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

Inheritance diagram for ObjCryst::MolBond:

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.
void	CalcGradient (std::map< MolAtom *, XYZ > &m) const
	Calc log(likelihood) gradient - versus all atomic coordinates.
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)
Public Member Functions inherited from ObjCryst::Restraint
	Restraint ()
	Default constructor, sets RefParType to gpRefParTypeObjCryst.
	Restraint (const RefParType *type)
	constructor specifying the type
virtual const RefParType *	GetType () const
virtual void	SetType (const RefParType *type)

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.

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 $length < length_{0}-\delta$ : $-\log(likelihood)= \log\left(2\delta+\sqrt{2\pi\sigma^2}\right) + \left(\frac{(length+\delta)-length_{0}}{\sigma} \right)^2$

virtual ObjCryst::MolBond::~MolBond ( )

virtual

Destructor.

Notifies the atoms that the bond has disappeared.

Member Function Documentation

void ObjCryst::MolBond::CalcGradient ( std::map< MolAtom *, XYZ > & m ) const

Calc log(likelihood) gradient - versus all atomic coordinates.

Parameters:

m,:	this map should have been initialized by adding all possible atom pointers as keys, with all XYZ values equal to zeros. On return, the derivative of the log(likelihood) vs each atomic coordinates will added to each coordinate of the corresponding atoms.

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

mutableprivate

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

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

REAL ObjCryst::MolBond::mDerivLLKCoeff

mutableprivate

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

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

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

Molecule.h

Public Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation