ObjCryst::MolBond Class Reference

Bond between two atoms, also a restraint on the associated bond length. More...

Inheritance diagram for ObjCryst::MolBond:

Collaboration diagram for ObjCryst::MolBond:

List of all members.

Public Member Functions

MolBond (MolAtom &atom1, MolAtom &atom2, const REAL length, const REAL sigma, const REAL delta, Molecule &parent, const REAL bondOrder=1.)

Constructor.

virtual ~MolBond ()

Destructor.

const Molecule & GetMolecule () const

Molecule & GetMolecule ()

string GetName () const

Name of the bond, e.g. "C3-O4".

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.

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.

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.

REAL mLLK

Stored log(likelihood).

XYZ mDerivAtom1

Derivatives of the bond length with respect to the coordinates of the atoms.

XYZ mDerivAtom2

REAL mDerivLLKCoeff

The factor used to change the derivative of the length/angle, to the derivative of the log(likelihood).

Detailed Description

Bond between two atoms, also a restraint on the associated bond length.

Definition at line 141 of file Molecule.h.

Constructor & Destructor Documentation

ObjCryst::MolBond::MolBond	(	MolAtom &	atom1,
		MolAtom &	atom2,
		const REAL	length,
		const REAL	sigma,
		const REAL	delta,
		Molecule &	parent,
		const REAL	bondOrder = `1.`
	)

Constructor.

Both atoms of the bond are told of the creation of the bond, so that they can keep a list of bonds they are involved in.

Parameters:

	atom1,atom2,:	the atoms of the bond
	length,:	the expected bond length
	sigma,delta,:	depending on the calculated length, the log(likelihood) is equal to: within $[length_{0}-\delta;length_{0}+\delta]$ : $-\log(likelihood)= \log\left(2\delta+\sqrt{2\pi\sigma^2}\right)$ if $length > length_{0}+\delta$ : $-\log(likelihood)= \log\left(2\delta+\sqrt{2\pi\sigma^2}\right) + \left(\frac{(length-\delta)-length_{0}}{\sigma} \right)^2$ if $length < length_{0}-\delta$ : $-\log(likelihood)= \log\left(2\delta+\sqrt{2\pi\sigma^2}\right) + \left(\frac{(length+\delta)-length_{0}}{\sigma} \right)^2$

Definition at line 282 of file Molecule.cpp.

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

Destructor.

Notifies the atoms that the bond has disappeared.

Definition at line 293 of file Molecule.cpp.

Member Function Documentation

REAL ObjCryst::MolBond::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.

If llk=true, this will return the derivative of the llk rather than the derivative of the length or angle

Member Data Documentation

XYZ ObjCryst::MolBond::mDerivAtom1 [mutable, private]

Derivatives of the bond length with respect to the coordinates of the atoms.

The derivatives are calculated in MolBond::GetLogLikelihood(true)

Definition at line 216 of file Molecule.h.

REAL ObjCryst::MolBond::mDerivLLKCoeff [mutable, private]

The factor used to change the derivative of the length/angle, to the derivative of the log(likelihood).

e.g. (for mDelta=0) $mDerivLLKCoeff = \frac{L-L_0}{\sigma^2}$

Definition at line 220 of file Molecule.h.

The documentation for this class was generated from the following files:


Public Member Functions
	MolBond (MolAtom &atom1, MolAtom &atom2, const REAL length, const REAL sigma, const REAL delta, Molecule &parent, const REAL bondOrder=1.)
	Constructor.
virtual	~MolBond ()
	Destructor.
const Molecule &	GetMolecule () const
Molecule &	GetMolecule ()
string	GetName () const
	Name of the bond, e.g. "C3-O4".
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.
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.
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.
REAL	mLLK
	Stored log(likelihood).
XYZ	mDerivAtom1
	Derivatives of the bond length with respect to the coordinates of the atoms.
XYZ	mDerivAtom2
REAL	mDerivLLKCoeff
	The factor used to change the derivative of the length/angle, to the derivative of the log(likelihood).