Yo RDKitters,
I am stuck on something so basic, its embarrassing. But for the life of me
I cannot figure it out on my own. This is probably more of a python
question than an RDKit one.
I want to capture the RDKit warning/error message from python. e.g.
>>> import rdkit
>>> from rdkit import Chem
>>> Chem.MolFromSmiles('XXX')
[14:51:32] SMILES Parse Error: syntax error for input: XXX
I want to capture that error message (which in this case isn't very
informative, but if you read in a mol2 you can get something like
[14:25:46] 3ZGZ.A: warning - O.co2 with non C.2 or S.o2 neighbor. Which I
am also interested in). The big picture is that I built a web up where you
upload an sdf, mol, mol2 or smi file - and I want to show RDKit's error
message if there something funny in the query file.
I have tried the obvious (I think):
#!/usr/bin/env python
import sys
import rdkit
from rdkit import Chem
f = open("err.log", "w")
original_stderr = sys.stderr
sys.stderr = f
Chem.MolFromSmiles('XXX')
sys.stderr = original_stderr
f.close()
This still shows the error message in the terminal and not in the file. I
tried the same for stdout, still no cigar.
Any ideas ?
THANKS!
JP
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