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com.daylight
Class Molecule

java.lang.Object
  extended by com.daylight.DaylightCppObject
      extended by com.daylight.DaylightObject
          extended by com.daylight.AtomBondCollection
              extended by com.daylight.ConnectedAtomCollection
                  extended by com.daylight.Molecule

public class Molecule
extends ConnectedAtomCollection

Object representing a molecule

Field Summary
 
Fields inherited from class com.daylight.DaylightCppObject
ref
 
Constructor Summary
Molecule()
          from dt_allocmol.
Molecule(java.lang.String smiles)
          from dt_smilein.
Molecule(java.lang.String smiles, boolean addExplicitHydrogens)
          from dt_smilin_addh.
 
Method Summary
 Atom addAtom(int atomicNumber, int hydrogenCount)
          from dt_addatom.
 Molecule copy()
          from dt_copy.
protected  void finalize()
          Called by the garbage collector on an object when garbage collection determines that there are no more references to the object.
 
Methods inherited from class com.daylight.ConnectedAtomCollection
addImplicitHydrogens, convertToGraphRepresentation, createConformation, createDepiction, getArbitrarySmiles, getArbitraryStream, getCanonicalSmiles, getCanonicalStream, getExchangeSmiles, getOriginalStream, getOriginatingSmiles, isModifiable, setModifiable, suppressImplicitHydrogens
 
Methods inherited from class com.daylight.AtomBondCollection
generateFingerprint, getAtomCount, partialFingerprint, partialFingerprint
 
Methods inherited from class com.daylight.DaylightObject
appendStringProperty, checkProgramLicense, checkToolkitLicense, clearErrors, disableVirtualHandles, equals, getAdjunct, getAncestor, getBase, getBooleanProperty, getChiralClass, getChiralOrder, getCount, getErrors, getExistingObjectCount, getHandleProperty, getIntegerProperty, getParent, getPropertyNames, getPropertyType, getRealProperty, getRuntimeLibraryCreationDate, getRuntimeLibraryVersion, getStream, getStringProperty, getType, getTypename, getUniqueId, getUniqueIdRange, getWorstErrorType, hashCode, isNullObject, mpInitialize, mpLock, mpTrylock, mpUnlock, saveError, setAdjunct, setBooleanProperty, setHandleProperty, setIntegerProperty, setRealProperty, setStringProperty
 
Methods inherited from class java.lang.Object
clone, getClass, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

Molecule

public Molecule()
         throws DaylightException
from dt_allocmol. Allocates a new molecule object. The molecule is initially empty.

Throws:
DaylightException

Molecule

public Molecule(java.lang.String smiles)
         throws DaylightException
from dt_smilein.

Throws:
DaylightException

Molecule

public Molecule(java.lang.String smiles,
                boolean addExplicitHydrogens)
         throws DaylightException
from dt_smilin_addh.

Throws:
DaylightException
Method Detail

copy

public Molecule copy()
              throws DaylightException
from dt_copy.

Throws:
DaylightException

addAtom

public Atom addAtom(int atomicNumber,
                    int hydrogenCount)
             throws DaylightException
from dt_addatom.

Throws:
DaylightException

finalize

protected void finalize()
                 throws java.lang.Throwable
Called by the garbage collector on an object when garbage collection determines that there are no more references to the object.

Overrides:
finalize in class ConnectedAtomCollection
Throws:
java.lang.Throwable
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