ObjCryst::StretchModeBondLength Struct Reference

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

Inheritance diagram for ObjCryst::StretchModeBondLength:

[legend]Collaboration diagram for ObjCryst::StretchModeBondLength:

[legend]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
MolAtom *	mpAtom0
	The first atom (fixed).
MolAtom *	mpAtom1
	The second atom (first atom moved).
const MolBond *	mpBond
	The (optional) bond length which this stretch mode should respect.
set< MolAtom * >	mvTranslatedAtomList
	The set of atoms that are to be translated, including at1.

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Detailed Description

Group of atoms for random moves changing a bond length.

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

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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]

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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.

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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.

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

• Molecule.h

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