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.