Class IteratorFactory.BondNeighbourIterator

  • All Implemented Interfaces:
    Iterator<MolBond>
    Enclosing class:
    IteratorFactory

    public class IteratorFactory.BondNeighbourIterator
    extends IteratorFactory.NeighbourIterator<MolBond>
    The BondNeighbourIterator class provides an iterator to process the bonds connecting to the specified atom according to the atom and bond related behavior of this factory. The following bonds are excluded:
    • bonds excluded in the bond related behavior of the factory and
    • bonds connecting to atoms that are excluded in the atom related behavior of the factory except that:

      If the atom related behavior of the factory is set to skip the multicenter and the bond related behavior is set to include the coordinate bonds the BondNeighbourIterator returns secondary bonds instead of coordinate bonds of multicenter atoms. Secondary bonds replace a coordinate bond to the multicenter with coordinate bonds from the metal to the represented atoms (represented atoms: the atoms in the MulticenterSgroup of the multicenter). These secondary bonds are NOT PART OF the molecule of the factory, so DO NOT USE Molecule.indexOf for the secondary bonds!

    • Constructor Detail

      • BondNeighbourIterator

        public BondNeighbourIterator​(MolAtom atom)
        Constructs an iterator to process the bonds connecting to the specified atom. The following bonds are excluded:
        • bonds excluded in the bond related behavior of the factory and
        • bonds connecting to atoms that are excluded in the atom related behavior of the factory except that:

          If the atom related behavior of the factory is set to skip the multicenter and the bond related behavior is set to include the coordinate bonds the BondNeighbourIterator returns secondary bonds instead of coordinate bonds of multicenter atoms. Secondary bonds replace a coordinate bond to the multicenter with coordinate bonds from the metal to the represented atoms (represented atoms: the atoms in the MulticenterSgroup of the multicenter). These secondary bond are NOT ADDED to the molecule of the factory, so DO NOT USE Molecule.indexOf for the secondary bonds!

        Parameters:
        atom - the atom whose bonds to be iterated
    • Method Detail

      • nextBond

        @Deprecated
        public MolBond nextBond()
        Deprecated.
        As of Marvin 6.2, Use next() instead.
        Returns the next bond in the iteration.
        Returns:
        the next bond in the iteration