On Apr 16, 2018, at 16:29, Guillaume GODIN <[email protected]>
wrote:
> And for this one C[C@@]12CC[C@@](C)(CC1)O2O any idea
>
> Cause your tool failed too.
It's true that smiview failed, in the sense that it shouldn't have tried to do
further analysis with a molecule that RDKit rejected.
However, RDKit does report the failure as "Explicit valence for atom # 8 O, 3,
is greater than permitted":
% smiview 'C[C@@]12CC[C@@](C)(CC1)O2O'
[16:45:37] Explicit valence for atom # 8 O, 3, is greater than permitted
Unable to generate a molecule: RDKit cannot parse the SMILES
Traceback (most recent call last):
File "/Users/dalke/venvs/py36-all/bin/smiview", line 11, in <module>
load_entry_point('smiview', 'console_scripts', 'smiview')()
.... failure report that smiview should have prevented from happening ...
A hypothetical future version of smiview will capture that RDKit error message
so it can pinpoint the error location more visually.
Cheers,
Andrew
[email protected]
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