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 > > > ------------------------------------------------------------------------------ _______________________________________________ Rdkit-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
