Class AromaticityResolver


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

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      boolean locateDelocalizedDoubleBonds​(boolean[] isAromaticBond)
      This method promotes all necessary bonds of the defined delocalized part of the molecule from single to double bonds in order to create a valid delocalized system of conjugated single and double bonds.
      boolean locateDelocalizedDoubleBonds​(boolean[] isAromaticBond, boolean mayChangeAtomCharges, boolean allHydrogensAreExplicit)
      This method promotes all necessary bonds of the defined delocalized part of the molecule from single to double bonds in order to create a valid delocalized system of conjugated single and double bonds.
      • Methods inherited from class java.lang.Object

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

      • AromaticityResolver

        public AromaticityResolver​(ExtendedMolecule mol)
        Creates a new AromaticityResolver for molecule mol.
        Parameters:
        mol -
    • Method Detail

      • locateDelocalizedDoubleBonds

        public boolean locateDelocalizedDoubleBonds​(boolean[] isAromaticBond)
        This method promotes all necessary bonds of the defined delocalized part of the molecule from single to double bonds in order to create a valid delocalized system of conjugated single and double bonds. The delocalized part of the molecule may be defined by passing an array to isAromaticBond that has all bonds flagged, which are part of a delocalized area. In this case these bonds are assumed to have bond type cBondTypeSingle. Alternatively, one may pass null and indicate affected bonds with bond type cBondTypeDelocalized. Non-cyclic atom chains defined to be delocalized are treated depending on whether we have a molecule or a query fragment. For fragments the respective bond types will be set to cBondTypeDelocalized; for molecules the chain will have alternating single and double bonds starting with double at a non-ring end.
        Returns:
        true if all bonds of the delocalized area could be consistently converted.
      • locateDelocalizedDoubleBonds

        public boolean locateDelocalizedDoubleBonds​(boolean[] isAromaticBond,
                                                    boolean mayChangeAtomCharges,
                                                    boolean allHydrogensAreExplicit)
        This method promotes all necessary bonds of the defined delocalized part of the molecule from single to double bonds in order to create a valid delocalized system of conjugated single and double bonds. The delocalized part of the molecule may be defined by passing an array to isAromaticBond that has all bonds flagged, which are part of a delocalized area. In this case these bonds are assumed to have bond type cBondTypeSingle. Alternatively, one may pass null and indicate affected bonds with bond type cBondTypeDelocalized. Non-cyclic atom chains defined to be delocalized are treated depending on whether we have a molecule or a query fragment. For fragments the respective bond types will be set to cBondTypeDelocalized; for molecules the chain will have alternating single and double bonds starting with double at a non-ring end.
        Parameters:
        isAromaticBond - if null, then bond type cBondTypeDelocalized is used to indicate delocalized bonds
        mayChangeAtomCharges - true if input molecule doesn't carry atom charges and these may be added to achieve aromaticity
        allHydrogensAreExplicit - true this method can rely on all hydrogens being explicitly present
        Returns:
        true if all bonds of the delocalized area could be consistently converted.