CDKToBeam NPE double bond stereo with labelled R-atoms #812
Description
String smiles = "N[C@H](C(N/C=C\\C[C@@H](O*)C/C=C(/*)\\C)=O)C(C)(C)C>C(=C/C(=O)O)\\C#C.CCN=C=NCCCN(C)C.Cl>N([C@H](C(N/C=C\\C[C@@H](O*)C/C=C(/*)\\C)=O)C(C)(C)C)C(=O)/C=C/C#C |$;;;;;;;;;R;;;;Y;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;R;;;;Y$,f:2.3|";
SmilesParser smilesParser = new SmilesParser(SilentChemObjectBuilder.getInstance());
smilesParser.kekulise(true);
SmilesGenerator smilesGenerator = new SmilesGenerator(SmiFlavor.Isomeric);
IReaction reaction = smilesParser.parseReactionSmiles(smiles);
for (IAtomContainer reactant : reaction.getReactants().atomContainers()) {
System.out.println(smilesGenerator.create(reactant));
}gives
Exception in thread "main" java.lang.NullPointerException
at org.openscience.cdk.smiles.CDKToBeam.addGeometricConfiguration(CDKToBeam.java:320)
at org.openscience.cdk.smiles.CDKToBeam.toBeamGraph(CDKToBeam.java:154)
at org.openscience.cdk.smiles.SmilesGenerator.create(SmilesGenerator.java:446)
at org.openscience.cdk.smiles.SmilesGenerator.create(SmilesGenerator.java:402)
at org.openscience.cdk.smiles.SmilesGenerator.create(SmilesGenerator.java:363)
Note that this doesn't occur if the extended SMILES atom labels are omitted.
Tested with CDK 2.7.1