Class MoleculeNeutralizer


  • public class MoleculeNeutralizer
    extends java.lang.Object
    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      int neutralizeChargedMolecule​(StereoMolecule mol)
      Tries to neutralize all charged atoms of the molecule unless a charged atom has a neighbour atom with opposite charge.
      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    • Constructor Detail

      • MoleculeNeutralizer

        public MoleculeNeutralizer()
    • Method Detail

      • neutralizeChargedMolecule

        public int neutralizeChargedMolecule​(StereoMolecule mol)
        Tries to neutralize all charged atoms of the molecule unless a charged atom has a neighbour atom with opposite charge. Quarternary ammonium or B(-) won't be touched. If positive charges remain, this method tries to deprotonate halogenes and acidic oxygen atoms to neutralize the molecule.
        Parameters:
        mol -
        Returns:
        remaining overall charge, which may be different from 0 if complete neutralization cannot be achieved