Class MMFFMolecule

  • All Implemented Interfaces:
    java.io.Serializable

    public final class MMFFMolecule
    extends StereoMolecule
    MMFF molecule is a wrapper class for the ExtendedMolecule. It holds some additional data such as a cache of the atom types, whether the molecule is valid for MMFF and the ring mmff aromaticity property.
    See Also:
    Serialized Form
    • Method Detail

      • getAtomType

        public int getAtomType​(int a)
        Get the MMFF atom type of an atom. This returns the cached value.
        Parameters:
        a - The atom index in the molecule.
        Returns:
        The MMFF atom type.
      • getHydrogenMap

        public int[] getHydrogenMap()
      • ringIsMMFFAromatic

        public boolean ringIsMMFFAromatic​(int r)
        Determine if a ring is aromatic according to MMFF criteria. Only designed to work with rings of size 5 and 6. Returns the cached value.
        Parameters:
        r - The ring index in the molecule.
        Returns:
        True if the ring is aromatic, false otherwise.
      • isSetRingMMFFAromaticity

        public boolean isSetRingMMFFAromaticity​(int r)
        Returns true if the given ring has had its MMFF aromaticity flag set.
        Parameters:
        r - The ring index in the molecule.
        Returns:
        True if the ring has had its flag set, false otherwise.