.hh.

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

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

Constructor.

Definition at line 89 of file MultiConstraint.cc.

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.

Definition at line 99 of file MultiConstraint.cc.

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.

Definition at line 104 of file MultiConstraint.hh.

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.

Definition at line 230 of file MultiConstraint.cc.

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

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

Definition at line 64 of file MultiConstraint.hh.

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.

Definition at line 163 of file MultiConstraint.hh.

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.

Definition at line 73 of file MultiConstraint.hh.

References MultiConstraint().

Referenced by remapped_clone().

void core::scoring::constraints::MultiConstraint::fill_f1_f2	(	AtomID const &	atom,
		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, core::scoring::constraints::AmbiguousConstraint, and protocols::constraints_additional::AmbiguousMultiConstraint.

Definition at line 166 of file MultiConstraint.cc.

References AtomID_to_Csts_.

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

inline

Definition at line 146 of file MultiConstraint.hh.

References member_constraints_.

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

inlinevirtual

number of atoms involved in this MultiConstraint container

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

Definition at line 78 of file MultiConstraint.hh.

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.

Definition at line 61 of file MultiConstraint.cc.

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,
		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.

Definition at line 33 of file MultiConstraint.cc.

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, core::scoring::constraints::AmbiguousConstraint, and protocols::constraints_additional::AmbiguousMultiConstraint.

Definition at line 136 of file MultiConstraint.cc.

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.

Definition at line 149 of file MultiConstraint.cc.

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.

Definition at line 111 of file MultiConstraint.hh.

References member_residues_.

void core::scoring::constraints::MultiConstraint::score	(	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, core::scoring::constraints::AmbiguousConstraint, and protocols::constraints_additional::AmbiguousMultiConstraint.

Definition at line 81 of file MultiConstraint.cc.

References member_constraints_.

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

inline

Definition at line 155 of file MultiConstraint.hh.

References report_this_as_effective_sequence_separation_.

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

virtual

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

Definition at line 128 of file MultiConstraint.cc.

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

Definition at line 197 of file MultiConstraint.cc.

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 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.

Definition at line 208 of file MultiConstraint.cc.

References 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, core::scoring::constraints::AmbiguousConstraint, and protocols::constraints_additional::AmbiguousMultiConstraint.

Definition at line 217 of file MultiConstraint.cc.

References member_constraints_.

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

inline

number of constraints data

Definition at line 83 of file MultiConstraint.hh.

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(), protocols::constraints_additional::AmbiguousMultiConstraint::score(), and core::scoring::constraints::KofNConstraint::score().