For what it's worth, I think I fixed this (and cleared up some other
problems) in this PR:
https://github.com/rdkit/rdkit/pull/2482
On Tue, Jun 4, 2019 at 1:44 PM Paolo Tosco
wrote:
> Hi David,
>
> I think I already have a fix for this bug, I'll submit a PR later. If you
> can create a ?GitHub
Hi David,
I think I already have a fix for this bug, I'll submit a PR later. If
you can create a ?GitHub issue it would be great so I can link my PR to
the bug.
Thanks, cheers
p.
On 06/04/19 12:10, David Cosgrove wrote:
Hi Paolo,
Many thanks for the speedy reply. I'll do as you suggest
Hi Paolo,
Many thanks for the speedy reply. I'll do as you suggest for now. Do you
want me to file an issue on github, or even, maybe, see if I can fix it
myself?
Cheers,
Dave
On Mon, Jun 3, 2019 at 5:32 PM Paolo Tosco
wrote:
> Hi David,
>
> a workaround could be adding a final check after
Hi David,
a workaround could be adding a final check after the for loop:
#!/usr/bin/env python
from rdkit import Chem
suppl1 = Chem.SmilesMolSupplier('test1.smi', titleLine=False, nameColumn=1)
rec_num = 0
print("len(suppl1) = {0:d}".format(len(suppl1)))
for mol in suppl1:
rec_num += 1
Hi,
I'm trying to catch the line numbers of lines in a SMILES file that aren't
parsed by the SmilesMolSupplier. Example code is attached, along with 2
SMILES files. When there is a bad SMILES string on the last line, the
error is not reported, as in test2.smi. I've tried iterating through the
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