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 > > > > > > >
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