Runs into org.openscience.cdk.exception.CDKException: "A bond had undefined order, possible query bond?"
I'm not able to spot the undefined order / query bond, maybe you can help me out?
String smirks = "[#8;H1:2]-[#6:10]1:[#6:5](-[#8;H1:1]):[#6:6](-[*,#1:11]):[#6:7]:[#6:8]:[#6,#7:9]:1>>[#8&-:2]-[#6:10](=O)-[#6,#7:9]=[#6:8]-[#6:7]=[#6:6](-[*,#1:11])-[#6:5](-[#8&-:1])=O"; String smi = "String smi = "Oc1cccc(Cl)c1O";
It's the same reaction / target pair as in #100, but with explicit aromatization.
Problem already fixed in Ambit snapshot: ambit2-smarts-3.0.3-20160628.065959-20.jar
Fixed in latest 3.0.3-SNAPSHOT