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ObjCryst::MolDihedralAngle Class Reference

Dihedral angle restraint between 4 atoms. More...

Inheritance diagram for ObjCryst::MolDihedralAngle:

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Collaboration diagram for ObjCryst::MolDihedralAngle:

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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.

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 ()

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
 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.

XYZ mDerivAtom4
 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).

Detailed Description

Dihedral angle restraint between 4 atoms.

The atoms involved need not be bonded.

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.

Member Function Documentation

REAL& ObjCryst::MolDihedralAngle::Angle0 (   ) 
 

REAL& ObjCryst::MolDihedralAngle::AngleDelta (   ) 
 

REAL& ObjCryst::MolDihedralAngle::AngleSigma (   ) 
 

REAL ObjCryst::MolDihedralAngle::GetAngle (   )  const
 

REAL ObjCryst::MolDihedralAngle::GetAngle0 (   )  const
 

REAL ObjCryst::MolDihedralAngle::GetAngleDelta (   )  const
 

REAL ObjCryst::MolDihedralAngle::GetAngleSigma (   )  const
 

MolAtom& ObjCryst::MolDihedralAngle::GetAtom1 (   ) 
 

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

MolAtom& ObjCryst::MolDihedralAngle::GetAtom2 (   ) 
 

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

MolAtom& ObjCryst::MolDihedralAngle::GetAtom3 (   ) 
 

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

MolAtom& ObjCryst::MolDihedralAngle::GetAtom4 (   ) 
 

const MolAtom& ObjCryst::MolDihedralAngle::GetAtom4 (   )  const
 

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

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

Get -ln(likelihood) for this restraint.

Reimplemented from ObjCryst::Restraint.

Molecule& ObjCryst::MolDihedralAngle::GetMolecule (   ) 
 

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

string ObjCryst::MolDihedralAngle::GetName (   )  const
 

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

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

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

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

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

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

void ObjCryst::MolDihedralAngle::SetAtom4 (  MolAtom &  at  ) 
 

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

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

Member Data Documentation

REAL ObjCryst::MolDihedralAngle::mAngle [private]
 

REAL ObjCryst::MolDihedralAngle::mAngle0 [private]
 

REAL ObjCryst::MolDihedralAngle::mDelta [private]
 

XYZ ObjCryst::MolDihedralAngle::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::MolDihedralAngle::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::MolDihedralAngle::mDerivAtom3 [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::MolDihedralAngle::mDerivAtom4 [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::MolDihedralAngle::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) $ mDerivLLKCoeff = \frac{L-L_0}{\sigma^2} $

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

Stored log(likelihood).

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

Parent Molecule.

REAL ObjCryst::MolDihedralAngle::mSigma [private]
 

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

The vector of the 4 atoms involved in the bond angle.

The documentation for this class was generated from the following file:
Generated on Tue Nov 14 15:03:59 2006 for ObjCryst++ by doxygen 1.3.6