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
  • 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