From: Vincent Le G. <vin...@gm...> - 2010-04-19 12:54:34
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2010/4/19 Egon Willighagen <ego...@gm...> > On Mon, Apr 19, 2010 at 11:42 AM, Vincent Le Guilloux > <vin...@gm...> wrote: > > When the CDK load a molecule having aromatic bond flag set to 4, the bond > > order is set to 1. For example, if I load benzene with aromatic flag set > to > > 4, and I write the molecule back, I will get cyclohexane. I think this is > > quite important issue that should be fixed asap. > > That situation was recently discussed on this mailing list. Yes indeed, my fault... I forgot (yet I was the topic starter as far as I remember) :) The > molfile specification does not have a bonder order 4, just 1-3. Many > files write, however, molfile query structures, where 4 indicates an > aromatic atom, but it is not a bond order. > Yep. > > Now, the CDK current does not have a unknown bond order (we need a > patch for that), so upon reading it (incorrectly?) defaults to > SINGLE... causing the cyclohexane... now, please let us know what > software created the incorrect MDL molfile, and please file a bug > report against that project... > It's not really a software specific problem (well at least not in my experience). I've encountered various situations... few people know in details each chemical format, and even more few people know how various softwares handle it. In my (short and modest) experience, I've already seen modeler / chemist that aromatize molecules (using Marvin for example -> if you aromatize a molecule and save it as SDF, the bond flag will be set to 4), or SDF files sent by chemical provider which contains aromatized molecules... In such cases, even if structures should no be defined using this flag, setting the bond order to 1 is clearly dangerous, even more dangerous because it is made silently. I guess that, until an appropriate flag is defined, the DeduceBondOrder should be used by default (along with a proper warning) in the reader when these specific cases are encountered. > Otherwise, use the DeduceBondOrder (or so) class to assign proper bond > orders... > > Egon > > -- > Post-doc @ Uppsala University > Proteochemometrics / Bioclipse Group of Prof. Jarl Wikberg > Homepage: http://egonw.github.com/ > Blog: http://chem-bla-ics.blogspot.com/ > PubList: http://www.citeulike.org/user/egonw/tag/papers > |