Class IteratingMDLConformerReader

  • All Implemented Interfaces:

    public class IteratingMDLConformerReader
    extends Object
    implements Iterator
    Iterate over conformers of a collection of molecules stored in SDF format. This class is analogous to the IteratingSDFReader except that rather than return a single IAtomContainer at each iteration this class will return all the conformers for a given molecule at each iteration. The class assumes that the molecules are stored in SDF format and that all conformers for a given molecule are in sequential order. Currently, the code uses the title of each molecule in the SD file to perform te conformer check and so it is important that all conformers for a given molecule have the same title field, but different from the title fields of conformers of other molecules. In the future the class will allow the user to perform the check using either the title or a more rigorous (but more time-consuming) graph isomorphism check. Example usage is
     String filename = "/Users/rguha/conf2.sdf";
     IteratingMDLConformerReader2 reader = new IteratingMDLConformerReader2(
             new FileReader(new File(filename)), DefaultChemObjectBuilder.getInstance());
     while (reader.hasNext()) {
          ConformerContainer2 cc = (ConformerContainer2);
     // do something with this set of conformers
    Rajarshi Guha
    See Also:
    Source code:
    Belongs to CDK module:
    file format SDF, conformer conformation