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
I am working on evaluating the RD Kit Postgresql data cartridge for use as the
back end of a Web Application. The app will use a JavaScript sketcher to allow
the user to input a SMILES of SMARTS that will be sent to the RD Kit cartridge.
In evaluating RD Kit I found that it doesn't support
Hi Fio,
Thanks for the tips. I’ve found that I need PandasTools to convert a smiles to
a mol though, I’ve not had MolFromSmiles work on a dataframe.
Have you found that this works?
Cheers,
mike
From: Fiorella Ruggiu
Sent: 31 October 2019 15:48
To: Mike Mazanetz
Cc: Jan Halborg
Hello Mike,
you could create a function with your if else structure and use apply on
the pandas dataframe. For example, if you have a SMILES column in your df:
def addMol(smiles):
if Chem.MolFromSmiles(smiles) is None:
Etc
return None # or whatever you
Dear RDKit’ers
I’ve been trying to skip failed molecules in
PandasTools.AddMoleculeColumnToFrame.
This is possible if I chuck each row to a different processor, but what I
really want to do is return a missing row entry.
Normally I’d go:
If mol is None:
Etc
Else:
Hi Taka and Jan,
Thanks for your help.
Worked out that I shouldn’t have added the names=[] when I read in my csv file
(woops).
It fails if you have a mol which is None, I’ll have to add a line asking it to
check that ROMol isn’t None first. Annoying.
Thanks for your help,
mike
Hi,
Pandas apply function will work too.
AddMoleculeColumnToFrame(DF, "Smiles") at first.
Default setting, rdkit mol object will be added "ROMol" column in your
dataframe.
https://www.rdkit.org/docs/source/rdkit.Chem.PandasTools.html
Then call apply function to apply a calculation function
Hi Mike
This should work
DF[‘HAC’] = [Chem.Lipinski.HeavyAtomCount(mol) for mol in DF[‘Molecule’]]
Best regards, Jan
On 31 Oct 2019, at 10.16, Mike Mazanetz
mailto:mi...@novadatasolutions.co.uk>> wrote:
Hi RDKit Gurus,
I’ve followed the docs and created a molecule column in my Pandas
Hi RDKit Gurus,
I've followed the docs and created a molecule column in my Pandas dataframe.
However, I do not seem to be able to do molecular operations on the column.
For example, if you had a SMILES column, how would you calculate heavy atom
count and append this result to a new
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