Abstract base Stretch Mode for Molecule objects. More...
Inheritance diagram for ObjCryst::StretchMode:
Collaboration diagram for ObjCryst::StretchMode:
Public Member Functions | |
| 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. More... | |
| virtual void | Print (ostream &os, bool full=true) const =0 |
| Print one-line list of atoms moved. | |
| virtual void | Stretch (const REAL change, const bool keepCenter=true)=0 |
| Move the atoms according to this mode. | |
| virtual void | RandomStretch (const REAL amplitude, const bool keepCenter=true)=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. | |
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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. | |
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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
Abstract base Stretch Mode for Molecule objects.
Definition at line 520 of file Molecule.h.
Member Function Documentation
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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
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derivllk if false, the derivative of the overall llk will not be computed, only the derivative of the atomic positions.
Implemented in ObjCryst::StretchModeTwist, ObjCryst::StretchModeTorsion, ObjCryst::StretchModeBondAngle, and ObjCryst::StretchModeBondLength.
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.
Definition at line 560 of file Molecule.h.
The documentation for this struct was generated from the following files:
