!
Giovanni
From: Ivan Tubert-Brohman
Sent: 14 April 2022 12:58
To: Giovanni Tricarico
Cc: rdkit-discuss@lists.sourceforge.net
Subject: Re: [Rdkit-discuss] how to report SDF records for which
Chem.ForwardSDMolSupplier returns None?
You don't often get email from
ivan.tubert-broh...@schrodinger.com
On Apr 14, 2022, at 12:57, Ivan Tubert-Brohman
wrote:
> How about splitting the file on lines consisting of "", and then parsing
> each record? If the parsing fails, you can write out the bad record for
> future inspection. (This addresses the basic use case, but not the "even
> better"
How about splitting the file on lines consisting of "", and then
parsing each record? If the parsing fails, you can write out the bad record
for future inspection. (This addresses the basic use case, but not the
"even better" one.)
Here's a proof of concept:
from rdkit import Chem
def
On Apr 14, 2022, at 09:16, Gyro Funch wrote:
> I don't know the sdf format well, so please excuse my ignorance, but instead
> of a custom parser, would it be possible to write a preprocessor to eliminate
> the offending information? Perhaps something using regular expressions in
> python,
will
then have to read them in another application for inspection.
Thanks
Giovanni
-Original Message-
From: Nils Weskamp
Sent: 13 April 2022 22:55
To: Giovanni Tricarico ;
rdkit-discuss@lists.sourceforge.net
Subject: Re: [Rdkit-discuss] how to report SDF records for which
for inspection.
Thanks
Giovanni
-Original Message-
From: Nils Weskamp
Sent: 13 April 2022 22:55
To: Giovanni Tricarico ;
rdkit-discuss@lists.sourceforge.net
Subject: Re: [Rdkit-discuss] how to report SDF records for which
Chem.ForwardSDMolSupplier returns None?
[You don't often get
Hello Giovanni,
have you tried using the ForwardSDMolSupplier with sanitize = False and
/ or strictParsing = False ?
This should at least reduce the number of cases where molecules are not
accepted. You would then have to sanitize the structures yourself
afterwards and handle possible
Hello,
I am using rdkit to read data from SD files.
My goal is to extract both the molecules and their associated properties (which
for our purposes are separate entities) from the SDF.
[For 100% clarity: by 'properties' I don't mean calculated properties or atom
or bond properties, but the
8 matches
Mail list logo
