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ObjCryst::StretchModeTorsion Struct Reference

Atoms moved when rotated around a bond at0-at1-at2-at3. More...

Inheritance diagram for ObjCryst::StretchModeTorsion:

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Collaboration diagram for ObjCryst::StretchModeTorsion:

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List of all members.

Public Member Functions

 StretchModeTorsion (MolAtom &at1, MolAtom &at2, const MolDihedralAngle *pDihedralAngle)
 Constructor If pDihedralAngle!=0, the dihedral angle length restraint is respected.

virtual ~StretchModeTorsion ()
virtual void CalcDeriv (const bool derivllk=true) const
 Calculate the derivative of the Molecule's Log(likelihood) and atomic positions versus a change of the bond length.

virtual void Print (ostream &os, bool full=true) const
 Print one-line list of atoms moved.

virtual void Stretch (const REAL change)
 Move the atoms according to this mode.

virtual void RandomStretch (const REAL amplitude)
 Move the atoms according to this mode, randomly.


Public Attributes

MolAtommpAtom1
 The first atom.

MolAtommpAtom2
 The second atom.

const MolDihedralAnglempDihedralAngle
 The (optional) bond angle restraint which this stretch mode should respect.

set< MolAtom * > mvRotatedAtomList
 The set of atoms that are to be rotated around at1-at2.


Detailed Description

Atoms moved when rotated around a bond at0-at1-at2-at3.

This should be merged (or have an inheritance relation) with MolDihedralAngle


Constructor & Destructor Documentation

ObjCryst::StretchModeTorsion::StretchModeTorsion MolAtom at1,
MolAtom at2,
const MolDihedralAngle pDihedralAngle
 

Constructor If pDihedralAngle!=0, the dihedral angle length restraint is respected.

virtual ObjCryst::StretchModeTorsion::~StretchModeTorsion  )  [virtual]
 


Member Function Documentation

virtual void ObjCryst::StretchModeTorsion::CalcDeriv const bool  derivllk = true  )  const [virtual]
 

Calculate the derivative of the Molecule's Log(likelihood) and atomic positions versus a change of the bond length.

The result is stored in mLLKDeriv and mLLKDerivXYZ, as well as in the various lists of restraints broken by this mode.

Parameters:
derivllk: if false, the derivative of the overall llk will not be computed, only the derivative of the atomic positions.

Implements ObjCryst::StretchMode.

virtual void ObjCryst::StretchModeTorsion::Print ostream &  os,
bool  full = true
const [virtual]
 

Print one-line list of atoms moved.

Implements ObjCryst::StretchMode.

virtual void ObjCryst::StretchModeTorsion::RandomStretch const REAL  amplitude  )  [virtual]
 

Move the atoms according to this mode, randomly.

Implements ObjCryst::StretchMode.

virtual void ObjCryst::StretchModeTorsion::Stretch const REAL  change  )  [virtual]
 

Move the atoms according to this mode.

Implements ObjCryst::StretchMode.


Member Data Documentation

MolAtom* ObjCryst::StretchModeTorsion::mpAtom1
 

The first atom.

MolAtom* ObjCryst::StretchModeTorsion::mpAtom2
 

The second atom.

const MolDihedralAngle* ObjCryst::StretchModeTorsion::mpDihedralAngle
 

The (optional) bond angle restraint which this stretch mode should respect.

The mpAtom1 and mpAtom2 must be the central atoms of this restraint.

set<MolAtom *> ObjCryst::StretchModeTorsion::mvRotatedAtomList
 

The set of atoms that are to be rotated around at1-at2.


The documentation for this struct was generated from the following file:
Generated on Tue Nov 14 15:04:10 2006 for ObjCryst++ by doxygen 1.3.6