Hi Hao,
Good question! I had to do a bit of digging to figure that out
Here's what's going on:
The Morgan fingerprint code uses CIP codes when you set useChirality=True
Atomic CIP codes are stored as an atomic property
When you use the multiprocessing module everything ends up being pickled
and
Hello,
I have two sets of conforms (ca. 2000 each) of a molecule. I’d like to find the
relative complement of set A in set B (i.e., unique conformers in set B that
are not in set A).
I’m thinking of calculating the distance matrix of each conformer, then looping
through all conformers to find
Hello,
This was a very strange bug that I saw. I was getting inconsistent
fingerprints using GetMorganFingerprint with useChirality=True, when I used
multiprocessing vs when I ran serially on rdkit 2017.09.1 and 2018.03.2. It
seems to have been fixed in the latest version. Woo! I was just
Hi Theo,
I don't think the RDKit version should make a difference; did you notice
that rdmolops.AdjustQueryProperties() does not modify the molecule in
place, but rather returns a modified copy?
pattern_generic_bonds = Chem.AdjustQueryProperties(pattern, query_params)
That might be the
Hi Paolo,
thank you very much for your detailed answer.
I tried to reproduce your last suggestion (but I don't have Jupyter Notebook).
However, my bonds are still SINGLE and DOUBLE instead of UNSPECIFIED.
Does this maybe depend on the RDKit Version, I have 2019.03... ?
Maybe, I should update and
Hi Theo,
the lack of match is due to different aromaticity flags on atoms and
bonds in the larger molecule.
This gist provides some explanation and a possible solution:
https://gist.github.com/ptosco/e410e45278b94e8f047ff224193d7788
Cheers,
p.
On 19/05/2020 14:13, theozh wrote:
Dear
The original file is around 25MB.
I changed the content in the dataframe (from sdf) and wrote:
PandasTools.WriteSDF( dataframe, 'path',
properties= dataframe .columns,
idName='ID')
Thanks, Mario
On Tue, May 19, 2020 at 9:13 AM Greg Landrum wrote:
> Hi
Dear RDKit-users,
I would like to do a very simple substructure search.
The chapter 3.5 "Substructure Searching" in RDKit Documentation (2019.09.1) is
pretty short and doesn't point to a solution. So far, I've learned that you can
create your search pattern via Chem.MolFromSmiles() or
Hi Mario,
how big is the file?
did you *add* properties to it or just modify existing values?
-greg
On Fri, May 15, 2020 at 11:34 AM Mario Lovrić
wrote:
> Dear all,
>
>
> I have loaded a SDF file (lets call it file1) with PandasTools, corrected
> some properties and wrote it with PandasTools
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