ggl::chem::MoleculeOB Class Reference

OpenBabel molecule object port. More...

#include <MoleculeOB.hh>

Public Member Functions
double	getMolEnergy ()
double	getMolWeight (const bool implicitH=true)
	MoleculeOB (const ggl::chem::Molecule &mol)

Static Public Member Functions
static OpenBabel::OBMol	convert (const Molecule &mol)
static Molecule	convert (const OpenBabel::OBMol &mol)

Protected Attributes
OpenBabel::OBMol	curMol
	current molecule working on More...

Detailed Description

   Wrapper class around an OpenBabel molecule object (OBMol).

   It utilizes the OpenBabel library (http://openbabel.org) for the
   conversion.

Author

Martin Mann (c) 2009 http://www.bioinf.uni-freiburg.de/~mmann/

Definition at line 30 of file MoleculeOB.hh.

Constructor & Destructor Documentation

ggl::chem::MoleculeOB::MoleculeOB

(

const ggl::chem::Molecule &

mol

)

Construction

      NOTE: the protons of the molecule are removed during construction.

Parameters

mol	the molecule to be represented by this object

Member Function Documentation

static OpenBabel::OBMol ggl::chem::MoleculeOB::convert ( const Molecule &  mol )

static

Converts a Molecule into an OpenBabel molecule instance.

NOTE: conversion is done via CML encoding and thus currently inefficient.

Parameters

mol	the molecule to convert

Returns

the according OBMol instance

static Molecule ggl::chem::MoleculeOB::convert ( const OpenBabel::OBMol &  mol )

static

Converts an OpenBabel molecule object into a Molecule instance.

NOTE: only atom label and formal charge are considered for each atom.

Parameters

mol	the molecule to convert

Returns

the according Molecule instance

double ggl::chem::MoleculeOB::getMolEnergy

(

)

Access to the complete energy of the molecule, calculated via force field methods

      In error case (e.g. force field not loadable) NaN is returned.

Returns

the complete energy of this molecule (in kJ/mol)

double ggl::chem::MoleculeOB::getMolWeight

(

const bool

implicitH = true

)

Access to the molar mass of the molecule

Parameters

implicitH

flag whether hydrogens should be added implicitly by openbabel or not

Returns

the standard molar mass given by IUPAC atomic masses (amu)

Field Documentation

OpenBabel::OBMol ggl::chem::MoleculeOB::curMol

protected

Definition at line 35 of file MoleculeOB.hh.

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

• src/ggl/chem/MoleculeOB.hh