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com.daylight
Class Reaction

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.Reaction

public class Reaction
extends ConnectedAtomCollection

Object representing a reaction

Field Summary
 
Fields inherited from class com.daylight.DaylightCppObject
ref
 
Constructor Summary
Reaction()
          from dt_alloc_reaction.
Reaction(java.lang.String smiles)
          from dt_smilin.
 
Method Summary
 Molecule addComponent(Molecule molecule, Role role)
          from dt_addcomponent.
 Reaction 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.
 Fingerprint getDifferenceFingerprint(int minStep, int maxStep, int size)
          from dt_fp_differencefp.
 Role getRole(Atom atom)
          from dt_getrole.
 Role getRole(Bond bond)
          from dt_getrole.
 Role getRole(Cycle cycle)
          from dt_getrole.
 Role getRole(Molecule molecule)
          from dt_getrole.
 
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

Reaction

public Reaction()
         throws DaylightException
from dt_alloc_reaction.

Throws:
DaylightException

Reaction

public Reaction(java.lang.String smiles)
         throws DaylightException
from dt_smilin.

Throws:
DaylightException
Method Detail

copy

public Reaction copy()
              throws DaylightException
from dt_copy.

Throws:
DaylightException

getDifferenceFingerprint

public Fingerprint getDifferenceFingerprint(int minStep,
                                            int maxStep,
                                            int size)
                                     throws DaylightException
from dt_fp_differencefp.

Throws:
DaylightException

addComponent

public Molecule addComponent(Molecule molecule,
                             Role role)
                      throws DaylightException
from dt_addcomponent.

Throws:
DaylightException

getRole

public Role getRole(Atom atom)
             throws DaylightException
from dt_getrole.

Throws:
DaylightException

getRole

public Role getRole(Bond bond)
             throws DaylightException
from dt_getrole.

Throws:
DaylightException

getRole

public Role getRole(Cycle cycle)
             throws DaylightException
from dt_getrole.

Throws:
DaylightException

getRole

public Role getRole(Molecule molecule)
             throws DaylightException
from dt_getrole.

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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