Bond angle restraint between 3 atoms. More...

Inheritance diagram for ObjCryst::MolBondAngle:

Collaboration diagram for ObjCryst::MolBondAngle:

Public Member Functions
	MolBondAngle (MolAtom &atom1, MolAtom &atom2, MolAtom &atom3, const REAL angle, const REAL sigma, const REAL delta, Molecule &parent)
	Constructor. More...

virtual	~MolBondAngle ()
	Destructor. More...

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. More...

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

void	SetAtom1 (MolAtom &at)

void	SetAtom2 (MolAtom &at)

void	SetAtom3 (MolAtom &at)

MolAtom &	GetAtom1 ()

MolAtom &	GetAtom2 ()

MolAtom &	GetAtom3 ()

bool	IsFlexible () const

void	SetFlexible (const bool isInRing)

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 3 atoms involved in the bond angle.

REAL	mAngle0

REAL	mDelta

REAL	mSigma

Molecule *	mpMol
	Parent Molecule.

bool	mIsFlexible
	When using the user-chosen flexibility model, this allows some flexibility for this bond angle, i.e. More...

REAL	mLLK
	Stored log(likelihood)

XYZ	mDerivAtom1
	Partial derivatives of the angle with respect to the coordinates of the atoms. More...

XYZ	mDerivAtom2

XYZ	mDerivAtom3

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

Detailed Description

Bond angle restraint between 3 atoms.

The atoms involved need not be bonded.

Definition at line 256 of file Molecule.h.

Constructor & Destructor Documentation

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

Constructor.

Definition at line 626 of file Molecule.cpp.

ObjCryst::MolBondAngle::~MolBondAngle ( )

virtual

Destructor.

Definition at line 639 of file Molecule.cpp.

Member Function Documentation

void ObjCryst::MolBondAngle::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.

Definition at line 863 of file Molecule.cpp.

Member Data Documentation

XYZ ObjCryst::MolBondAngle::mDerivAtom1

mutableprivate

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

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

Definition at line 325 of file Molecule.h.

REAL ObjCryst::MolBondAngle::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) $mDerivLLKCoeff = \frac{L-L_0}{\sigma^2}$

Definition at line 329 of file Molecule.h.

bool ObjCryst::MolBondAngle::mIsFlexible

private

When using the user-chosen flexibility model, this allows some flexibility for this bond angle, i.e.

the bond angle does not remain strictly rigid, and is still restrained.

Definition at line 318 of file Molecule.h.

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

Public Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation