Thanks for both tips, Andrew!
Everything works as expected now.
> -Original Message-
> From: Andrew Dalke [mailto:da...@dalkescientific.com]
> Sent: Friday, May 19, 2017 2:13 PM
> To: Markus Heller <mhel...@cdrd.ca>
> Cc: rdkit-discuss@lists.sourceforge.net
> Sub
Hi all,
I'm trying to work with Chembl23, calculating ChemFP fingerprints. Some
compounds contain non-standard heavy atoms, e.g. this one containing Te:
CC(C)(/C(=C\\Cl)/[Te](c1ccc(cc1)OC)(Cl)Cl)O
My workflow is to convert SDF format to SMILES as I find it easier to correct
any minor errors.
Hi everyone,
This issue was solved with Greg off-list.
Turns out that the receptor contains 5 amino acids with AltLoc. 4 of these
were cleaned up during preparation of the receptor for docking; the 5th was
missed, and that turned out to be the culprit.
Cheers
Markus
From: Greg Landrum
Solved:
The script we used (from deepchem) converts the ligand into PDB format, and I
assume that based on spatial proximity, a covalent bond between an oxygen and a
fluorine was formed erroneously.
From: Greg Landrum
Sent: Thursday, June 6, 2019 8:25 PM
To: Mateo Vacacela
Cc:
Hi,
In a Jupyter notebook, the following code does not show renderings of the
molecules in a Pandas dataframe:
from rdkit import Chem
from rdkit.Chem import PandasTools
from rdkit.Chem.Draw import MolsToGridImage
from rdkit.Chem.Draw import IPythonConsole
from rdkit.Chem import rdDepictor
Hi Paolo,
Thank you very much for this! This clarified issues I hadn’t even thought
about yet
Cheers
Markus
From: Paolo Tosco
Sent: Tuesday, November 5, 2019 2:49 PM
To: Markus Heller ; rdkit-discuss
(rdkit-discuss@lists.sourceforge.net)
Subject: Re: [Rdkit-discuss] Explicit H
/tuning-substructure-queries-ii.html
From: Greg Landrum
Sent: Tuesday, November 5, 2019 11:26 PM
To: Markus Heller
Cc: rdkit-discuss (rdkit-discuss@lists.sourceforge.net)
Subject: Re: [Rdkit-discuss] Explicit H in substructure searches
Paolo's answer was completely correct, but there's
)
# rebuild query with explicit H removed, not what I want
query = Chem.MolFromSmiles('c1cn[nH]c(N([H])([H]))1')
m1.HasSubstructMatch(query)
m2.HasSubstructMatch(query)
m3.HasSubstructMatch(query)
--
Markus Heller, PhD
Senior Scientist
Direct: 604.827.1122 Main: 604.827.1147
[A027228F]
2405
Hi Mike,
As a general comment, "This doesn't work" is not very helpful, because if it
did, you wouldn't be asking :)
Including error messages etc. would be very helpful and would also (most
likely) get you an answer much faster ...
Markus
From: Mike Mazanetz
Sent: Thursday, October 31, 2019
Hello,
As per subject: how can I plot similarity maps side by side, and not below each
other?
I tried matplotlib's add_subplot approach and failed, since
SimilarityMaps.GetSimilarityMapForFingerprint returns a figure object, not an
axes object.
I realize that this is more of a Python
This line of code works for me on a data frame with over 6M compounds …
PandasTools.AddMoleculeColumnToFrame(df, 'smiles', 'mol',
includeFingerprints=True)
‘smiles’ is the name of the column containing the SMILES, ‘mol’ is the name of
the new column with the mol objects.
Once that’s done, you
Hi all,
I have an issue with molecule rendering in a pandas dataframe. I read a csv
file with SMILES strings and names into a dataframe, and add a mol column to
the dataframe based on the SMILES. I then display the molecules in the
dataframe like so:
from IPython.display import HTML
Hello all,
Is there a method for adjusting a molecule's protonation state to pH 7? A
search of the mailing list (archive) revealed that some effort was put towards
implementing this functionality, but that it was discontinued.
Thanks
Markus
___
are highlighted in the molecule column in my dataframe.
I still haven't figured out how to turn this highlighting off though. Neither
web searches nor searches in the RDkit docs were successful, or I have searched
using the wrong terms ... How can this be done?
Cheers
Markus
From: Markus Heller
Sent
Hello,
When plotting molecules contained in a dataframe as image, I use
`PandasTools.FrameToGridImage`. One of the optional parameters is
`legendsCol`, which allows me to define a column in the df to be used as legend.
Can this be tweaked to include two columns as legend that would be printed
Probably not the reason, but there was an older version of pandas, 0.24 IIRC,
that dinner render the molecules correctly.
Can you perform calculations on the mol objects?
On Mar 29, 2020, at 4:07 AM, Tim Dudgeon wrote:
I'm finding that if I create a pandas dataframe using
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