ObjCryst::MolDihedralAngle Class Reference

Dihedral angle restraint between 4 atoms. More...

Inheritance diagram for ObjCryst::MolDihedralAngle:

List of all members.

Public Member Functions
	MolDihedralAngle (MolAtom &atom1, MolAtom &atom2, MolAtom &atom3, MolAtom &atom4, const REAL angle, const REAL sigma, const REAL delta, Molecule &parent)
	Constructor.
virtual	~MolDihedralAngle ()
	Destructor.
const Molecule &	GetMolecule () const
Molecule &	GetMolecule ()
string	GetName () const
virtual void	XMLOutput (ostream &os, int indent=0) const
virtual void	XMLInput (istream &is, const XMLCrystTag &tag)
virtual REAL	GetLogLikelihood () const
	Get -ln(likelihood) for this restraint.
REAL	GetLogLikelihood (const bool calcDeriv, const bool recalc) const
REAL	GetDeriv (const std::map< const MolAtom *, XYZ > &m, const bool llk=false) const
	Get the derivative of the Angle, given the derivatives of the atom positions This requires that GetLogLikelihood(calcDeriv=true) be called first If llk=true, this will return the derivative of the llk rather than the derivative of the length or angle.
void	CalcGradient (std::map< MolAtom *, XYZ > &m) const
	Calc log(likelihood) gradient - versus all atomic coordinates.
REAL	GetAngle () const
REAL &	Angle0 ()
REAL &	AngleDelta ()
REAL &	AngleSigma ()
REAL	GetAngle0 () const
REAL	GetAngleDelta () const
REAL	GetAngleSigma () const
void	SetAngle0 (const REAL angle)
void	SetAngleDelta (const REAL delta)
void	SetAngleSigma (const REAL sigma)
const MolAtom &	GetAtom1 () const
const MolAtom &	GetAtom2 () const
const MolAtom &	GetAtom3 () const
const MolAtom &	GetAtom4 () const
void	SetAtom1 (MolAtom &at)
void	SetAtom2 (MolAtom &at)
void	SetAtom3 (MolAtom &at)
void	SetAtom4 (MolAtom &at)
MolAtom &	GetAtom1 ()
MolAtom &	GetAtom2 ()
MolAtom &	GetAtom3 ()
MolAtom &	GetAtom4 ()
Public Member Functions inherited from ObjCryst::Restraint
	Restraint ()
	Default constructor, sets RefParType to gpRefParTypeObjCryst.
	Restraint (const RefParType *type)
	constructor specifying the type
virtual const RefParType *	GetType () const
virtual void	SetType (const RefParType *type)

Private Attributes
vector< MolAtom * >	mvpAtom
	The vector of the 4 atoms involved in the bond angle.
REAL	mAngle
REAL	mAngle0
REAL	mDelta
REAL	mSigma
Molecule *	mpMol
	Parent Molecule.
REAL	mLLK
	Stored log(likelihood)
XYZ	mDerivAtom1
	Partial derivatives of the angle with respect to the coordinates of the atoms.
XYZ	mDerivAtom2
XYZ	mDerivAtom3
XYZ	mDerivAtom4
REAL	mDerivLLKCoeff
	The factor used to change the derivative of the length/angle, to the derivative of the log(likelihood).

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Detailed Description

Dihedral angle restraint between 4 atoms.

The atoms involved need not be bonded.

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Constructor & Destructor Documentation

ObjCryst::MolDihedralAngle::MolDihedralAngle	(	MolAtom &	atom1,
		MolAtom &	atom2,
		MolAtom &	atom3,
		MolAtom &	atom4,
		const REAL	angle,
		const REAL	sigma,
		const REAL	delta,
		Molecule &	parent
	)

Constructor.

virtual ObjCryst::MolDihedralAngle::~MolDihedralAngle ( )

virtual

Destructor.

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Member Function Documentation

void ObjCryst::MolDihedralAngle::CalcGradient

(

std::map< MolAtom *, XYZ > &

m

)

const

Calc log(likelihood) gradient - versus all atomic coordinates.

Parameters:

m,:	this map should have been initialized by adding all possible atom pointers as keys, with all XYZ values equal to zeros. On return, the derivative of the log(likelihood) vs each atomic coordinates will added to each coordinate of the corresponding atoms.

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Member Data Documentation

XYZ ObjCryst::MolDihedralAngle::mDerivAtom1

mutableprivate

Partial derivatives of the angle with respect to the coordinates of the atoms.

The derivatives are calculated in MolBondAngle::GetLogLikelihood(true)

REAL ObjCryst::MolDihedralAngle::mDerivLLKCoeff

mutableprivate

The factor used to change the derivative of the length/angle, to the derivative of the log(likelihood).

e.g. (for mDelta=0)

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

• Molecule.h