Hi, That SMILES-string doesn’t look valid. You have half the six-membered ring specified as aromatic and the other half as aliphatic. It seems like AddHydrogens is fixing this and adds hydrogens to match up the “aromatic” carbons.
Med vänliga hälsningar, Fredrik On 11 Sep 2019, 20:41 +0200, Scalfani, Vincent <vfscalf...@ua.edu>, wrote: > Hi Noel, > > Thanks very much, this works great! Also, If I add the DoNotAddH InChI option > without adding explicit hydrogens with OBMol.AddHydrogens(), to the molecule > before writing InChI, I get InChIs with no H’s. > > So, C (methane), becomes: > InChI=1S/C > > Instead of > InChI=1S/CH4/h1H4 > > But you are right, it seems that I was specifying the default options anyway, > and I do not need to add explicit H nor add the DoNotAddH option. Thanks for > the explanation. In general I found the InChIs are the same between the two > methods (i.e., no options vs. DoNotAddH). I did find a few examples where > these two methods produce different InChIs with Open Babel. However, I think > this is an unrelated bug, maybe related to OBMol.AddHydrogens(), and not > InChI? I’m not sure though. I’m happy to file a bug report if I uncovered > something real. > > Here is a Gist for an example of a molecule that has a different InChI based > on the two methods. The first InChI is calculated with no InChI options, and > the second with specifying DoNotAddH, and adding explicit hydrogens before > calculation. > > https://nbviewer.jupyter.org/gist/vfscalfani/724c47df3880edf4c0588001ba72d69e > > Thanks again. > > Vin > > > From: Noel O'Boyle <baoille...@gmail.com> > Sent: Wednesday, September 11, 2019 6:05 AM > To: Scalfani, Vincent <vfscalf...@ua.edu> > Cc: openbabel-discuss@lists.sourceforge.net > Subject: Re: [Open Babel] Error handling with smi file in pybel? > > Hi Vin, > > By default the command-line application stops on error, a behavior that can > be overridden by "-e". I have to say that this behavior drives me bananas. > But anyway... > > I've just been trying to do the same through Python, but have been failing. > Adding obconversion.AddOption("e", obconversion.GENOPTIONS) should work but > doesn't. So I'll file a bug. > > But for your purposes you don't need this. Just do what I always do :-) > > # loop through molecules and print InChI strings to a file > with open("mySMILES.smi") as inp: > with open("InChI_ouput.inchi", 'w') as f: > for line in inp: > try: > mol = pybel.readstring("smi", line) > except IOError: > f.write("Open_Babel_Error\n") > continue > > Pro-tip: name your file handles "inp" and "out" instead of "f", etc. I've > been there. :-) > > Regarding what you're trying to do, AddHydrogens doesn't actually add > hydrogens (I know, I know), it converts from implicit hydrogens to explicit. > The hydrogens are already there on every atom. But it's no harm making them > explicit, and you should get the same InChI either way. Similarly, I'd have > to check to be sure, but I think the code that uses the InChI has "/DoNoAddH" > implicitly (it's done through the API). Again, no harm specifying it. > > On Mon, 9 Sep 2019 at 22:05, Scalfani, Vincent <vfscalf...@ua.edu> wrote: > > Dear All, > > > > I am trying to process a SMILES file (.smi) and calculate InChIs, where > > there are some SMILES that Open Babel will not be able to read, due to > > syntax or other errors. In those cases, I would like to print a string such > > as “Open_Babel_Error” on the line (or something even more descriptive). > > > > However, everything I have tried results in Open Babel stopping once it > > reads a SMILES string it cannot parse. Here is where I am at (code below), > > I did read the Errors and Warnings documentation with OBMessageHandler > > class, but I could not figure out how to incorporate that. Any > > direction/examples would be much appreciated. > > > > Thanks > > > > Vin > > -- > > import pybel > > > > # Set up conversion to InChI > > conv = pybel.ob.OBConversion() > > conv.SetOutFormat("inchi") > > conv.AddOption("X", conv.OUTOPTIONS, "DoNotAddH") > > > > # Read a SMILES file > > mols = pybel.readfile("smi","mySMILES.smi") > > > > # loop through molecules and print InChI strings to a file > > with open("InChI_ouput.inchi", 'w') as f: > > for mol in mols: > > if not mol: > > f.write("Open_Babel_Error\n".format(inchi)) > > continue > > # N.B. Adding H's to OB Molecular Object, and not through InChI > > mol.OBMol.AddHydrogens() > > inchi = conv.WriteString(mol.OBMol) > > f.write("{}".format(inchi)) > > f.close() > > > > —- > > Vincent F. Scalfani, Ph.D. > > University Libraries > > The University of Alabama > > > > _______________________________________________ > > OpenBabel-discuss mailing list > > OpenBabel-discuss@lists.sourceforge.net > > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
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