ObjCryst::StretchMode Struct Reference

Abstract base Stretch Mode for Molecule objects. More...

Inheritance diagram for ObjCryst::StretchMode:

[legend]Collaboration diagram for ObjCryst::StretchMode:

[legend]List of all members.

Public Member Functions
virtual	~StretchMode ()
virtual void	CalcDeriv (const bool derivllk=true) const=0
	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=0
	Print one-line list of atoms moved.
virtual void	Stretch (const REAL change)=0
	Move the atoms according to this mode.
virtual void	RandomStretch (const REAL amplitude)=0
	Move the atoms according to this mode, randomly.
Public Attributes
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.

---

Detailed Description

Abstract base Stretch Mode for Molecule objects.

---

Constructor & Destructor Documentation

virtual ObjCryst::StretchMode::~StretchMode (   )  [virtual]

---

Member Function Documentation

virtual void ObjCryst::StretchMode::CalcDeriv (  const bool  derivllk = true  )  const [pure 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. Implemented in ObjCryst::StretchModeBondLength, ObjCryst::StretchModeBondAngle, ObjCryst::StretchModeTorsion, and ObjCryst::StretchModeTwist.

virtual void ObjCryst::StretchMode::Print (  ostream &  os, bool  full = true )  const [pure virtual]

Print one-line list of atoms moved. Implemented in ObjCryst::StretchModeBondLength, ObjCryst::StretchModeBondAngle, ObjCryst::StretchModeTorsion, and ObjCryst::StretchModeTwist.

virtual void ObjCryst::StretchMode::RandomStretch (  const REAL  amplitude  )  [pure virtual]

Move the atoms according to this mode, randomly. Implemented in ObjCryst::StretchModeBondLength, ObjCryst::StretchModeBondAngle, ObjCryst::StretchModeTorsion, and ObjCryst::StretchModeTwist.

virtual void ObjCryst::StretchMode::Stretch (  const REAL  change  )  [pure virtual]

Move the atoms according to this mode. Implemented in ObjCryst::StretchModeBondLength, ObjCryst::StretchModeBondAngle, ObjCryst::StretchModeTorsion, and ObjCryst::StretchModeTwist.

---

Member Data Documentation

REAL ObjCryst::StretchMode::mBaseAmplitude

The recommended change amplitude, for a base global optimization displacement, to obtain an average 0.1 Angstroem displacement. This is learnt at the beginning of an optimization. This can be superseeded to respect any restraint.

std::map<const MolAtom*,XYZ> ObjCryst::StretchMode::mDerivXYZ [mutable]

Derivative of the atomic positions versus a change of the bond length.

REAL ObjCryst::StretchMode::mLLKDeriv [mutable]

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

Molecule* ObjCryst::StretchMode::mpMol

The Molecule corresponding to this stretch mode.

std::map<const MolBond*,REAL> ObjCryst::StretchMode::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> ObjCryst::StretchMode::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> ObjCryst::StretchMode::mvpBrokenDihedralAngle

List of dihedral angle restraints modified by this mode The key is the restraint, the value is the derivative of the LLK associated.

---

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

• Molecule.h

---