Package org.openscience.cdk.fragment

Class ExhaustiveFragmenter

java.lang.Object
org.openscience.cdk.fragment.ExhaustiveFragmenter
All Implemented Interfaces:
IFragmenter
public class ExhaustiveFragmenter extends Object implements IFragmenter
Generate fragments exhaustively. This fragmentation scheme simply breaks single non-ring bonds. By default fragments smaller than 6 atoms in size are not considered, but this can be changed by the user. Side chains are retained.
Author:
Rajarshi Guha
Source code:
main
Belongs to CDK module:
fragment
Keywords:
fragment

  • Constructor Details

    • ExhaustiveFragmenter

      public ExhaustiveFragmenter()
      Instantiate fragmenter with default minimum fragment size.

    • ExhaustiveFragmenter

      public ExhaustiveFragmenter(int minFragSize)
      Instantiate fragmenter with user specified minimum fragment size.
      Parameters:
      minFragSize - the minimum fragment size desired

  • Method Details

    • setMinimumFragmentSize

      public void setMinimumFragmentSize(int minFragSize)
      Set the minimum fragment size.
      Parameters:
      minFragSize - the smallest size fragment that will be returned

    • generateFragments

      public void generateFragments(IAtomContainer atomContainer) throws CDKException
      Generate fragments for the input molecule.
      Specified by:
      generateFragments in interface IFragmenter
      Parameters:
      atomContainer - The input molecule.
      Throws:
      CDKException - if ring detection fails

    • getFragments

      public String[] getFragments()
      Get the fragments generated as SMILES strings.
      Specified by:
      getFragments in interface IFragmenter
      Returns:
      a String[] of the fragments.

    • getFragmentsAsContainers

      public IAtomContainer[] getFragmentsAsContainers()
      Get the fragments generated as IAtomContainer objects..
      Specified by:
      getFragmentsAsContainers in interface IFragmenter
      Returns:
      a IAtomContainer[] of the fragments.