ObjCryst::MolBondAngle Class Reference

Bond angle restraint between 3 atoms. More...

Inheritance diagram for ObjCryst::MolBondAngle:

[legend]Collaboration diagram for ObjCryst::MolBondAngle:

[legend]List of all members.

Public Member Functions
	MolBondAngle (MolAtom &atom1, MolAtom &atom2, MolAtom &atom3, const REAL angle, const REAL sigma, const REAL delta, Molecule &parent)
	Constructor.
virtual	~MolBondAngle ()
	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.
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)
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.
REAL	mLLK
	Stored log(likelihood).
XYZ	mDerivAtom1
	Partial derivatives of the angle with respect to the coordinates of the atoms.
XYZ	mDerivAtom2
	Partial derivatives of the angle with respect to the coordinates of the atoms.
XYZ	mDerivAtom3
	Partial derivatives of the angle with respect to the coordinates of the atoms.
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

Bond angle restraint between 3 atoms.

The atoms involved need not be bonded.

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Constructor & Destructor Documentation

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

Constructor.

virtual ObjCryst::MolBondAngle::~MolBondAngle (   )  [virtual]

Destructor.

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Member Function Documentation

REAL& ObjCryst::MolBondAngle::Angle0 (   )

REAL& ObjCryst::MolBondAngle::AngleDelta (   )

REAL& ObjCryst::MolBondAngle::AngleSigma (   )

REAL ObjCryst::MolBondAngle::GetAngle (   )  const

REAL ObjCryst::MolBondAngle::GetAngle0 (   )  const

REAL ObjCryst::MolBondAngle::GetAngleDelta (   )  const

REAL ObjCryst::MolBondAngle::GetAngleSigma (   )  const

MolAtom& ObjCryst::MolBondAngle::GetAtom1 (   )

const MolAtom& ObjCryst::MolBondAngle::GetAtom1 (   )  const

MolAtom& ObjCryst::MolBondAngle::GetAtom2 (   )

const MolAtom& ObjCryst::MolBondAngle::GetAtom2 (   )  const

MolAtom& ObjCryst::MolBondAngle::GetAtom3 (   )

const MolAtom& ObjCryst::MolBondAngle::GetAtom3 (   )  const

REAL ObjCryst::MolBondAngle::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.

REAL ObjCryst::MolBondAngle::GetLogLikelihood (  const bool  calcDeriv, const bool  recalc )  const

virtual REAL ObjCryst::MolBondAngle::GetLogLikelihood (   )  const [virtual]

Get -ln(likelihood) for this restraint. Reimplemented from ObjCryst::Restraint.

Molecule& ObjCryst::MolBondAngle::GetMolecule (   )

const Molecule& ObjCryst::MolBondAngle::GetMolecule (   )  const

string ObjCryst::MolBondAngle::GetName (   )  const

bool ObjCryst::MolBondAngle::IsFlexible (   )  const

void ObjCryst::MolBondAngle::SetAngle0 (  const REAL  angle  )

void ObjCryst::MolBondAngle::SetAngleDelta (  const REAL  delta  )

void ObjCryst::MolBondAngle::SetAngleSigma (  const REAL  sigma  )

void ObjCryst::MolBondAngle::SetAtom1 (  MolAtom &  at  )

void ObjCryst::MolBondAngle::SetAtom2 (  MolAtom &  at  )

void ObjCryst::MolBondAngle::SetAtom3 (  MolAtom &  at  )

void ObjCryst::MolBondAngle::SetFlexible (  const bool  isInRing  )

virtual void ObjCryst::MolBondAngle::XMLInput (  istream &  is, const XMLCrystTag &  tag )  [virtual]

virtual void ObjCryst::MolBondAngle::XMLOutput (  ostream &  os, int  indent = 0 )  const [virtual]

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Member Data Documentation

REAL ObjCryst::MolBondAngle::mAngle0 [private]

REAL ObjCryst::MolBondAngle::mDelta [private]

XYZ ObjCryst::MolBondAngle::mDerivAtom1 [mutable, private]

Partial derivatives of the angle with respect to the coordinates of the atoms. The derivatives are calculated in MolBondAngle::GetLogLikelihood(true)

XYZ ObjCryst::MolBondAngle::mDerivAtom2 [mutable, private]

Partial derivatives of the angle with respect to the coordinates of the atoms. The derivatives are calculated in MolBondAngle::GetLogLikelihood(true)

XYZ ObjCryst::MolBondAngle::mDerivAtom3 [mutable, private]

Partial derivatives of the angle with respect to the coordinates of the atoms. The derivatives are calculated in MolBondAngle::GetLogLikelihood(true)

REAL ObjCryst::MolBondAngle::mDerivLLKCoeff [mutable, private]

The factor used to change the derivative of the length/angle, to the derivative of the log(likelihood). e.g. (for mDelta=0)

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.

REAL ObjCryst::MolBondAngle::mLLK [mutable, private]

Stored log(likelihood).

Molecule* ObjCryst::MolBondAngle::mpMol [private]

Parent Molecule.

REAL ObjCryst::MolBondAngle::mSigma [private]

vector<MolAtom*> ObjCryst::MolBondAngle::mvpAtom [private]

The vector of the 3 atoms involved in the bond angle.

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

• Molecule.h

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