#108 arom bond not added in smirks with smarts bonds

[Martin Gütlein]

String smirks = "[#6:9]=,:[#6:10]@-C:6([#8:2][H:11])C:5(@-[#6:7]=,:[#6:8])[#8:1][H:12]>>[H:12][#8:1]-c:5:c:6:[c:10]:[c:9]";
String smi = "O[C@@H]1C=CC=C(Cl)[C@@H]1O";
String expectedSmiles = "C1=CC(=C(C(=C1)Cl)O)O";

We are not quite sure if our smirks is correct. However, at the moment your library produces a product that does NOT match the right side of the smirks, which should never happen, I guess.

see also https://github.com/mguetlein/TestAmbitSmarts/blob/master/src/test/java/org/kramerlab/test/TestAmbit.java

[Martin Gütlein]

just rembered sth (okay, I have to admit, I found sth in my notes):
we cannot make sth aromatic like this, e.g. this smirks does not work in your library as well:
[#6:1]1-[#6:2]=[#6:3]-[#6:4]=[#6:5]-[#6:6]-1>>[c:1]1:[c:2]:[c:3]:[c:4]:[c:5]:[c:6]:1
correct?

accordingly, the solution for the above smirks would be to introduce explict single and double bonds on the product side, correct?

in this special case, we think that we have to remove the smarts bonds "=,:" and make it explicit, therefore, we have to make 4 smirks out of 1

[Martin Gütlein]

smirks above should be

[#6:9]=,:[#6:10]@-[C:6]([H])([#8:2][H:11])[C:5]([H])(@-[#6:7]=,:[#6:8])[#8:1][H:12]>>[H:12][#8:1]-[c:5](:[c:7]:[c:8]):[c:6](-[#8:2][H:11]):[c:10]:[c:9]

[Nikolay Kochev]

Yes, the solution is to define explicitely the bond orders on the product side. Whether particular bonds will become aromatic or not will be a result from aromaticity detector.

It is not correct to have bonds with undefined order on the product side because the software does not know what order to set within the CDK atom container.
The only exception which is allowed to have aromatic bonds on the product side is when their correspondint bonds from the reactant side are also defined as aromatic i.e. in this case no bond order change is done so the software can work "without knowing the bond orders"

The proposed above SMIRKS is not ok - because produtc bonds are aromatic without specified order.