Super, I'll test it. Thanks :-)
Br Esben Jannik Bjerrum cand.pharm, Ph.D /Sent from my Ubuntu Touch Phone Phone +45 2823 8009 http://dk.linkedin.com/in/esbenbjerrum http://www.wildcardconsulting.dk On Friday, January 8, 2016 9:56 AM, Greg Landrum <[email protected]> wrote: Esben, We ended up with a glitch in the new RDKit code-review "process" with this, but this has been fixed and the new version is checked in. Please let me know if you still see problems, -greg On Wed, Dec 23, 2015 at 9:49 AM, Esben Jannik Bjerrum <[email protected]> wrote: Thanks, sounds good if its a simple fix to the .ToBinary() function. Simple if you know ;-) "Interesting" explanation about the rB0 values, are they used at all in the RDkit code or are they just historic remnants? > >Esben Jannik Bjerrum >cand.pharm, Ph.D > >/Sent from my Ubuntu Touch Phone > >Phone +45 2823 8009 >http://dk.linkedin.com/in/esbenbjerrum >http://www.wildcardconsulting.dk > > > > >On Tuesday, December 22, 2015 7:01 AM, Greg Landrum <[email protected]> >wrote: > > > >Hi Esben, > > >On Thu, Dec 17, 2015 at 12:04 PM, Esben Jannik Bjerrum ><[email protected]> wrote: > > >> >>A problem is that in depictions the atomic number gets "wrapped" so it comes >>out as '*' >> >>I traced it down to a conversion in MolDrawing.py >> >> >>mol = Chem.Mol(mol.ToBinary()) >>and it can be reproduced in the python session: >> >> >>mol = Chem.Mol(mol.ToBinary()) >>mol.GetAtoms()[0].GetSymbol() >> >>returns '*' which is the pseudo atom with atomic number 0. >> >>My guess is that it has something to do with the atomic number being limited >>to 7 bit in the ToBinary() function? 128 = 10000000 => 0000000 = 0? Any .cpp >>guru who knows the ToBinary() who can help and suggest a solution? >> > >You've hit the nail on the head. I think it's "just" a matter of changing >To/FromBinary() to use all 8 bits when serializing/deserializing. I also think >I can make this change easily without affecting backwards compatibility, but >I'm going to have to confirm that. > >Also it would be best to start the atomic numbering of the pseudo atoms from >147 so that it matches MDL ISIS draw and Proteax pseudo atom numbering, but >RDkit assumes that the atomic numbering are forth running. I guess its >possible to add a lot of placeholders in between 112 and 147, but is there >another solution? >> >> > >Unfortunately not. The periodic table data structure uses a vector to store >the data which is indexed by atomic number. > > >>Bonus question: What is the rB0 in the atomic_data.cpp file? >> > >Hmm, the origin of some of that stuff is almost lost in antiquity. Here's an >explanation: https://sourceforge.net/p/openbabel/mailman/message/7048411/ > >-greg > > > > >>P/S. don't use the above pseudo atoms for anything but tested, it need more >>testing with regard to the behavior of the combinations of outer shell >>electrons and allowed valences. >> >>Esben Jannik Bjerrum >>cand.pharm, Ph.D >> >>/Sent from my Ubuntu Touch Phone >> >>Phone +45 2823 8009 >>http://dk.linkedin.com/in/esbenbjerrum >>http://www.wildcardconsulting.dk >> >>------------------------------------------------------------------------------ >> >>_______________________________________________ >>Rdkit-discuss mailing list >>[email protected] >>https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >> >> >> > ------------------------------------------------------------------------------ Site24x7 APM Insight: Get Deep Visibility into Application Performance APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month Monitor end-to-end web transactions and take corrective actions now Troubleshoot faster and improve end-user experience. Signup Now! http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140 _______________________________________________ Rdkit-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
