Inheritance diagram for ObjCryst::StretchMode:
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. |
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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.
Implemented in ObjCryst::StretchModeBondLength, ObjCryst::StretchModeBondAngle, ObjCryst::StretchModeTorsion, and ObjCryst::StretchModeTwist. |
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Print one-line list of atoms moved.
Implemented in ObjCryst::StretchModeBondLength, ObjCryst::StretchModeBondAngle, ObjCryst::StretchModeTorsion, and ObjCryst::StretchModeTwist. |
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Move the atoms according to this mode, randomly.
Implemented in ObjCryst::StretchModeBondLength, ObjCryst::StretchModeBondAngle, ObjCryst::StretchModeTorsion, and ObjCryst::StretchModeTwist. |
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Move the atoms according to this mode.
Implemented in ObjCryst::StretchModeBondLength, ObjCryst::StretchModeBondAngle, ObjCryst::StretchModeTorsion, and ObjCryst::StretchModeTwist. |
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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. |
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Derivative of the atomic positions versus a change of the bond length.
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Derivative of the Molecule's Log(likelihood) versus a change of the bond length.
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The Molecule corresponding to this stretch mode.
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List of bond restraints affected by this mode The key is the restraint, the value is the derivative of the LLK associated.
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List of bond angle restraints modified by this mode The key is the restraint, the value is the derivative of the LLK associated.
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List of dihedral angle restraints modified by this mode The key is the restraint, the value is the derivative of the LLK associated.
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