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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:

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Collaboration diagram for ObjCryst::StretchModeTwist:

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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

MolAtommpAtom1
 The first atom.

MolAtommpAtom2
 The second atom.

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


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.


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]
 


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.


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.


The documentation for this struct was generated from the following file:
Generated on Tue Nov 14 15:04:13 2006 for ObjCryst++ by doxygen 1.3.6