On Thu, Jun 6, 2019 at 8:00 PM Mateo Vacacela <mvacac...@cdrd.ca> wrote:
> Just as a follow up, I’m getting a similar error with the following ligand
> molecule:
>
> ValueError: Sanitization error: Explicit valence for atom # 21 F, 2, is
> greater than permitted
>
Again, the error message is telling you what the problem is: there's an F
atom in the structure (#21) that has a valence of 2. That's illegal for F.
Two notes about the SDF that you included in your message:
1) the SDF format is an old one and is sensitive to the amount of
whitespace. When you copied the text into your email some spaces got lost,
which makes the file unuseable.
2) The structure in that file does not produce the error message you
report. After editng the file by hand to add the spaces back in (I've
attached the editing file to the message), I was able to read it without
problems:
In [16]: m = Chem.MolFromMolFile('/tmp/ligand.mol')
In [17]:
Best,
-greg
ligand.mol
Description: Binary data
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