Interface IChemObject

All Superinterfaces:
Cloneable, ICDKObject
All Known Subinterfaces:
IAminoAcid, IAtom, IAtomContainer, IAtomContainerSet, IAtomType, IBioPolymer, IBond, IChemFile, IChemModel, IChemSequence, ICrystal, IElectronContainer, IElement, IFragmentAtom, IIsotope, ILonePair, IMapping, IMonomer, IPDBAtom, IPDBMonomer, IPDBPolymer, IPolymer, IPseudoAtom, IQueryAtom, IQueryAtomContainer, IQueryBond, IReaction, IReactionScheme, IReactionSet, IRGroupQuery, IRing, IRingSet, ISingleElectron, IStrand, ISubstance
All Known Implementing Classes:
AliphaticAtom, AliphaticSymbolAtom, AminoAcid, AminoAcid, AnyAtom, AnyOrderQueryBond, AromaticAtom, AromaticOrSingleQueryBond, AromaticQueryBond, AromaticSymbolAtom, Association, Atom, Atom, AtomContainer, AtomContainer, AtomContainerSet, AtomContainerSet, AtomicNumberAtom, AtomRef, AtomType, AtomType, BioPolymer, BioPolymer, Bond, Bond, BondRef, ChargeGroup, ChemFile, ChemFile, ChemModel, ChemModel, ChemObject, ChemObject, ChemSequence, ChemSequence, ChiralityAtom, Crystal, Crystal, CTFileQueryBond, DebugAminoAcid, DebugAtom, DebugAtomContainer, DebugAtomContainerSet, DebugAtomType, DebugBioPolymer, DebugBond, DebugChemFile, DebugChemModel, DebugChemObject, DebugChemSequence, DebugCrystal, DebugElectronContainer, DebugElement, DebugFragmentAtom, DebugIsotope, DebugLonePair, DebugMapping, DebugMonomer, DebugPDBAtom, DebugPDBMonomer, DebugPDBPolymer, DebugPDBStructure, DebugPolymer, DebugPseudoAtom, DebugReaction, DebugReactionScheme, DebugReactionSet, DebugRing, DebugRingSet, DebugSingleElectron, DebugStrand, DebugSubstance, ElectronContainer, ElectronContainer, Element, Element, EnzymeResidueLocator, ExplicitConnectionAtom, FormalChargeAtom, FragmentAtom, FragmentAtom, HybridizationNumberAtom, HydrogenAtom, ImplicitHCountAtom, InverseSymbolSetQueryAtom, Isotope, Isotope, LogicalOperatorAtom, LogicalOperatorBond, LonePair, LonePair, Mapping, Mapping, MassAtom, MDMolecule, Monomer, Monomer, NonCHHeavyAtom, OrderQueryBond, OrderQueryBond, OrderQueryBondOrderOnly, PDBAtom, PDBAtom, PDBMonomer, PDBMonomer, PDBPolymer, PDBPolymer, PDBStrand, PDBStructure, PDBStructure, PeriodicGroupNumberAtom, PharmacophoreAngleBond, PharmacophoreAtom, PharmacophoreBond, PharmacophoreQuery, PharmacophoreQueryAngleBond, PharmacophoreQueryAtom, PharmacophoreQueryBond, Polymer, Polymer, PseudoAtom, PseudoAtom, QueryAtom, QueryAtomContainer, QueryBond, QueryChemObject, Reaction, Reaction, ReactionChain, ReactionRoleQueryAtom, ReactionScheme, ReactionScheme, ReactionSet, ReactionSet, RecursiveSmartsAtom, Residue, RGroupQuery, Ring, Ring, RingBond, RingIdentifierAtom, RingMembershipAtom, RingSet, RingSet, SingleElectron, SingleElectron, SmallestRingAtom, SMARTSAtom, SMARTSBond, StereoBond, Strand, Strand, Substance, Substance, SymbolAndChargeQueryAtom, SymbolChargeIDQueryAtom, SymbolQueryAtom, SymbolSetQueryAtom, TotalConnectionAtom, TotalHCountAtom, TotalRingConnectionAtom, TotalValencyAtom

public interface IChemObject extends ICDKObject
The base class for all chemical objects in this cdk. It provides methods for adding listeners and for their notification of events, as well a a hash table for administration of physical or chemical properties
Author:
egonw
Source code:
main
Belongs to CDK module:
interfaces
  • Method Summary

    Modifier and Type
    Method
    Description
    void
    Use this to add yourself to this IChemObject as a listener.
    void
    Add properties to this object, duplicate keys will replace any existing value.
    Returns a deep clone of this IChemObject.
    boolean
    getFlag(int mask)
    Returns the value of a given flag.
    boolean[]
    Returns the whole set of flags.
    Access the internal value used to store the flags.
    Returns the identifier (ID) of this object.
    int
    Returns the number of ChemObjectListeners registered with this object.
    boolean
    Returns the flag that indicates whether notification messages are sent around.
    Returns a Map with the IChemObject's properties.
    <T> T
    getProperty(Object description)
    Returns a property for the IChemObject - the object is automatically cast to the required type.
    <T> T
    getProperty(Object description, Class<T> c)
    Access a property of the given description and cast the specified class.
    void
    This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
    void
    This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
    void
    Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.
    void
    removeProperty(Object description)
    Removes a property for a IChemObject.
    void
    setFlag(int mask, boolean value)
    Sets the value of some flag.
    void
    setFlags(boolean[] newFlags)
    Sets the whole set of flags.
    void
    setID(String identifier)
    Sets the identifier (ID) of this object.
    void
    setNotification(boolean bool)
    Set a flag to use or not use notification.
    void
    Set the properties of this object to the provided map (shallow copy).
    void
    setProperty(Object description, Object property)
    Sets a property for a IChemObject.
    Returns a one line description of this IChemObject.

    Methods inherited from interface org.openscience.cdk.interfaces.ICDKObject

    getBuilder
  • Method Details

    • addListener

      void addListener(IChemObjectListener col)
      Use this to add yourself to this IChemObject as a listener. In order to do so, you must implement the ChemObjectListener Interface.
      Parameters:
      col - the ChemObjectListener
      See Also:
    • getListenerCount

      int getListenerCount()
      Returns the number of ChemObjectListeners registered with this object.
      Returns:
      the number of registered listeners.
    • removeListener

      void removeListener(IChemObjectListener col)
      Use this to remove a ChemObjectListener from the ListenerList of this IChemObject. It will then not be notified of change in this object anymore.
      Parameters:
      col - The ChemObjectListener to be removed
      See Also:
    • setNotification

      void setNotification(boolean bool)
      Set a flag to use or not use notification. By default it should be set to true.
      Parameters:
      bool - if true, then notification messages are sent.
      See Also:
    • getNotification

      boolean getNotification()
      Returns the flag that indicates whether notification messages are sent around.
      Returns:
      true if messages are sent.
      See Also:
    • notifyChanged

      void notifyChanged()
      This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
    • notifyChanged

      void notifyChanged(IChemObjectChangeEvent evt)
      This should be triggered by an method that changes the content of an object to that the registered listeners can react to it. This is a version of notifyChanged() which allows to propagate a change event while preserving the original origin.
      Parameters:
      evt - A ChemObjectChangeEvent pointing to the source of where the change happend
    • setProperty

      void setProperty(Object description, Object property)
      Sets a property for a IChemObject.
      Parameters:
      description - An object description of the property (most likely a unique string)
      property - An object with the property itself
      See Also:
    • removeProperty

      void removeProperty(Object description)
      Removes a property for a IChemObject.
      Parameters:
      description - The object description of the property (most likely a unique string)
      See Also:
    • getProperty

      <T> T getProperty(Object description)
      Returns a property for the IChemObject - the object is automatically cast to the required type. This does however mean if the wrong type is provided then a runtime ClassCastException will be thrown.
      
      
           IAtom atom = new Atom("C");
           atom.setProperty("number", 1); // set an integer property
      
           // access the property and automatically cast to an int
           Integer number = atom.getProperty("number");
      
           // if the method is in a chain or needs to be nested the type
           // can be provided
           methodAcceptingInt(atom.getProperty("number", Integer.class));
      
           // the type cannot be checked and so...
           String number = atom.getProperty("number"); // ClassCastException
      
           // if the type is provided a more meaningful error is thrown
           atom.getProperty("number", String.class); // IllegalArgumentException
      
       
      Type Parameters:
      T - generic return type
      Parameters:
      description - An object description of the property (most likely a unique string)
      Returns:
      The object containing the property. Returns null if property is not set.
      See Also:
    • getProperty

      <T> T getProperty(Object description, Class<T> c)
      Access a property of the given description and cast the specified class.
      
      
           IAtom atom = new Atom("C");
           atom.setProperty("number", 1); // set an integer property
      
           // access the property and automatically cast to an int
           Integer number = atom.getProperty("number");
      
           // if the method is in a chain or needs to be nested the type
           // can be provided
           methodAcceptingInt(atom.getProperty("number", Integer.class));
      
           // the type cannot be checked and so...
           String number = atom.getProperty("number"); // ClassCastException
      
           // if the type is provided a more meaningful error is thrown
           atom.getProperty("number", String.class); // IllegalArgumentException
      
       
      Type Parameters:
      T - generic type (of provided class)
      Parameters:
      description - description of a property (normally a string)
      c - type of the value to be returned
      Returns:
      the value stored for the specified description.
      See Also:
    • getProperties

      Map<Object,Object> getProperties()
      Returns a Map with the IChemObject's properties.
      Returns:
      The object's properties as an Map
      See Also:
    • getID

      String getID()
      Returns the identifier (ID) of this object.
      Returns:
      a String representing the ID value
      See Also:
    • setID

      void setID(String identifier)
      Sets the identifier (ID) of this object.
      Parameters:
      identifier - a String representing the ID value
      See Also:
    • setFlag

      void setFlag(int mask, boolean value)
      Sets the value of some flag. The flag is a mask from a given CDKConstant (e.g. CDKConstants.ISAROMATIC or CDKConstants.VISITED). The flags are intrinsic internal properties and should not be used to store custom values, please use setProperty(Object, Object).
      
       // set this chem object to be aromatic
       chemObject.setFlag(CDKConstants.ISAROMATIC, Boolean.TRUE);
       // ...
       // indicate we have visited this chem object
       chemObject.setFlag(CDKConstants.VISITED, Boolean.TRUE);
       
      Parameters:
      mask - flag to set the value for
      value - value to assign to flag
      See Also:
    • getFlag

      boolean getFlag(int mask)
      Returns the value of a given flag. The flag is a mask from a given CDKConstant (e.g. CDKConstants.ISAROMATIC).
      
       if(chemObject.getFlag(CDKConstants.ISAROMATIC)){
           // handle aromatic flag on this chem object
       }
       
      Parameters:
      mask - flag to retrieve the value of
      Returns:
      true if the flag flag_type is set
      See Also:
    • setProperties

      void setProperties(Map<Object,Object> properties)
      Set the properties of this object to the provided map (shallow copy). Any existing properties are removed.
      Parameters:
      properties - map key-value pairs
    • addProperties

      void addProperties(Map<Object,Object> properties)
      Add properties to this object, duplicate keys will replace any existing value.
      Parameters:
      properties - a Map specifying the property values
      See Also:
    • setFlags

      void setFlags(boolean[] newFlags)
      Sets the whole set of flags. This set will iteratively invoke setFlag(int, boolean) for each value in the array and use CDKConstants.FLAG_MASKS to look up the correct mask. If only a single flag is being set it is a lot faster to use setFlag(int, boolean).
      Parameters:
      newFlags - the new flags to set.
      See Also:
    • getFlags

      boolean[] getFlags()
      Returns the whole set of flags. This method will create a new array on each invocation and it is recommend you use getFlagValue() if you need all the flags. For individual flags please use getFlag(int)
      Returns:
      the flags.
      See Also:
    • getFlagValue

      Number getFlagValue()
      Access the internal value used to store the flags. The flags are stored on a single numeric value and are set/cleared.
      Returns:
      numeric representation of the flags
    • toString

      String toString()
      Returns a one line description of this IChemObject.
      Overrides:
      toString in class Object
      Returns:
      a String representation of this object
    • clone

      Returns a deep clone of this IChemObject.
      Returns:
      Object the clone of this IChemObject.
      Throws:
      CloneNotSupportedException - if the IChemObject cannot be cloned