Package chemaxon.util.iterator
Class IteratorFactory
java.lang.Object
chemaxon.util.iterator.IteratorFactory
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:
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Nested Class Summary
Modifier and TypeClassDescriptionclass
TheAtomIterator
class provides an iterator for the atoms of the specified molecule of the factory according to the atom related behavior set in the factory.class
TheAtomNeighbourIterator
class provides an iterator to process the atoms connecting to a specified atom according to the atom and bond related behavior of this factory.class
TheBondIterator
class provides an iterator to process the bonds of the specified molecule in this factory according to the bond related behavior of this factory.class
TheBondNeighbourIterator
class provides an iterator to process the bonds connecting to the specified atom according to the atom and bond related behavior of this factory.class
TheNeighbourIterator
class provides an iterator to process the bonds connecting to the specified atom according to the atom and bond related behavior of this factory.class
TheRgComponentIterator
class provides an iterator to process the rgroup definition components in the specified molecule of the factory.class
TheRxnComponentIterator
class provides an iterator to process the components (reactant, product and agent components) in the reaction molecule of the factory.class
TheSgroupIterator
class provides an iterator for the s-groups of the specified molecule of the factory. -
Field Summary
Modifier and TypeFieldDescriptionstatic final int
Include all atoms: chemical atoms, explicit hydrogen, multicenter, lone pair and pseudo atoms in atom iterations.static final int
Include all bonds: covalent and coordinate bonds in bond iteration.static final int
Deprecated, for removal: This API element is subject to removal in a future version.static final int
Include only chemical atoms in iteration, skip multicenters, lone pairs and pseudo atoms.static final int
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
Exclude coordinate bonds from bond iteration.static final int
Exclude covalent bonds from bond iteration.static final int
Exclude explicit hydrogens from atom iteration.static final int
Exclude lone pairs from atom iteration.static final int
Exclude multicenters from atom iteration.static final int
Exclude pseudo atoms from atom iteration. -
Constructor Summary
ConstructorDescriptionIteratorFactory
(Molecule mol) Constructs an iterator factory for the specified molecule with default atom and bond related behavior to include all atoms and bonds.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) Constructs an iterator factory for the specified molecule with a specified atom and bond related behavior. -
Method Summary
Modifier and TypeMethodDescriptionConstructs an atom iterator for the specified molecule of the factory according to the atom related behavior set in the factory.Constructs an iterator to get the atom neighbours of the specified atom.Constructs a bond iterator for the specified molecule of the factory according to bond related behavior set in the factory.Constructs an iterator to get the bonds connecting to the specified atom.Constructs an rgroup definition component iterator for the specified molecule of the factory if the molecule is an RgMolecule, an empty iterator otherwise.Constructs a reaction component iterator for the specified molecule of the factory if the molecule is an RxnMolecule, an empty iterator otherwise.Constructs an s-group iterator for the specified molecule of the factory.boolean
isExcludedAtom
(MolAtom atom) By overriding this method, the inclusion pattern of IteratorFactory can be rewritten to exclude more atoms, than it would normally.boolean
isExcludedBond
(MolBond bond) By overriding this method, the inclusion pattern of IteratorFactory can be rewritten to exclude more bonds, than it would normally.int
Returns the number of atoms iterated by AtomIterator.int
Returns the number of bonds iterated by BondIterator.int
numberOfNeighbours
(MolAtom atom) Returns the number of atoms/bonds iterated by (Atom/Bond)NeighbourIterator (the two values are the same).
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Field Details
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INCLUDE_ALL_BONDS
public static final int INCLUDE_ALL_BONDSInclude all bonds: covalent and coordinate bonds in bond iteration.- See Also:
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SKIP_COORDINATE_BONDS
public static final int SKIP_COORDINATE_BONDSExclude coordinate bonds from bond iteration.- See Also:
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SKIP_COVALENT_BONDS
public static final int SKIP_COVALENT_BONDSExclude covalent bonds from bond iteration.- See Also:
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REPLACE_COORDINATE_BONDS
public static final int REPLACE_COORDINATE_BONDSReplace 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:
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INCLUDE_ALL_ATOMS
public static final int INCLUDE_ALL_ATOMSInclude all atoms: chemical atoms, explicit hydrogen, multicenter, lone pair and pseudo atoms in atom iterations.- See Also:
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SKIP_EXPLICIT_H
public static final int SKIP_EXPLICIT_HExclude explicit hydrogens from atom iteration.- See Also:
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SKIP_MULTICENTER
public static final int SKIP_MULTICENTERExclude multicenters from atom iteration.- See Also:
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SKIP_LONE_PAIR
public static final int SKIP_LONE_PAIRExclude lone pairs from atom iteration.- See Also:
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SKIP_PSEUDO_ATOM
public static final int SKIP_PSEUDO_ATOMExclude pseudo atoms from atom iteration.- See Also:
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INCLUDE_CHEMICAL_ATOMS
@Deprecated(forRemoval=true) @SubjectToRemoval(date=JUL_01_2025) public static final int INCLUDE_CHEMICAL_ATOMSDeprecated, for removal: This API element is subject to removal in a future version.As of Marvin 6.2, UseINCLUDE_CHEMICAL_ATOMS_ONLY
instead.Include only chemical atoms in iteration, skip multicenters, lone pairs and pseudo atoms.- See Also:
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INCLUDE_CHEMICAL_ATOMS_ONLY
public static final int INCLUDE_CHEMICAL_ATOMS_ONLYInclude only chemical atoms in iteration, skip multicenters, lone pairs and pseudo atoms.- See Also:
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Constructor Details
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IteratorFactory
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
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IteratorFactory
Constructs an iterator factory for the specified molecule with default atom and bond related behavior to include all atoms and bonds.- See Also:
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IteratorFactory
Constructs an iterator factory for the specified molecule with default atom and bond related behavior to include all atoms and bonds.- See Also:
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Method Details
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createAtomIterator
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
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createBondIterator
Constructs a bond iterator for the specified molecule of the factory according to bond related behavior set in the factory.- Returns:
- the bond iterator
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createSgroupIterator
Constructs an s-group iterator for the specified molecule of the factory.- Returns:
- the s-group iterator
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createAtomNeighbourIterator
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
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createBondNeighbourIterator
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
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createRxnComponentIterator
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
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createRgComponentIterator
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
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isExcludedAtom
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
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isExcludedBond
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
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numberOfAtoms
public int numberOfAtoms()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
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numberOfBonds
public int numberOfBonds()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
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numberOfNeighbours
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
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INCLUDE_CHEMICAL_ATOMS_ONLY
instead.