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, 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:

master

Belongs to CDK module:

interfaces

Method Summary

Modifier and Type	Method and 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.
Object	clone() Returns a deep clone of this IChemObject.
boolean	getFlag(int mask) Returns the value of a given flag.
boolean[]	getFlags() Returns the whole set of flags.
Number	getFlagValue() Access the internal value used to store the 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.
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	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

Method Detail

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:

removeListener(org.openscience.cdk.interfaces.IChemObjectListener)

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:

addListener(org.openscience.cdk.interfaces.IChemObjectListener)

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()

getNotification

boolean getNotification()

Returns the flag that indicates whether notification messages are sent around.

Returns:

true if messages are sent.

See Also:

setNotification(boolean)

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:

getProperty(java.lang.Object), removeProperty(java.lang.Object)

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:

setProperty(java.lang.Object, java.lang.Object), getProperty(java.lang.Object)

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:

setProperty(java.lang.Object, java.lang.Object), getProperty(Object, Class), removeProperty(java.lang.Object)

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:

getProperty(Object), addProperties(java.util.Map)

getProperties

Map<Object,Object> getProperties()

Returns a Map with the IChemObject's properties.

Returns:

The object's properties as an Map

See Also:

addProperties(java.util.Map<java.lang.Object, java.lang.Object>)

getID

String getID()

Returns the identifier (ID) of this object.

Returns:

a String representing the ID value

See Also:

setID(java.lang.String)

setID

void setID(String identifier)

Sets the identifier (ID) of this object.

Parameters:

identifier - a String representing the ID value

See Also:

getID()

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(int), CDKConstants

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:

setFlag(int, boolean), CDKConstants

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:

getProperties()

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:

setFlag(int, boolean), getFlags()

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:

setFlags(boolean[]), getFlag(int), getFlagValue()

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

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