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

Inheritance diagram for ObjCryst::StretchModeBondLength:

Collaboration diagram for ObjCryst::StretchModeBondLength:

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

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. More...

virtual void	Print (ostream &os, bool full=true) const
	Print one-line list of atoms moved.

virtual void	Stretch (const REAL change, const bool keepCenter=true)
	Move the atoms according to this mode.

virtual void	RandomStretch (const REAL amplitude, const bool keepCenter=true)
	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.

Public Attributes inherited from ObjCryst::StretchMode
std::map< const MolBond *, REAL >	mvpBrokenBond
	List of bond restraints affected by this mode The key is the restraint, the value is the derivative of the LLK associated.

std::map< const MolBondAngle *, REAL >	mvpBrokenBondAngle
	List of bond angle restraints modified by this mode The key is the restraint, the value is the derivative of the LLK associated.

std::map< const MolDihedralAngle *, REAL >	mvpBrokenDihedralAngle
	List of dihedral angle restraints modified by this mode The key is the restraint, the value is the derivative of the LLK associated.

REAL	mLLKDeriv
	Derivative of the Molecule's Log(likelihood) versus a change of the bond length.

std::map< const MolAtom *, XYZ >	mDerivXYZ
	Derivative of the atomic positions versus a change of the bond length.

Molecule *	mpMol
	The Molecule corresponding to this stretch mode.

REAL	mBaseAmplitude
	The recommended change amplitude, for a base global optimization displacement, to obtain an average 0.1 Angstroem displacement. More...

Detailed Description

Group of atoms for random moves changing a bond length.

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

Definition at line 567 of file Molecule.h.

Member Function Documentation

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.

Definition at line 1514 of file Molecule.cpp.

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