Class MMPFragmenter


  • public class MMPFragmenter
    extends java.lang.Object
    • Field Detail

      • KEYS_MIN_ATOMS

        public static final java.lang.Integer KEYS_MIN_ATOMS
      • FRAGMENT_DELIMITER

        public static final java.lang.String FRAGMENT_DELIMITER
        See Also:
        Constant Field Values
    • Constructor Detail

    • Method Detail

      • createR1HMoleculeID

        public static java.lang.String createR1HMoleculeID()
        Generates the idCode for the R-[H] molecule
        Returns:
        idCode String
      • getMoleculeIndexesID

        public java.util.List<MMPFragmenter.MoleculeIndexID> getMoleculeIndexesID​(boolean generateWholeMoleculeVariations)
        Returns an ArrayList of MoleculeIndexID containing
        IDCodes of keys and values of single and double cuts.
        Parameters:
        generateWholeMoleculeVariations - true/false to generate whole molecule variations, used for identification of H-replacements
      • getMoleculeFragmentsID

        public java.util.List<java.lang.String[]> getMoleculeFragmentsID()
        Returns an ArrayList of {R-group, "clean" (without R-groups)}
        fragmentsID used for Hydrogen replacements.
      • getMoleculeIndexesIDByte

        public java.util.List<MMPFragmenter.MoleculeIndexIDByte> getMoleculeIndexesIDByte​(boolean generateWholeMoleculeVariations)
        Returns an ArrayList of MoleculeIndexIDByte containing bytes of IDCodes of keys and values of single and double cuts.
        Parameters:
        generateWholeMoleculeVariations - true/false to generate whole molecule variations, used for identification of H-replacements
      • getRotBondsIndex

        public java.util.ArrayList<java.lang.Integer> getRotBondsIndex()
        Returns the indexes of the rotatable bonds
        Returns:
        Array of integers
      • fragmentMolecule

        public void fragmentMolecule()
      • fragmentMolecule

        public void fragmentMolecule​(boolean generateWholeMoleculeVariations)
        Fragments one StereoMolecule into keys-value pairs of StereoMolecules;
        - for single cuts, keys is an array containing one fragment
        ('constant' part of the molecule), value the 'variable' part;
        - for double cuts, keys in an array containing two fragments
        (constant parts of the molecule, i.e. 'left' and 'right' part), value the 'middle' part.
        An array containing all 'single cut' fragments is available for Hydrogen replacements.
        Parameters:
        generateWholeMoleculeVariations - true/false to generate whole molecule variations, used for identification of H-replacements
      • generateWholeMoleculeVariations

        public void generateWholeMoleculeVariations()
        Generates all variations of Hydrogen replacements on the whole molecule;
        fragments are added to the moleculeIndexesID.