Thanks for the tip! Hi, Greg I will check it another for cases. SetNoImplicit and SetNoExplicit are very confused ones. What this makes it soluble?
Best, Noki. On Fri, Nov 2, 2018 at 1:01 PM Greg Landrum <greg.land...@gmail.com> wrote: > You're going to reach the limit of what this simple approach can do can do > very quickly. :-) > When you express the sulfur atom as [SH] in the SMILES, you tell the RDKit > that it must have an H attached. That information is preserved when you > connect the S to the other molecule, so you end up with a valence that's > too high. > > I added a function combine2 to the gist ( > https://gist.github.com/greglandrum/fd488309268cb085be218f26178e13b8) > that can handle this case, > > On Thu, Nov 1, 2018 at 9:33 AM Noki Lee <noki.le...@gmail.com> wrote: > >> Hi, Greg >> >> Recently, I got the code producing a combined molecule from one core and >> several functional groups: >> https://gist.github.com/greglandrum/fd488309268cb085be218f26178e13b8 >> >> Here is the exception case that I encountered. >> >> core = Chem.MolFromSmiles('N(=N/c1ccccc1)\c2ccccc2') >> pieces = [Chem.MolFromSmiles(x) for x in ('C(=O)O','O=[SH](=O)O')] >> connections = ((7,0),(4,1)) >> newMol = combine(core,pieces,connections) >> Draw.MolToImage(core).show() >> Draw.MolToImage(pieces[0]).show() >> Draw.MolToImage(pieces[1]).show() >> Draw.MolToImage(newMol).show() >> print(Chem.MolToSmiles(newMol)) >> >> I tried using all canonicalized smiles. I worked for 'O=S(=O)O' which is >> not canonicalized one. >> If I put 'O=[SH](=O)O', it works. But it's not what I wanted. The tail of >> H(hydrogen) tags along the S atom. >> I tried [S-] instead [SH], but it is also not what I expected. S in the >> result of 'combine' function has a negative charge. Can you suggest >> something? >> >> _______________________________________________ >> Rdkit-discuss mailing list >> Rdkit-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >> >
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