Package chemaxon.struc

Class IteratorFactory

java.lang.Object
chemaxon.struc.IteratorFactory
@PublicApi @Deprecated(forRemoval=true) @SubjectToRemoval(date=JUL_01_2027) public class IteratorFactory extends Object
Deprecated, for removal: This API element is subject to removal in a future version.
This class is deprecated and subject to removal in a future release. Please use the appropriate methods of MoleculeGraph and Molecule instead.
The IteratorFactory class provides implementations of Iterator to ease the handling of atoms and bonds used in Molecule objects and its descendants. The following iterators are included in this class:
  • AtomIterator
  • BondIterator
  • AtomNeighbourIterator
  • BondNeighbourIterator
  • RxnComponentIterator
  • RgComponentIterator

API usage example: 

      //initialize an RgMolecule;
      RgMolecule mol = ... ;
      //create the iterator factory with the specified molecule and parameters related to atoms and bonds.
      IteratorFactory factory = new IteratorFactory(mol, IteratorFactory.INCLUDE_ALL_ATOMS, IteratorFactory.INCLUDE_ALL_BONDS);
      RgComponentIterator rgIterator = factory.createRgComponentIterator();
      //iteration on the components of the RgMolecule.
      while (rgIterator.hasNext()) {
          Molecule component = rgIterator.next();
          IteratorFactory ifc = new IteratorFactory(component, IteratorFactory.SKIP_PSEUDO_ATOM | IteratorFactory.SKIP_EXPLICIT_H,
                  IteratorFactory.SKIP_COORDINATE_BONDS);
          AtomIterator atomIterator = ifc.createAtomIterator();
          //iteration on the atoms of a component
          while (atomIterator.hasNext()){
              MolAtom atom = atomIterator.next();
              //process the atom
              ...
          }
          //iteration on the bonds of a component
          BondIterator bondIterator = ifc.createBondIterator();
          while (bondIterator.hasNext()){
              MolBond bond = bondIterator.next();
              //process the bond
              ...
          }
      }

      //the inclusion pattern of IteratorFactory can be rewritten to exclude
      //more atoms and/or bonds, for example:
      IteratorFactory factory2 = new IteratorFactory(mol,
          IteratorFactory.INCLUDE_CHEMICAL_ATOMS_ONLY, IteratorFactory.INCLUDE_ALL_BONDS) {
          //this ensures that only chemical atoms with properties are iterated
          public boolean isExcludedAtom(MolAtom atom) {
          return (atom.propertyCount() == 0);
          }
          //the same can be done for bonds with isExcludedBond(MolBond bond)
      };
Since:
Marvin 5.1
See Also:

  • Nested Class Summary

    Nested Classes
    Modifier and Type
    Class
    Description
    class 
    IteratorFactory.AtomIterator
    Deprecated, for removal: This API element is subject to removal in a future version.
    class 
    IteratorFactory.AtomNeighbourIterator
    Deprecated, for removal: This API element is subject to removal in a future version.
    class 
    IteratorFactory.BondIterator
    Deprecated, for removal: This API element is subject to removal in a future version.
    class 
    IteratorFactory.BondNeighbourIterator
    Deprecated, for removal: This API element is subject to removal in a future version.
    class 
    IteratorFactory.NeighbourIterator<E>
    Deprecated, for removal: This API element is subject to removal in a future version.
    class 
    IteratorFactory.RgComponentIterator
    Deprecated, for removal: This API element is subject to removal in a future version.
    class 
    IteratorFactory.RxnComponentIterator
    Deprecated, for removal: This API element is subject to removal in a future version.
    class 
    IteratorFactory.SgroupIterator
    Deprecated, for removal: This API element is subject to removal in a future version.

  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    static final int
    INCLUDE_ALL_ATOMS
    Deprecated, for removal: This API element is subject to removal in a future version.
    Include all atoms: chemical atoms, explicit hydrogen, multicenter, lone pair and pseudo atoms in atom iterations.
    static final int
    INCLUDE_ALL_BONDS
    Deprecated, for removal: This API element is subject to removal in a future version.
    Include all bonds: covalent and coordinate bonds in bond iteration.
    static final int
    INCLUDE_CHEMICAL_ATOMS_ONLY
    Deprecated, for removal: This API element is subject to removal in a future version.
    Include only chemical atoms in iteration, skip multicenters, lone pairs and pseudo atoms.
    static final int
    REPLACE_COORDINATE_BONDS
    Deprecated, for removal: This API element is subject to removal in a future version.
    Replace coordinate bonds to multicenter atoms with coordinate bonds from the metal to the represented atoms (in the MulticenterSgroup of the multicenter).
    static final int
    SKIP_COORDINATE_BONDS
    Deprecated, for removal: This API element is subject to removal in a future version.
    Exclude coordinate bonds from bond iteration.
    static final int
    SKIP_COVALENT_BONDS
    Deprecated, for removal: This API element is subject to removal in a future version.
    Exclude covalent bonds from bond iteration.
    static final int
    SKIP_EXPLICIT_H
    Deprecated, for removal: This API element is subject to removal in a future version.
    Exclude explicit hydrogens from atom iteration.
    static final int
    SKIP_LONE_PAIR
    Deprecated, for removal: This API element is subject to removal in a future version.
    Exclude lone pairs from atom iteration.
    static final int
    SKIP_MULTICENTER
    Deprecated, for removal: This API element is subject to removal in a future version.
    Exclude multicenters from atom iteration.
    static final int
    SKIP_PSEUDO_ATOM
    Deprecated, for removal: This API element is subject to removal in a future version.
    Exclude pseudo atoms from atom iteration.

  • Constructor Summary

    Constructors
    Constructor
    Description
    IteratorFactory(Molecule mol)
    Deprecated, for removal: This API element is subject to removal in a future version.
    Constructs an iterator factory for the specified molecule with default atom and bond related behavior to include all atoms and bonds.
    IteratorFactory(MoleculeGraph mol)
    Deprecated, for removal: This API element is subject to removal in a future version.
    Constructs an iterator factory for the specified molecule with default atom and bond related behavior to include all atoms and bonds.
    IteratorFactory(Molecule mol, int atomRelatedBehavior, int bondRelatedBehavior)
    Deprecated, for removal: This API element is subject to removal in a future version.
    Constructs an iterator factory for the specified molecule with a specified atom and bond related behavior.

  • Method Summary

    Modifier and Type
    Method
    Description
    IteratorFactory.AtomIterator
    createAtomIterator()
    Deprecated, for removal: This API element is subject to removal in a future version.
    Constructs an atom iterator for the specified molecule of the factory according to the atom related behavior set in the factory.
    IteratorFactory.AtomNeighbourIterator
    createAtomNeighbourIterator(MolAtom atom)
    Deprecated, for removal: This API element is subject to removal in a future version.
    Constructs an iterator to get the atom neighbours of the specified atom.
    IteratorFactory.BondIterator
    createBondIterator()
    Deprecated, for removal: This API element is subject to removal in a future version.
    Constructs a bond iterator for the specified molecule of the factory according to bond related behavior set in the factory.
    IteratorFactory.BondNeighbourIterator
    createBondNeighbourIterator(MolAtom atom)
    Deprecated, for removal: This API element is subject to removal in a future version.
    Constructs an iterator to get the bonds connecting to the specified atom.
    IteratorFactory.RgComponentIterator
    createRgComponentIterator()
    Deprecated, for removal: This API element is subject to removal in a future version.
    Constructs an rgroup definition component iterator for the specified molecule of the factory if the molecule is an RgMolecule, an empty iterator otherwise.
    IteratorFactory.RxnComponentIterator
    createRxnComponentIterator()
    Deprecated, for removal: This API element is subject to removal in a future version.
    Constructs a reaction component iterator for the specified molecule of the factory if the molecule is an RxnMolecule, an empty iterator otherwise.
    IteratorFactory.SgroupIterator
    createSgroupIterator()
    Deprecated, for removal: This API element is subject to removal in a future version.
    Constructs an s-group iterator for the specified molecule of the factory.
    boolean
    isExcludedAtom(MolAtom atom)
    Deprecated, for removal: This API element is subject to removal in a future version.
    By overriding this method, the inclusion pattern of IteratorFactory can be rewritten to exclude more atoms, than it would normally.
    boolean
    isExcludedBond(MolBond bond)
    Deprecated, for removal: This API element is subject to removal in a future version.
    By overriding this method, the inclusion pattern of IteratorFactory can be rewritten to exclude more bonds, than it would normally.
    int
    numberOfAtoms()
    Deprecated, for removal: This API element is subject to removal in a future version.
    Returns the number of atoms iterated by AtomIterator.
    int
    numberOfBonds()
    Deprecated, for removal: This API element is subject to removal in a future version.
    Returns the number of bonds iterated by BondIterator.
    int
    numberOfNeighbours(MolAtom atom)
    Deprecated, for removal: This API element is subject to removal in a future version.
    Returns the number of atoms/bonds iterated by (Atom/Bond)NeighbourIterator (the two values are the same).

    Methods inherited from class java.lang.Object

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

  • Field Details

    • INCLUDE_ALL_BONDS

      public static final int INCLUDE_ALL_BONDS
      Deprecated, for removal: This API element is subject to removal in a future version.
      Include all bonds: covalent and coordinate bonds in bond iteration.
      See Also:

    • SKIP_COORDINATE_BONDS

      public static final int SKIP_COORDINATE_BONDS
      Deprecated, for removal: This API element is subject to removal in a future version.
      Exclude coordinate bonds from bond iteration.
      See Also:

    • SKIP_COVALENT_BONDS

      public static final int SKIP_COVALENT_BONDS
      Deprecated, for removal: This API element is subject to removal in a future version.
      Exclude covalent bonds from bond iteration.
      See Also:

    • REPLACE_COORDINATE_BONDS

      public static final int REPLACE_COORDINATE_BONDS
      Deprecated, for removal: This API element is subject to removal in a future version.
      Replace coordinate bonds to multicenter atoms with coordinate bonds from the metal to the represented atoms (in the MulticenterSgroup of the multicenter). These secondary bonds are not added to the molecule of the factory, so do not use Molecule.indexOf for the secondary bonds!
      See Also:

    • INCLUDE_ALL_ATOMS

      public static final int INCLUDE_ALL_ATOMS
      Deprecated, for removal: This API element is subject to removal in a future version.
      Include all atoms: chemical atoms, explicit hydrogen, multicenter, lone pair and pseudo atoms in atom iterations.
      See Also:

    • SKIP_EXPLICIT_H

      public static final int SKIP_EXPLICIT_H
      Deprecated, for removal: This API element is subject to removal in a future version.
      Exclude explicit hydrogens from atom iteration.
      See Also:

    • SKIP_MULTICENTER

      public static final int SKIP_MULTICENTER
      Deprecated, for removal: This API element is subject to removal in a future version.
      Exclude multicenters from atom iteration.
      See Also:

    • SKIP_LONE_PAIR

      public static final int SKIP_LONE_PAIR
      Deprecated, for removal: This API element is subject to removal in a future version.
      Exclude lone pairs from atom iteration.
      See Also:

    • SKIP_PSEUDO_ATOM

      public static final int SKIP_PSEUDO_ATOM
      Deprecated, for removal: This API element is subject to removal in a future version.
      Exclude pseudo atoms from atom iteration.
      See Also:

    • INCLUDE_CHEMICAL_ATOMS_ONLY

      public static final int INCLUDE_CHEMICAL_ATOMS_ONLY
      Deprecated, for removal: This API element is subject to removal in a future version.
      Include only chemical atoms in iteration, skip multicenters, lone pairs and pseudo atoms.
      See Also:

  • Constructor Details

    • IteratorFactory

      public IteratorFactory(Molecule mol, int atomRelatedBehavior, int bondRelatedBehavior)
      Deprecated, for removal: This API element is subject to removal in a future version.
      Constructs an iterator factory for the specified molecule with a specified atom and bond related behavior. Atom and bond related behavior can be set with the constants below, using the bitwise | operator (which means AND here) to combine them.
      Parameters:
      mol - the molecule whose atoms and bonds to be iterated.
      atomRelatedBehavior - the behavior how to iterate on atoms. Specify with the constants:
      • INCLUDE_ALL_ATOMS
      • INCLUDE_CHEMICAL_ATOMS_ONLY
      • SKIP_EXPLICIT_H
      • SKIP_MULTICENTER
      • SKIP_LONE_PAIR
      • SKIP_PSEUDO_ATOM
      bondRelatedBehavior - the behavior how to iterate on bonds. Specify with the constants:
      • INCLUDE_ALL_BONDS
      • SKIP_COORDINATE_BONDS
      • SKIP_COVALENT_BONDS
      • REPLACE_COORDINATE_BONDS

    • IteratorFactory

      public IteratorFactory(Molecule mol)
      Deprecated, for removal: This API element is subject to removal in a future version.
      Constructs an iterator factory for the specified molecule with default atom and bond related behavior to include all atoms and bonds.
      See Also:

    • IteratorFactory

      public IteratorFactory(MoleculeGraph mol)
      Deprecated, for removal: This API element is subject to removal in a future version.
      Constructs an iterator factory for the specified molecule with default atom and bond related behavior to include all atoms and bonds.
      See Also:

  • Method Details

    • createAtomIterator

      public IteratorFactory.AtomIterator createAtomIterator()
      Deprecated, for removal: This API element is subject to removal in a future version.
      Constructs an atom iterator for the specified molecule of the factory according to the atom related behavior set in the factory.
      Returns:
      the atom iterator

    • createBondIterator

      public IteratorFactory.BondIterator createBondIterator()
      Deprecated, for removal: This API element is subject to removal in a future version.
      Constructs a bond iterator for the specified molecule of the factory according to bond related behavior set in the factory.
      Returns:
      the bond iterator

    • createSgroupIterator

      public IteratorFactory.SgroupIterator createSgroupIterator()
      Deprecated, for removal: This API element is subject to removal in a future version.
      Constructs an s-group iterator for the specified molecule of the factory.
      Returns:
      the s-group iterator

    • createAtomNeighbourIterator

      public IteratorFactory.AtomNeighbourIterator createAtomNeighbourIterator(MolAtom atom)
      Deprecated, for removal: This API element is subject to removal in a future version.
      Constructs an iterator to get the atom neighbours of the specified atom. The following atoms are excluded:
      • atoms excluded in the atom related behavior of the factory and
      • atoms connecting with bonds that are excluded in the bond related behavior of the factory.
      Parameters:
      atom - the atom whose neighbour atoms to be iterated
      Returns:
      the atom neighbour iterator of the specified atom

    • createBondNeighbourIterator

      public IteratorFactory.BondNeighbourIterator createBondNeighbourIterator(MolAtom atom)
      Deprecated, for removal: This API element is subject to removal in a future version.
      Constructs an iterator to get 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.
      Parameters:
      atom - the atom whose bonds to be iterated
      Returns:
      the bond neighbour iterator of the specified atom

    • createRxnComponentIterator

      public IteratorFactory.RxnComponentIterator createRxnComponentIterator()
      Deprecated, for removal: This API element is subject to removal in a future version.
      Constructs a reaction component iterator for the specified molecule of the factory if the molecule is an RxnMolecule, an empty iterator otherwise.
      Returns:
      the reaction component iterator

    • createRgComponentIterator

      public IteratorFactory.RgComponentIterator createRgComponentIterator()
      Deprecated, for removal: This API element is subject to removal in a future version.
      Constructs an rgroup definition component iterator for the specified molecule of the factory if the molecule is an RgMolecule, an empty iterator otherwise.
      Returns:
      the rgroup component iterator

    • isExcludedAtom

      public boolean isExcludedAtom(MolAtom atom)
      Deprecated, for removal: This API element is subject to removal in a future version.
      By overriding this method, the inclusion pattern of IteratorFactory can be rewritten to exclude more atoms, than it would normally. By default, this method returns false.
      Parameters:
      atom - the atom to be checked
      Returns:
      whether the atom should be excluded

    • isExcludedBond

      public boolean isExcludedBond(MolBond bond)
      Deprecated, for removal: This API element is subject to removal in a future version.
      By overriding this method, the inclusion pattern of IteratorFactory can be rewritten to exclude more bonds, than it would normally. By default, this method returns false.
      Parameters:
      bond - the bond to be checked
      Returns:
      whether the bond should be excluded

    • numberOfAtoms

      public int numberOfAtoms()
      Deprecated, for removal: This API element is subject to removal in a future version.
      Returns the number of atoms iterated by AtomIterator. It currently works by creating an AtomIterator, and iterating through it. This might make it unsuitable for some uses, where performance is important.
      Returns:
      the number of atoms

    • numberOfBonds

      public int numberOfBonds()
      Deprecated, for removal: This API element is subject to removal in a future version.
      Returns the number of bonds iterated by BondIterator. It currently works by creating a BondIterator, and iterating through it. This might make it unsuitable for some uses, where performance is important.
      Returns:
      the number of bonds

    • numberOfNeighbours

      public int numberOfNeighbours(MolAtom atom)
      Deprecated, for removal: This API element is subject to removal in a future version.
      Returns the number of atoms/bonds iterated by (Atom/Bond)NeighbourIterator (the two values are the same). It currently works by creating a BondNeighbourIterator, and iterating through it. This might make it unsuitable for some uses, where performance is important.
      Returns:
      the number of neighbours