ObjCryst::StretchModeBondAngle Struct Reference
Atoms moved when changing a bond angle. More...
Inheritance diagram for ObjCryst::StretchModeBondAngle:
Collaboration diagram for ObjCryst::StretchModeBondAngle:
Public Member Functions | |
| StretchModeBondAngle (MolAtom &at0, MolAtom &at1, MolAtom &at2, const MolBondAngle *pBondAngle) | |
| Constructor If pBondAngle!=0, the bond 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 * | mpAtom0 |
| The first atom. | |
| MolAtom * | mpAtom1 |
| The second atom. | |
| MolAtom * | mpAtom2 |
| The third atom. | |
| const MolBondAngle * | mpBondAngle |
| The (optional) bond angle restraint which this stretch mode should respect. | |
| set< MolAtom * > | mvRotatedAtomList |
| The set of atoms that are to be rotated around the direction going through at1 and perpendicular to the at0-at1-at2 plane. More... | |
| 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. | |
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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
Atoms moved when changing a bond angle.
This should be merged (or have an inheritance relation) with MolBondAngle.
Definition at line 595 of file Molecule.h.
Member Function Documentation
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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.
Implements ObjCryst::StretchMode.
Definition at line 1593 of file Molecule.cpp.
Member Data Documentation
| set<MolAtom *> ObjCryst::StretchModeBondAngle::mvRotatedAtomList |
The set of atoms that are to be rotated around the direction going through at1 and perpendicular to the at0-at1-at2 plane.
Definition at line 620 of file Molecule.h.
The documentation for this struct was generated from the following files:
