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com.daylight
Class ConnectedAtomCollection

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

A collection of atoms joined by bonds

Field Summary
 
Fields inherited from class com.daylight.DaylightCppObject
ref
 
Constructor Summary
protected ConnectedAtomCollection()
          implicit superconstructor.
 
Method Summary
 void addImplicitHydrogens(boolean allNonSpecialHydrogens)
          from dt_addh.
 void convertToGraphRepresentation()
          from dt_molgraph.
 Conformation createConformation()
          from dt_alloc_conformation.
 Depiction createDepiction()
          from dt_alloc_depiction.
protected  void finalize()
          Called by the garbage collector on an object when garbage collection determines that there are no more references to the object.
 java.lang.String getArbitrarySmiles(boolean includeIsomericInfo)
          from dt_arbsmiles.
 Stream getArbitraryStream(DaylightObjectType type, boolean includeIsomericInfo, boolean addOrdinaryHydrogens)
          from dt_arbstream.
 java.lang.String getCanonicalSmiles(boolean includeIsomericInfo)
          from dt_cansmiles.
 Stream getCanonicalStream(DaylightObjectType type, boolean includeIsomericInfo, boolean addOrdinaryHydrogens)
          from dt_canstream.
 java.lang.String getExchangeSmiles(boolean includeIsomericInfo, boolean showImplicitProperties)
          from dt_xsmiles.
 Stream getOriginalStream(DaylightObjectType type)
          from dt_origstream.
 java.lang.String getOriginatingSmiles()
          from dt_info.
 boolean isModifiable()
          from dt_mod_is_on.
 void setModifiable(boolean value)
          from dt_mod_off and dt_mod_on.
 void suppressImplicitHydrogens(boolean allNonSpecialHydrogens)
          from dt_suppressh.
 
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

ConnectedAtomCollection

protected ConnectedAtomCollection()
                           throws DaylightException
implicit superconstructor.

Throws:
DaylightException
Method Detail

getArbitrarySmiles

public java.lang.String getArbitrarySmiles(boolean includeIsomericInfo)
                                    throws DaylightException
from dt_arbsmiles.

Throws:
DaylightException

getCanonicalSmiles

public java.lang.String getCanonicalSmiles(boolean includeIsomericInfo)
                                    throws DaylightException
from dt_cansmiles.

Throws:
DaylightException

getExchangeSmiles

public java.lang.String getExchangeSmiles(boolean includeIsomericInfo,
                                          boolean showImplicitProperties)
                                   throws DaylightException
from dt_xsmiles.

Throws:
DaylightException

getOriginatingSmiles

public java.lang.String getOriginatingSmiles()
                                      throws DaylightException
from dt_info.

Throws:
DaylightException

getOriginalStream

public Stream getOriginalStream(DaylightObjectType type)
                         throws DaylightException
from dt_origstream. Allocates a stream of 'type', in original order, for the reaction or molecule.

Throws:
DaylightException

getArbitraryStream

public Stream getArbitraryStream(DaylightObjectType type,
                                 boolean includeIsomericInfo,
                                 boolean addOrdinaryHydrogens)
                          throws DaylightException
from dt_arbstream.

Throws:
DaylightException

getCanonicalStream

public Stream getCanonicalStream(DaylightObjectType type,
                                 boolean includeIsomericInfo,
                                 boolean addOrdinaryHydrogens)
                          throws DaylightException
from dt_canstream.

Throws:
DaylightException

createConformation

public Conformation createConformation()
                                throws DaylightException
from dt_alloc_conformation.

Throws:
DaylightException

createDepiction

public Depiction createDepiction()
                          throws DaylightException
from dt_alloc_depiction.

Throws:
DaylightException

addImplicitHydrogens

public void addImplicitHydrogens(boolean allNonSpecialHydrogens)
                          throws DaylightException
from dt_addh.

Throws:
DaylightException

suppressImplicitHydrogens

public void suppressImplicitHydrogens(boolean allNonSpecialHydrogens)
                               throws DaylightException
from dt_suppressh.

Throws:
DaylightException

isModifiable

public boolean isModifiable()
                     throws DaylightException
from dt_mod_is_on.

Throws:
DaylightException

setModifiable

public void setModifiable(boolean value)
                   throws DaylightException
from dt_mod_off and dt_mod_on.

Throws:
DaylightException

convertToGraphRepresentation

public void convertToGraphRepresentation()
                                  throws DaylightException
from dt_molgraph. Modifies the molecule or reaction object to generate an oxidation-suppressed representation of the object. The function calls dt_mod_on(3), then performs the following operations: all bond orders are set to "single", aromaticity is turned off, hydrogen counts are set to the lowest "normal" count, charges and masses are set to zero, and isolated Hydrogen atoms (not connected to any other atoms) are removed. Then dt_mod_off(3) is called before returning. The resulting structure is essentially what's used to generate a GRAPH SMILES in Thor. The canonical SMILES of this object generates the graph string. For molecules, the canonical smiles is used directly as the GRAPH. For reactions, the string is postprocessed to convert the ">" characters to ".". Note that this function operates directly on the object; if one wants to preserve the original molecule or reaction, make a copy of the molecule or reaction before calling. If it fails, the molecule object will be deallocated and set to the null object.

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 AtomBondCollection
Throws:
java.lang.Throwable
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