[Cdk-devel] [ cdk-Bugs-884991 ] Layout algorithm cannot handle diconnected structures

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Bugs item #884991, was opened at 2004-01-26 20:49
Message generated for change (Comment added) made by steinbeck
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Category: org.openscience.cdk.layout
Group: None
>Status: Closed
>Resolution: Invalid
Priority: 5
Submitted By: Anatoli Krassavine (akrassavine)
Assigned to: Christoph Steinbeck (steinbeck)
Summary: Layout algorithm cannot handle diconnected structures

Initial Comment:
  Presently CDK cannot layout a disconnected structure 
(structure consisting of several unconnected 
fragments). This is most simply shown when entering 
structure from smiles

CCCC.CCCCCCC will fail with the following exception:

java.lang.NullPointerException
        at 
org.openscience.cdk.layout.AtomPlacer.getNextBondVect
or(AtomPlacer.java:338)
        at 
org.openscience.cdk.layout.StructureDiagramGenerator.
handleAliphatics(StructureDiagramGenerator.java:410)
        at 
org.openscience.cdk.layout.StructureDiagramGenerator.
generateCoordinates
(StructureDiagramGenerator.java:293)
        at 
org.openscience.cdk.layout.StructureDiagramGenerator.
generateCoordinates
(StructureDiagramGenerator.java:310)

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>Comment By: Christoph Steinbeck (steinbeck)
Date: 2004-01-27 10:08

Message:
Logged In: YES 
user_id=54358

This behaviour is documented in the javadoc. 
Use ConnectivitiyChecker.partitionIntoMolecules() first and
then do the layout. 

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