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I'd like to be able to create a table displaying different substituents and bonds inside the different members of drug groups like the morphinan opioids and as part of that it would be great if I could create a atom-numbered diagram of morphinan to refer to in said table. I'd just like to know if it is possible to do this in MarvinSketch and, if so, how. I am using MarvinSketch 5.12.3 if it is relevant.

EDIT: I would like MarvinSketch to automatically number each atom. That is, I would like each atom to be assigned the number it is given when naming in IUPAC.

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You can use the manual mapping function (mouseover + m and the number you wish to add to the atom) to reorder the default atom numbering. There is more information about using the manual mapping function in Marvin here.

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Um, sorry I wasn't as specific as I had originally thought, please refer to my latest edit (after "EDIT:"). –  Brenton Horne Apr 20 '13 at 21:57
    
There is an IUPAC module in biopython. A Python scripting question would be a topic for Stackoverflow. –  karel Apr 20 '13 at 23:55
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