#102 aromaticity ring with oxygen treated as non aromatic?

[Emanuel Schmid]

Result should be empty:

String smirks = "[#6:4]@-[#6;!$(C1(=O)C=CC(=O)C=C1)!$(C(=O)CC=O):1](@-[#6:2])=[O:5]>>[#6:2]@-[#8]@-[#6:1](@-[#6:4])=[O:5]";
String smi = "COc1cc(O)c2c(c1)oc(cc2=O)-c1ccc(O)cc1";

On the other hand, for these targets the result is as expected:

        smi = "O=C1CCOC=C1";
        smi = "O=c1ccocc1";
        smi = "O=C1C=COC=C1";

[Emanuel Schmid]

more explicitly: "O=C1CCOC=C1" is a target, the other two "O=c1ccocc1" and "O=C1C=COC=C1" are not triggering a reaction.

[Emanuel Schmid]

after changeing the '@-' bonds to '@-!:' aromatic rings are not a target anymore - but non ring molecules are:

String smirks = "[#6:4]@-!:[#6:1](@-!:[#6:2])=[O:5]>>[#6:2]@-[#8]@-[#6:1](@-[#6:4])=[O:5]"
String smiles = "O=C(C)C";

Expected products: none

[Nikolay Kochev]

Indeed, this bond

[#6:4]@-!:[#6:1]

must not match non-ring bonds.

The bug is fixed in snapshot: ambit2-smarts-3.0.3-20160630.051729-23.jar

Also working alternatives to this expression are:

[#6:4]@-&!:[#6:1]   and   [#6:4]@-;!:[#6:1]    

The latter worked in the previous version as well.

[Nina Jeliazkova]

Fixed in latest 3.0.3-SNAPSHOT