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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