OK, error messages where hidden by IPython for me too.
I used "Knime" to look at the sdf file, and it seems that the errors are
"real" - polymers, organometallic compounds or completely daft, two
examples:
The structure in the first column is the input sdf.
Simple workflow was:
"RDKit Fr
I also got this to run with no problem in a Jupyter notebook.
BUT...I did see the error messages Milinda mentioned in the terminal that
was running the jupyter notebook server. If I do *from rdkit.Chem.Draw
import IPythonConsole *before running the code, I see all the
errors/warnings in Jupyter.
On 2017-01-11 19:26, Milinda Samaraweera wrote:
Dear Experts,
I was trying to read in the attached SD file (downloaded from HMDB)
and trying to calculate the exact mass of each entry:
[...]
By running the script, I got a barrage of errors as:
[13:15:14] ERROR: Could not sanitize molecule
With same code and fresh file download, works fine for me without error.
ms contains 35177 molecules. Perhaps your download was corrupt?
On 11/01/2017 18:26, Milinda Samaraweera wrote:
Dear Experts,
I was trying to read in the attached SD file (downloaded from HMDB)
and trying to calculate th
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