Package org.openscience.cdk.config

Class Isotopes

java.lang.Object

org.openscience.cdk.config.IsotopeFactory

org.openscience.cdk.config.Isotopes

public class Isotopes
extends IsotopeFactory

List of isotopes. Data is taken from the Blue Obelisk Data Repository, version 10 [Willighagen, E. and Hutchinson, G. and Niehaus, C. and Buchwald, J. and Pfeiffer, M. and Leidert, D. and Brefort, J., Blue Obelisk Data Repository (version 10)]. The data set is described in the first Blue Obelisk paper [Guha, R. et. al.. J. Chem. Inf. Model.. 2006. 46].

The isotopes.dat file that is used by this class is a binary class of this data, improving loading times over the BODR XML representation. It is created from the original BODR files using tools from the cdk-build-util repository.

Author:

egonw

Source code:

main

Belongs to CDK module:

core

Field Summary

Fields inherited from class org.openscience.cdk.config.IsotopeFactory

EMPTY_ISOTOPE_ARRAY

Method Summary

Modifier and Type	Method	Description
static void	clearMajorIsotopes(IAtomContainer mol)	Clear the isotope information from atoms that are major isotopes (e.g.
static void	clearMajorIsotopes(IMolecularFormula formula)	Clear the isotope information from istopes that are major (e.g.
static Isotopes	getInstance()	Returns a singleton instance of this class.

Methods inherited from class org.openscience.cdk.config.IsotopeFactory

add, configure, configure, configureAtoms, getElement, getElement, getElementSymbol, getExactMass, getIsotope, getIsotope, getIsotopes, getIsotopes, getIsotopes, getIsotopes, getMajorIsotope, getMajorIsotope, getMajorIsotopeMass, getNaturalMass, getNaturalMass, getSize, isElement

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Method Details

getInstance

public static Isotopes getInstance()
                            throws IOException

Returns a singleton instance of this class.

Returns:

the singleton

Throws:

IOException - when reading of the data file did not work

clearMajorIsotopes

public static void clearMajorIsotopes(IAtomContainer mol)

Clear the isotope information from atoms that are major isotopes (e.g. ¹²C, ¹H, etc).

Parameters:

mol - the molecule

clearMajorIsotopes

public static void clearMajorIsotopes(IMolecularFormula formula)

Clear the isotope information from istopes that are major (e.g. ¹²C, ¹H, etc).

Parameters:

formula - the formula