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Can't kekulize mol #917
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Is this a known problem ? |
Just busy and haven't had a chance to take a look at it. |
OK. For the moment, I will just ignore those molecules. |
One piece of information that would really help: which piece of software produced the mol2 files? |
Conformer generation was performed with omega (from openeye). |
And that wrote the mol2 file? |
I hope so. |
Hmm. Let me think; maybe there was an additional pass with open babel to ensure the partial charges were Gasteiger ones. |
The reader is not super robust. It really expects that the input files have atom types that match what Corina produces. There's a bit of documentation of that here: http://www.rdkit.org/Python_Docs/rdkit.Chem.rdmolfiles-module.html#MolFromMol2File |
If possible, you will have much better luck creating molecules from a Mol (or SDF) file |
Thanks for the tip. |
That would indeed be nice, but it doesn't know that. It just knows that a ring was encountered that it could not kekulize. Having some reporting that tells you which ring had the problem may help some. |
* improve error reporting for kekulization failures Connected to #917 * better phrasing of the message.
Now that the error reporting has been improved (at least I think so), I'm closing this. |
Using the following script:
and rdkit-Release_2016_03_1; I got all the following molecules in error:
https://gist.github.com/UnixJunkie/c8c500f9b18d80daf59d0990c8bc964e
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