chemaxon.util.iterator

Class IteratorFactory.BondNeighbourIterator

java.lang.Object

chemaxon.util.iterator.IteratorFactory.NeighbourIterator<MolBond>

chemaxon.util.iterator.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!

Field Summary

Fields inherited from class chemaxon.util.iterator.IteratorFactory.NeighbourIterator

atom, currentBond, secondaryBonds

Constructor Summary

Constructors

Constructor and Description
IteratorFactory.BondNeighbourIterator(MolAtom atom) Constructs an iterator to process the bonds connecting to the specified atom.

Method Summary

Methods

Modifier and Type	Method and Description
MolBond	next() Returns the next bond in the iteration.
MolBond	nextBond() Deprecated. As of Marvin 6.2, Use next() instead.

Methods inherited from class chemaxon.util.iterator.IteratorFactory.NeighbourIterator

getBond, hasNext, nextBondIndex, remove

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

IteratorFactory.BondNeighbourIterator

public IteratorFactory.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

next

public MolBond next()

Returns the next bond in the iteration.

Returns:

the next bond in the iteration

Throws:

NoSuchElementException