I have a question regarding the Aromatic ring count.
There was a publication regarding the Heteroaromatic Rings of the Future and I used the
Instant-JChem module for curating some structures.
However for 2H,3H-imidazo[1,5-c]pyrimidin-3-one O=c1[nH]cc2ccncn12
I got two different aromatic ring counts depending on the aromatization state.
With dearomatization I got aromaticringcount = 2
with aromatization I got aromaticringcount = 1
Is that correct, because for naphthalene (2 rings) I get always aromaticringcount = 2
in aromatized and dearomatized state.
I added some more examples, see picture and see attached file.
I performed one calculation with aromatization (actually without doing anything) and
another one with explicit dearomatization using the standardizer.
Agin in very simple cases, naphthalene, the fusearomaticringcount is always the same,
in aromatized and dearomatized mode. For the attached examples there are many different
cases. So good practice always would be to dearomartize? But why the differences in some
cases and in some cases no difference?
Attached some thousand structures as SMI, SDF and XLS.
Thanks for the bug report, we will fix it.
See also this topic.
We fixed this bug in our main development version. It will be available in JChem version 5.3 (due this autumn) and in the next Instant JChem version using that version of JChem.
The bugfix unfortunately would require table regeneration, and to avoid that we do not plan to release it in a bugfix version (5.2.X). However, if we are forced to change the table version for any reason before version 5.3, we will include this bugfix in that version as well.
In the meantime, please use the dearomatized version of molecules.