ObjCryst::StretchModeTwist Struct Reference

Atoms moved *between* two other atoms, using a "twist" of their positions - only small twists of their positions are allowed to avoid breaking restraints too much. More...

Inheritance diagram for ObjCryst::StretchModeTwist:

[legend]Collaboration diagram for ObjCryst::StretchModeTwist:

[legend]List of all members.

Public Member Functions
	StretchModeTwist (MolAtom &at1, MolAtom &at2)
	Constructor If pDihedralAngle!=0, the dihedral angle length restraint is respected.
virtual	~StretchModeTwist ()
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.
set< MolAtom * >	mvRotatedAtomList
	The set of atoms that are to be rotated around at1-at2.

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Detailed Description

Atoms moved *between* two other atoms, using a "twist" of their positions - only small twists of their positions are allowed to avoid breaking restraints too much.

Also, the atoms in the middle between the two reference atoms are more displaced than the one closer, to help avoid breaking restraints.

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Constructor & Destructor Documentation

ObjCryst::StretchModeTwist::StretchModeTwist (  MolAtom &  at1, MolAtom &  at2 )

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

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

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Member Function Documentation

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

Print one-line list of atoms moved. Implements ObjCryst::StretchMode.

virtual void ObjCryst::StretchModeTwist::RandomStretch (  const REAL  amplitude  )  [virtual]

Move the atoms according to this mode, randomly. Implements ObjCryst::StretchMode.

virtual void ObjCryst::StretchModeTwist::Stretch (  const REAL  change  )  [virtual]

Move the atoms according to this mode. Implements ObjCryst::StretchMode.

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Member Data Documentation

MolAtom* ObjCryst::StretchModeTwist::mpAtom1

The first atom.

MolAtom* ObjCryst::StretchModeTwist::mpAtom2

The second atom.

set<MolAtom *> ObjCryst::StretchModeTwist::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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