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Public Member Functions |
| MolBond (MolAtom &atom1, MolAtom &atom2, const REAL length, const REAL sigma, const REAL delta, Molecule &parent, const REAL bondOrder=1.) |
| Constructor.
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virtual | ~MolBond () |
| Destructor.
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const Molecule & | GetMolecule () const |
Molecule & | GetMolecule () |
string | GetName () const |
| Name of the bond, e.g. "C3-O4".
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virtual void | XMLOutput (ostream &os, int indent=0) const |
virtual void | XMLInput (istream &is, const XMLCrystTag &tag) |
virtual REAL | GetLogLikelihood () const |
| Get -ln(likelihood) for this restraint.
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REAL | GetLogLikelihood (const bool calcDeriv, const bool recalc) const |
REAL | GetDeriv (const std::map< const MolAtom *, XYZ > &m, const bool llk=false) const |
| Get the derivative of the bond length, given the derivatives of the atom positions This requires that GetLogLikelihood(calcDeriv=true) be called first.
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const MolAtom & | GetAtom1 () const |
const MolAtom & | GetAtom2 () const |
MolAtom & | GetAtom1 () |
MolAtom & | GetAtom2 () |
void | SetAtom1 (MolAtom &at1) |
void | SetAtom2 (MolAtom &at2) |
REAL | GetLength () const |
REAL | GetLength0 () const |
REAL | GetLengthDelta () const |
REAL | GetLengthSigma () const |
REAL | GetBondOrder () const |
REAL & | Length0 () |
REAL & | LengthDelta () |
REAL & | LengthSigma () |
REAL & | BondOrder () |
void | SetLength0 (const REAL length) |
void | SetLengthDelta (const REAL length) |
void | SetLengthSigma (const REAL length) |
void | SetBondOrder (const REAL length) |
bool | IsFreeTorsion () const |
void | SetFreeTorsion (const bool isInRing) |
Private Attributes |
pair< MolAtom *, MolAtom * > | mAtomPair |
REAL | mLength0 |
REAL | mDelta |
REAL | mSigma |
REAL | mBondOrder |
bool | mIsFreeTorsion |
Molecule * | mpMol |
| Parent Molecule.
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REAL | mLLK |
| Stored log(likelihood).
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XYZ | mDerivAtom1 |
| Derivatives of the bond length with respect to the coordinates of the atoms.
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XYZ | mDerivAtom2 |
| Derivatives of the bond length with respect to the coordinates of the atoms.
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REAL | mDerivLLKCoeff |
| The factor used to change the derivative of the length/angle, to the derivative of the log(likelihood).
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