Package org.openscience.cdk.tools.manipulator

Class ChemModelManipulator

  • public class ChemModelManipulator
extends Object
    Class with convenience methods that provide methods from methods from ChemObjects within the ChemModel. For example: 
     ChemModelManipulator.removeAtom(chemModel, atom);
    will find the Atom in the model by traversing the ChemModel's MoleculeSet, Crystal and ReactionSet fields and remove it with the removeAtom(Atom) method.
    See Also:
    AtomContainer.removeAtomAndConnectedElectronContainers(IAtom)
    Source code:
    main
    Belongs to CDK module:
    standard

    • Constructor Detail

      • ChemModelManipulator

        public ChemModelManipulator()

    • Method Detail

      • getAtomCount

        public static int getAtomCount​(IChemModel chemModel)
        Get the total number of atoms inside an IChemModel.
        Parameters:
        chemModel - The IChemModel object.
        Returns:
        The number of Atom object inside.

      • getBondCount

        public static int getBondCount​(IChemModel chemModel)
        Get the total number of bonds inside an IChemModel.
        Parameters:
        chemModel - The IChemModel object.
        Returns:
        The number of Bond object inside.

      • removeAtomAndConnectedElectronContainers

        public static void removeAtomAndConnectedElectronContainers​(IChemModel chemModel,
                                                            IAtom atom)
        Remove an Atom and the connected ElectronContainers from all AtomContainers inside an IChemModel.
        Parameters:
        chemModel - The IChemModel object.
        atom - The Atom object to remove.

      • removeElectronContainer

        public static void removeElectronContainer​(IChemModel chemModel,
                                           IElectronContainer electrons)
        Remove an ElectronContainer from all AtomContainers inside an IChemModel.
        Parameters:
        chemModel - The IChemModel object.
        electrons - The ElectronContainer to remove.

      • createNewMolecule

        public static IAtomContainer createNewMolecule​(IChemModel chemModel)
        Adds a new Molecule to the MoleculeSet inside a given ChemModel. Creates a MoleculeSet if none is contained.
        Parameters:
        chemModel - The ChemModel object.
        Returns:
        The created Molecule object.

      • newChemModel

        public static IChemModel newChemModel​(IAtomContainer atomContainer)
        Create a new ChemModel containing an IAtomContainer. It will create an IAtomContainer from the passed IAtomContainer when needed, which may cause information loss.
        Parameters:
        atomContainer - The AtomContainer to have inside the ChemModel.
        Returns:
        The new IChemModel object.

      • getRelevantAtomContainer

        public static IAtomContainer getRelevantAtomContainer​(IChemModel chemModel,
                                                      IAtom atom)
        This badly named methods tries to determine which AtomContainer in the ChemModel is best suited to contain added Atom's and Bond's.

      • getRelevantAtomContainer

        public static IAtomContainer getRelevantAtomContainer​(IChemModel chemModel,
                                                      IBond bond)
        Retrieves the first IAtomContainer containing a given IBond from an IChemModel.
        Parameters:
        chemModel - The IChemModel object.
        bond - The IBond object to search.
        Returns:
        The IAtomContainer object found, null if none is found.

      • getRelevantReaction

        public static IReaction getRelevantReaction​(IChemModel chemModel,
                                            IAtom atom)
        Retrieves the first IReaction containing a given IAtom from an IChemModel.
        Parameters:
        chemModel - The IChemModel object.
        atom - The IAtom object to search.
        Returns:
        The IAtomContainer object found, null if none is found.

      • getAllAtomContainers

        public static List<IAtomContainer> getAllAtomContainers​(IChemModel chemModel)
        Returns all the AtomContainer's of a ChemModel.

      • setAtomProperties

        public static void setAtomProperties​(IChemModel chemModel,
                                     Object propKey,
                                     Object propVal)
        Sets the AtomProperties of all Atoms inside an IChemModel.
        Parameters:
        chemModel - The IChemModel object.
        propKey - The key of the property.
        propVal - The value of the property.

      • getAllChemObjects

        public static List<IChemObject> getAllChemObjects​(IChemModel chemModel)
        Retrieve a List of all ChemObject objects within an IChemModel.
        Parameters:
        chemModel - The IChemModel object.
        Returns:
        A List of all ChemObjects inside.