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 thecdk-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
All Methods Static Methods Concrete Methods 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
-
-
-
-
Method Detail
-
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
-
-