constraint on dihedral angle formed by 4 points More...

#include <BigBinConstraint.hh>

Inheritance diagram for core::scoring::constraints::BigBinConstraint:

Collaboration diagram for core::scoring::constraints::BigBinConstraint:

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

void	score (XYZ_Func const &xyz, EnergyMap const &, EnergyMap &emap) const
	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...

void	fill_f1_f2 (AtomID const &, XYZ_Func const &xyz, Vector &, Vector &, EnergyMap const &) const
	Fill the f1 and f2 vectors, necessary for considering the derivative this constraint during minimization. (someone please reference Bill Wedermeyer's paper here, as I'm in an airport and can't fill it in myself!) More...

	BigBinConstraint (AtomID C0, AtomID N1, AtomID CA1, AtomID C1, AtomID N2, AtomID CA2, char bin, ScoreType scotype=dihedral_constraint)
	c-tor More...

	BigBinConstraint ()

	BigBinConstraint (Size const res, char const bin, core::Real const sdev)

Size	natoms () const
	Returns the number of atoms involved in defining this constraint. If the constraint doesn't depend on particular atoms (e.g. a residue type constraint) this function can return zero. More...

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

void	read_def (std::istream &in, pose::Pose const &pose, FuncFactory const &func_factory)
	one line definition "BigBin res_number bin_char sdev" More...

char	bin () const

Size	res () const

Real	sdev () 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 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...

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	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 ConstraintOP	remap_resid (core::id::SequenceMapping const &) 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 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_scoring (XYZ_Func const &, ScoreFunction 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	show_def (std::ostream &, pose::Pose const &) 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 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 Size	show_violations (std::ostream &out, pose::Pose const &, Size, Real threshold=1) 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...

virtual Func const &	get_func () const
	Returns the Func object associated with this Constraint object. More...

virtual bool	operator== (Constraint const &) const
	possibility to do object comparison instead of pointer comparison More...

bool	operator!= (Constraint const &other) const
	possibility to do object comparison instead of pointer comparison More...

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

Private Attributes
AtomID	C0_

AtomID	N1_

AtomID	CA1_

AtomID	C1_

AtomID	N2_

AtomID	CA2_

Size	res_

char	bin_

core::Real	sdev_

utility::vector1< ConstraintOP >	my_csts_

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

Detailed Description

constraint on dihedral angle formed by 4 points

Definition at line 44 of file BigBinConstraint.hh.

Constructor & Destructor Documentation

core::scoring::constraints::BigBinConstraint::BigBinConstraint	(	AtomID	C0,
		AtomID	N1,
		AtomID	CA1,
		AtomID	C1,
		AtomID	N2,
		AtomID	CA2,
		char	bin,
		ScoreType	scotype = `dihedral_constraint`
	)

inline

c-tor

Definition at line 69 of file BigBinConstraint.hh.

core::scoring::constraints::BigBinConstraint::BigBinConstraint ( )

inline

Definition at line 89 of file BigBinConstraint.hh.

Referenced by clone().

core::scoring::constraints::BigBinConstraint::BigBinConstraint	(	Size const	res,
		char const	bin,
		core::Real const	sdev
	)

inline

Definition at line 96 of file BigBinConstraint.hh.

Member Function Documentation

AtomID const& core::scoring::constraints::BigBinConstraint::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 111 of file BigBinConstraint.hh.

References C0_, C1_, CA1_, CA2_, N1_, and N2_.

char core::scoring::constraints::BigBinConstraint::bin ( ) const

inline

Definition at line 136 of file BigBinConstraint.hh.

References bin_.

virtual ConstraintOP core::scoring::constraints::BigBinConstraint::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.

Definition at line 52 of file BigBinConstraint.hh.

References BigBinConstraint(), bin_, res_, and sdev_.

void core::scoring::constraints::BigBinConstraint::fill_f1_f2	(	AtomID const &	atom,
		XYZ_Func const &	xyz_func,
		Vector &	F1,
		Vector &	F2,
		EnergyMap const &	weights
	)		const

virtual

Fill the f1 and f2 vectors, necessary for considering the derivative this constraint during minimization. (someone please reference Bill Wedermeyer's paper here, as I'm in an airport and can't fill it in myself!)

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

Definition at line 152 of file BigBinConstraint.cc.

References core::sequence::end, and my_csts_.

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

inlinevirtual

Returns the number of atoms involved in defining this constraint. If the constraint doesn't depend on particular atoms (e.g. a residue type constraint) this function can return zero.

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 105 of file BigBinConstraint.hh.

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

virtual

one line definition "BigBin res_number bin_char sdev"

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

Definition at line 45 of file BigBinConstraint.cc.

References core::chemical::ResidueType::atom_index(), bin_, C0_, C1_, CA1_, CA2_, my_csts_, N1_, N2_, res_, core::pose::Pose::residue_type(), sdev_, and core::pose::Pose::total_residue().

Size core::scoring::constraints::BigBinConstraint::res ( ) const

inline

Definition at line 140 of file BigBinConstraint.hh.

References res_.

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

virtual

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.

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

Definition at line 141 of file BigBinConstraint.cc.

References core::sequence::end, and my_csts_.

Real core::scoring::constraints::BigBinConstraint::sdev ( ) const

inline

Definition at line 144 of file BigBinConstraint.hh.

References sdev_.

void core::scoring::constraints::BigBinConstraint::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.

Definition at line 135 of file BigBinConstraint.cc.

References bin_, res_, and sdev_.

virtual std::string core::scoring::constraints::BigBinConstraint::type ( ) const

inlinevirtual

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

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

Definition at line 48 of file BigBinConstraint.hh.

Member Data Documentation

char core::scoring::constraints::BigBinConstraint::bin_

private

Definition at line 152 of file BigBinConstraint.hh.

Referenced by bin(), clone(), read_def(), and show().

AtomID core::scoring::constraints::BigBinConstraint::C0_

private

Definition at line 150 of file BigBinConstraint.hh.

Referenced by atom(), and read_def().

AtomID core::scoring::constraints::BigBinConstraint::C1_

private

Definition at line 150 of file BigBinConstraint.hh.

Referenced by atom(), and read_def().

AtomID core::scoring::constraints::BigBinConstraint::CA1_

private

Definition at line 150 of file BigBinConstraint.hh.

Referenced by atom(), and read_def().

AtomID core::scoring::constraints::BigBinConstraint::CA2_

private

Definition at line 150 of file BigBinConstraint.hh.

Referenced by atom(), and read_def().

utility::vector1< ConstraintOP > core::scoring::constraints::BigBinConstraint::my_csts_

private

Definition at line 155 of file BigBinConstraint.hh.

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

AtomID core::scoring::constraints::BigBinConstraint::N1_

private

Definition at line 150 of file BigBinConstraint.hh.

Referenced by atom(), and read_def().

AtomID core::scoring::constraints::BigBinConstraint::N2_

private

Definition at line 150 of file BigBinConstraint.hh.

Referenced by atom(), and read_def().

Size core::scoring::constraints::BigBinConstraint::res_

private

Definition at line 151 of file BigBinConstraint.hh.

Referenced by clone(), read_def(), res(), and show().

core::Real core::scoring::constraints::BigBinConstraint::sdev_

private

Definition at line 153 of file BigBinConstraint.hh.

Referenced by clone(), read_def(), sdev(), and show().

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

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

Public Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation