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ObjCryst::StretchModeBondLength Struct Reference

Group of atoms for random moves changing a bond length. More...

Inheritance diagram for ObjCryst::StretchModeBondLength:

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Collaboration diagram for ObjCryst::StretchModeBondLength:

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List of all members.

Public Member Functions

 StretchModeBondLength (MolAtom &at0, MolAtom &at1, const MolBond *pBond)
 Constructor If pBond!=0, the bond length restraint is respected.

virtual ~StretchModeBondLength ()
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

MolAtommpAtom0
 The first atom (fixed).

MolAtommpAtom1
 The second atom (first atom moved).

const MolBondmpBond
 The (optional) bond length which this stretch mode should respect.

set< MolAtom * > mvTranslatedAtomList
 The set of atoms that are to be translated, including at1.


Detailed Description

Group of atoms for random moves changing a bond length.

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


Constructor & Destructor Documentation

ObjCryst::StretchModeBondLength::StretchModeBondLength MolAtom at0,
MolAtom at1,
const MolBond pBond
 

Constructor If pBond!=0, the bond length restraint is respected.

virtual ObjCryst::StretchModeBondLength::~StretchModeBondLength  )  [virtual]
 


Member Function Documentation

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

Print one-line list of atoms moved.

Implements ObjCryst::StretchMode.

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

Move the atoms according to this mode, randomly.

Implements ObjCryst::StretchMode.

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

Move the atoms according to this mode.

Implements ObjCryst::StretchMode.


Member Data Documentation

MolAtom* ObjCryst::StretchModeBondLength::mpAtom0
 

The first atom (fixed).

MolAtom* ObjCryst::StretchModeBondLength::mpAtom1
 

The second atom (first atom moved).

const MolBond* ObjCryst::StretchModeBondLength::mpBond
 

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

set<MolAtom *> ObjCryst::StretchModeBondLength::mvTranslatedAtomList
 

The set of atoms that are to be translated, including at1.


The documentation for this struct was generated from the following file:
Generated on Tue Nov 14 15:04:05 2006 for ObjCryst++ by doxygen 1.3.6