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
gives
Note that this doesn't occur if the extended SMILES atom labels are omitted.
Tested with CDK 2.7.1