#include <AmbiguousConstraint.hh>

Inheritance diagram for core::scoring::constraints::AmbiguousConstraint:

Collaboration diagram for core::scoring::constraints::AmbiguousConstraint:

Public Member Functions
	AmbiguousConstraint ()
	Constructor. More...

	AmbiguousConstraint (ConstraintCOPs &cst_in)
	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

void	init_cst_score_types ()

std::string	type () const
	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, FuncFactory const &func_factory)
	read in constraint defiinition More...

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

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

core::Real	calculate_total_cst_score (EnergyMap const &weights, EnergyMap &emap) const
	helper function to accumulate all constraint scores into one number 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...

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

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...

ConstraintCOP	active_constraint () const

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 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 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...

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...

Private Attributes
ConstraintCOP	active_constraint_

core::Real	low_total_cst_score_

EnergyMap	low_EMap_

EnergyMap	temp_EMap_

ScoreTypes	cst_score_types_

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_

Detailed Description

Definition at line 48 of file AmbiguousConstraint.hh.

Constructor & Destructor Documentation

core::scoring::constraints::AmbiguousConstraint::AmbiguousConstraint ( )

Constructor.

Definition at line 37 of file AmbiguousConstraint.cc.

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

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

core::scoring::constraints::AmbiguousConstraint::AmbiguousConstraint ( ConstraintCOPs & cst_in)

Constructor.

Definition at line 48 of file AmbiguousConstraint.cc.

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

Member Function Documentation

ConstraintCOP core::scoring::constraints::AmbiguousConstraint::active_constraint ( ) const

Definition at line 197 of file AmbiguousConstraint.cc.

References active_constraint_.

core::Real core::scoring::constraints::AmbiguousConstraint::calculate_total_cst_score	(	EnergyMap const &	weights,
		EnergyMap &	emap
	)		const

helper function to accumulate all constraint scores into one number

Definition at line 135 of file AmbiguousConstraint.cc.

References core::scoring::angle_constraint, core::scoring::atom_pair_constraint, core::scoring::backbone_stub_constraint, core::scoring::constant_constraint, core::scoring::coordinate_constraint, core::scoring::dihedral_constraint, and core::scoring::total_score.

Referenced by protocols::constraints_additional::AmbiguousMultiConstraint::score(), and score().

virtual ConstraintOP core::scoring::constraints::AmbiguousConstraint::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.

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

Definition at line 59 of file AmbiguousConstraint.hh.

References AmbiguousConstraint().

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

inlinevirtual

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

Definition at line 64 of file AmbiguousConstraint.hh.

References AmbiguousConstraint().

void core::scoring::constraints::AmbiguousConstraint::fill_f1_f2	(	AtomID const &	atom,
		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.

Reimplemented in protocols::constraints_additional::AmbiguousMultiConstraint.

Definition at line 168 of file AmbiguousConstraint.cc.

References active_constraint_.

void core::scoring::constraints::AmbiguousConstraint::init_cst_score_types ( )

Definition at line 60 of file AmbiguousConstraint.cc.

References core::scoring::angle_constraint, core::scoring::atom_pair_constraint, core::scoring::backbone_stub_constraint, core::scoring::constant_constraint, core::scoring::coordinate_constraint, cst_score_types_, and core::scoring::dihedral_constraint.

Referenced by AmbiguousConstraint().

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

virtual

possibility to compare constraint according to data and not just pointers

this function only checks whether the passed in cst is the same type and then hands off to the multi cst. probably overkill to also demand that the active cst is identical

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

Definition at line 76 of file AmbiguousConstraint.cc.

References core::scoring::constraints::MultiConstraint::operator==().

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

virtual

read in constraint defiinition

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

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

Definition at line 308 of file AmbiguousConstraint.cc.

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

ConstraintOP core::scoring::constraints::AmbiguousConstraint::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.

Reimplemented in protocols::constraints_additional::AmbiguousMultiConstraint.

Definition at line 145 of file AmbiguousConstraint.cc.

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

void core::scoring::constraints::AmbiguousConstraint::score	(	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.

Reimplemented in protocols::constraints_additional::AmbiguousMultiConstraint.

Definition at line 86 of file AmbiguousConstraint.cc.

References active_constraint_, core::scoring::angle_constraint, core::scoring::atom_pair_constraint, core::scoring::backbone_stub_constraint, calculate_total_cst_score(), core::scoring::constant_constraint, core::scoring::coordinate_constraint, cst_score_types_, core::scoring::dihedral_constraint, low_EMap_, core::scoring::constraints::MultiConstraint::member_constraints(), temp_EMap_, and core::scoring::EMapVector::zero().

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

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

Definition at line 183 of file AmbiguousConstraint.cc.

References core::scoring::constraints::MultiConstraint::member_constraints().

Size core::scoring::constraints::AmbiguousConstraint::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.

Reimplemented in protocols::constraints_additional::AmbiguousMultiConstraint.

Definition at line 228 of file AmbiguousConstraint.cc.

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

std::string core::scoring::constraints::AmbiguousConstraint::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.

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

Definition at line 72 of file AmbiguousConstraint.hh.

Referenced by show_violations().