Hi Charmaine,
my suggestion is to build starting from a conda environment. That will
significantly simplify your dependencies, since most packages are available
pre-built.
You can look into .azure-pipelines\vs_build_dll.yml for how to set up your
conda environment and for the cmake flags to use.
Thank you Ivan, that's great!
It does exactly what I wanted.
OK, I cannot read the properties for wrong records, but one could argue when
the molecule is wrong there is no point reading the properties.
I only adjusted a couple of details (made sure that the file is read as text,
not binary,
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,
Hello,
I've been trying to build RDKit on Windows so that I can get the RDKit
extension in pgAdmin (Postgres) but I've been unsuccessful.
I've tried to follow the instruction on https://www.rdkit.org/docs/Install.html
to build RDKit and encountered several problems.
Some of them I manage to
On 2022-04-14 08:12 AM, Giovanni Tricarico wrote:
Thank you Nils.
In fact I do want the sanitize + parse to happen, and I do some further checks
on the molecules, too (ChEMBL pipeline etc).
The issue is that whatever does not pass the initial steps just completely
disappears and cannot be
Thank you Nils.
In fact I do want the sanitize + parse to happen, and I do some further checks
on the molecules, too (ChEMBL pipeline etc).
The issue is that whatever does not pass the initial steps just completely
disappears and cannot be reported or inspected in any way.
Indeed, making a
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