Atoms moved when rotated around a bond at0-at1-at2-at3. More...

Inheritance diagram for ObjCryst::StretchModeTorsion:

Collaboration diagram for ObjCryst::StretchModeTorsion:

Public Member Functions
	StretchModeTorsion (MolAtom &at1, MolAtom &at2, const MolDihedralAngle *pDihedralAngle)
	Constructor If pDihedralAngle!=0, the dihedral angle 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 *	mpAtom1
	The first atom.

MolAtom *	mpAtom2
	The second atom.

const MolDihedralAngle *	mpDihedralAngle
	The (optional) bond angle restraint which this stretch mode should respect. More...

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

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

Atoms moved when rotated around a bond at0-at1-at2-at3.

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

Definition at line 626 of file Molecule.h.

Member Function Documentation

void ObjCryst::StretchModeTorsion::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 1693 of file Molecule.cpp.

const MolDihedralAngle* ObjCryst::StretchModeTorsion::mpDihedralAngle

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

The mpAtom1 and mpAtom2 must be the central atoms of this restraint.

Definition at line 647 of file Molecule.h.

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