ObjCryst::StretchModeTorsion Struct Reference

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

Inheritance diagram for ObjCryst::StretchModeTorsion:

[legend]Collaboration diagram for ObjCryst::StretchModeTorsion:

[legend]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
MolAtom *	mpAtom1
	The first atom.
MolAtom *	mpAtom2
	The second atom.
const MolDihedralAngle *	mpDihedralAngle
	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.

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Detailed Description

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

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

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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]

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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.

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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.

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

• Molecule.h

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