Hi Jean-Marc,
Just a thought, but SDMolSupplier has a lazy eval, if I am not mistaken.
Technically you should get all the rdkit warnings and errors at the time of
processing that bit of the sdf file. You can always read the stderror output,
parse it and throw exception every time a 'funny' molecule comes in.
I use a routine similar to this:
from io import StringIO
import sys
import rdkit
saved_std_err = sys.stderr
log = sys.stderr = StringIO()
rdkit.Chem.WrapLogs()
reader = Chem.SDMolSupplier('my_file.sdf')
for mol in reader:
error_msgs = log.getvalue()
# check error_msgs content if it there are any particular errors and
act accordingly, erhaps even flush the stream
sys.stderr = saved_std_err
Lukas
On 21/01/2019, 13:24, "Jean-Marc Nuzillard" <[email protected]> wrote:
Chem.SDMolSupplier
_______________________________________________
Rdkit-discuss mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
