I have a question related to the topic :
I have a big set of molecule having this issue :
since an implicit H is ambiguously defined in an aromatic ring (eg in COc1cc2nnnc2cc1C(=O)NCC3CCCN3CC=C) the dearomatization do not work on them (using jchem 3.1.5).
Since the structures in this set are pretty diverses, using the standardizer seem to be difficult. Would there be another way to dearomatize this kind of molecule ? (knowing that on which nitrogen the implicit hydrogen goes is not really important)
Dearomatization module has been improved.
Shortcoming of dearomatization about ambiguous “H” has been fixed.
Will be available soon in the new Marvin release.
Sorry, this is a little unclear to me. You mean it has been fixed in the latest jchem release (3.1.7) or it has been fixed and will be included in the next jchem release ? If it's the latest option, do you know when it will be available ?
The issue just has been fixed. Dearomatization is part of the Marvin library, but JChem contains Marvin.
Marvin 4.1 will be released first hopefully this month, but no JChem release (containing Marvin 4.1) can be expected before the end of August, I am afraid.
any update on when this new marvin will be released ?
You can expect it this week.