Package org.openscience.cdk.tools.manipulator

Class ChemModelManipulator

java.lang.Object
org.openscience.cdk.tools.manipulator.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:
Source code:
main
Belongs to CDK module:
standard

  • Constructor Details

    • ChemModelManipulator

      public ChemModelManipulator()

  • Method Details

    • 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.

    • getAllIDs

      public static List<String> getAllIDs(IChemModel chemModel)