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com.daylight
Class AtomBondCollection

java.lang.Object
  extended by com.daylight.DaylightCppObject
      extended by com.daylight.DaylightObject
          extended by com.daylight.AtomBondCollection
Direct Known Subclasses:
ConnectedAtomCollection, Cycle, Set
public class AtomBondCollection
extends DaylightObject

Base class for for any object for which object.stream(DaylightObject::Atom) and object.stream(DaylightObject::Bond) will return a stream of atoms and bonds, respectively.

Field Summary
 
Fields inherited from class com.daylight.DaylightCppObject
ref
 
Constructor Summary
protected AtomBondCollection()
          implicit superconstructor.
 
Method Summary
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 generateFingerprint(int minStep, int maxStep, int sizeInBits)
          from dt_fp_generatefp.
 int getAtomCount()
          from dt_count.
 Fingerprint partialFingerprint(Atom atom, int minStep, int maxStep, int sizeInBits)
          from dt_fp_partfp.
 Fingerprint partialFingerprint(Bond bond, int minStep, int maxStep, int sizeInBits)
          from dt_fp_partfp.
 
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

AtomBondCollection

protected AtomBondCollection()
                      throws DaylightException
implicit superconstructor.

Throws:
DaylightException
Method Detail

getAtomCount

public int getAtomCount()
                 throws DaylightException
from dt_count.

Throws:
DaylightException

generateFingerprint

public Fingerprint generateFingerprint(int minStep,
                                       int maxStep,
                                       int sizeInBits)
                                throws DaylightException
from dt_fp_generatefp.

Parameters:
minStep - minimum length path to be included in the fingerprint
maxStep - maximum length path to be included in the fingerprint
sizeInBits - values are 32 to 2^30
Returns:
Fingerprint
Throws:
DaylightException

partialFingerprint

public Fingerprint partialFingerprint(Atom atom,
                                      int minStep,
                                      int maxStep,
                                      int sizeInBits)
                               throws DaylightException
from dt_fp_partfp.

Parameters:
atom - the atom which is in the generated paths
minStep - minimum length path to be included in the fingerprint
maxStep - maximum length path to be included in the fingerprint
sizeInBits - values are 32 to 2^30
Returns:
Fingerprint
Throws:
DaylightException

partialFingerprint

public Fingerprint partialFingerprint(Bond bond,
                                      int minStep,
                                      int maxStep,
                                      int sizeInBits)
                               throws DaylightException
from dt_fp_partfp.

Parameters:
bond - the bond which is in the generated paths
minStep - minimum length path to be included in the fingerprint
maxStep - maximum length path to be included in the fingerprint
sizeInBits - values are 32 to 2^30
Returns:
Fingerprint
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 DaylightObject
Throws:
java.lang.Throwable
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