Class Aromaticity.Model

  • Enclosing class:
    Aromaticity

    public static class Aromaticity.Model
    extends Object
    Container for aromaticity models.
    • Field Detail

      • Daylight

        public static ElectronDonation Daylight
        A model similar to what Daylight used for SMILES/SMARTS. If you are using SMILES/SMARTS then this is a good model to use.
      • PiBonds

        public static ElectronDonation PiBonds
        Any atom connected to a single pi bond in a ring contributes 1 electron.
      • Mdl

        public static ElectronDonation Mdl
        A model similar to what MDL/Symyx used. This is similar to the PiBonds model but only allows certain atom types. Exo cyclic pi bonds are not allowed.
      • OpenSmiles

        public static ElectronDonation OpenSmiles
        Similar to the Daylight model but also allows boron and some arsenic variants as well as charge separated sulfinyl/seleninyl.
      • CDK_1x

        public static ElectronDonation CDK_1x
        Somewhere in between Mdl/Daylight, allows indole/pyrrole/furan but does not allow exo-cyclic bonds.
      • CDK_2x

        public static ElectronDonation CDK_2x
        Similar to the Daylight model but also allows boron, tellurium and some arsenic variants as well not allowing sulfinyl/seleninyl since these are Sp3.
      • CDK_AtomTypes

        public static ElectronDonation CDK_AtomTypes
        The old aromatic bond based on CDK atom types, this model requires atom types have been assigned before calling. Generally the CDK_1x should be indistinguishable and run faster.