Package org.openscience.cdk.interfaces

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, AtomContainerLegacy, AtomContainerLegacy, 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

  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    static final int
    ALIPHATIC
    Flag that is set if a ChemObject is part of an aliphatic chain.
    static final int
    AROMATIC
    Flag is set if ChemObject is part of an aromatic system.
    static final int
    CONJUGATED
    Flag is set if ChemObject is part of a conjugated system.
    static final int
    HYDROGEN_BOND_ACCEPTOR
    Sets to true if the atom is a hydrogen bond acceptor.
    static final int
    HYDROGEN_BOND_DONOR
    Sets to true if the atom is a hydrogen bond donor.
    static final int
    IN_RING
    Flag that is set when the ChemObject is part of a ring.
    static final int
    MAPPED
    Flag is set if a ChemObject is mapped to another ChemObject.
    static final int
    MARKUSH
    Flag to indicate a flattened molecule holds a Markush structure, you can work on it as is or it might make more sense to repack into something sensible like a RGroupQuery.
    static final int
    NOT_IN_RING
    Flag that is set when the ChemObject is part of a ring.
    static final int
    PLACED
    Flag that is set if the ChemObject is placed when calculating 2D/3D layouts.
    static final int
    REACTIVE_CENTER
    Flag is set if a ChemObject has reactive center.
    static final int
    SINGLE_OR_DOUBLE
    Flag used for marking uncertainty of the bond order.
    static final int
    TYPEABLE
    Flag is set if an atom could be typed.
    static final int
    VISITED
    Flag is set if ChemObject has been visited.

  • Method Summary

    Modifier and Type
    Method
    Description
    void
    addListener(IChemObjectListener col)
    Use this to add yourself to this IChemObject as a listener.
    void
    addProperties(Map<Object,Object> properties)
    Add properties to this object, duplicate keys will replace any existing value.
    void
    clear(int flags)
    Clear the provided flags.
    Object
    clone()
    Returns a deep clone of this IChemObject.
    int
    flags()
    Access the current value of the flags for this ChemObject.
    boolean
    getFlag(int mask)
    Returns the value of a given flag.
    boolean[]
    getFlags()
    Returns the whole set of flags.
    Number
    getFlagValue()
    Deprecated.
    used flags()
    String
    getID()
    Returns the identifier (ID) of this object.
    int
    getListenerCount()
    Returns the number of ChemObjectListeners registered with this object.
    boolean
    getNotification()
    Returns the flag that indicates whether notification messages are sent around.
    Map<Object,Object>
    getProperties()
    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.
    boolean
    is(int flags)
    Test if a flag(s) are set on this ChemObject.
    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.
    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.
    void
    removeListener(IChemObjectListener col)
    Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.
    void
    removeProperty(Object description)
    Removes a property for a IChemObject.
    void
    set(int flags)
    Set the provided flags.
    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
    setProperties(Map<Object,Object> properties)
    Set the properties of this object to the provided map (shallow copy).
    void
    setProperty(Object description, Object property)
    Sets a property for a IChemObject.
    String
    toString()
    Returns a one line description of this IChemObject.

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

    getBuilder

  • Field Details

    • PLACED

      static final int PLACED
      Flag that is set if the ChemObject is placed when calculating 2D/3D layouts.
      See Also:

    • IN_RING

      static final int IN_RING
      Flag that is set when the ChemObject is part of a ring.
      See Also:

    • NOT_IN_RING

      static final int NOT_IN_RING
      Flag that is set when the ChemObject is part of a ring. Note !isInRing() is preferred.
      See Also:

    • ALIPHATIC

      static final int ALIPHATIC
      Flag that is set if a ChemObject is part of an aliphatic chain. Since normally ALIPHATIC = !AROMATIC and AROMATIC = !ALIPHATIC.
      See Also:

    • VISITED

      static final int VISITED
      Flag is set if ChemObject has been visited.
      See Also:

    • AROMATIC

      static final int AROMATIC
      Flag is set if ChemObject is part of an aromatic system.
      See Also:

    • CONJUGATED

      static final int CONJUGATED
      Flag is set if ChemObject is part of a conjugated system.
      See Also:

    • MAPPED

      static final int MAPPED
      Flag is set if a ChemObject is mapped to another ChemObject. It is used for example in subgraph isomorphism search. Note this flag is not currently used.
      See Also:

    • HYDROGEN_BOND_DONOR

      static final int HYDROGEN_BOND_DONOR
      Sets to true if the atom is a hydrogen bond donor.
      See Also:

    • HYDROGEN_BOND_ACCEPTOR

      static final int HYDROGEN_BOND_ACCEPTOR
      Sets to true if the atom is a hydrogen bond acceptor.
      See Also:

    • REACTIVE_CENTER

      static final int REACTIVE_CENTER
      Flag is set if a ChemObject has reactive center. It is used for example in reaction.
      See Also:

    • TYPEABLE

      static final int TYPEABLE
      Flag is set if an atom could be typed.
      See Also:

    • SINGLE_OR_DOUBLE

      static final int SINGLE_OR_DOUBLE
      Flag used for marking uncertainty of the bond order. If used on an
      • IAtomContainer it means that one or several of the bonds have this flag raised (which may indicate aromaticity).
      • IBond it means that it's unclear whether the bond is a single or double bond.
      • IAtom it is a way for the Smiles parser to indicate that this atom was written with a lower case letter, e.g. 'c' rather than 'C'
      See Also:

    • MARKUSH

      static final int MARKUSH
      Flag to indicate a flattened molecule holds a Markush structure, you can work on it as is or it might make more sense to repack into something sensible like a RGroupQuery.
      See Also:

  • 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. AROMATIC or 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. AROMATIC). 
      
 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

      @Deprecated Number getFlagValue()
      Deprecated.
      used flags()
      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

    • set

      void set(int flags)
      Set the provided flags. Any on-bits in the input parameter are set on in the ChemObject.
      Parameters:
      flags - the flags

    • clear

      void clear(int flags)
      Clear the provided flags. Any on-bits in the input parameter are set on in the ChemObject.
      Parameters:
      flags - the flags

    • is

      boolean is(int flags)
      Test if a flag(s) are set on this ChemObject. If multiple flags are provided they must all be set to return true. 
      
 atom.set(IS_IN_RING);
 atom.is(IS_IN_RING); // false!
 atom.is(IS_IN_RING+IS_AROMATIC); // false!
 atom.set(IS_AROMATIC);
 atom.is(IS_IN_RING+IS_AROMATIC); // true!
      Parameters:
      flags - the flags

    • flags

      int flags()
      Access the current value of the flags for this ChemObject.
      Returns:
      the flag value (32-bit integer)

    • toString

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

    • clone

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