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<mailto: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<mailto:OpenBabel-discuss@lists.sourceforge.net> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
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