Hi Paul,
I am not sure if it is easily doable to get the pandas read_table function to
handle sd-files. However, there is some basic functionality for this already
built-in in the PandasTools module. If you check the docktest header there is a
small example. Basically,
frame =
PandasTools.LoadSDF(sdfFile,smilesName='SMILES',molColName='Molecule',includeFingerprints=True)
loads the data from an sd-file into a dataframe, such that every molecule entry
corresponds to a row with the molecule in the column 'Molecule'. The specified
smiles column is generated automatically and every sd-property ends up in a
column with the respective property name. Additionally, if there is a property
"_Name" set for the molecule that is used as a row identifier - I assume this
could be made customisable in the future.
Is this something you could use?
Kind regards,
Niko
On Jun 30, 2013, at 5:10 PM, paul.czodrow...@merckgroup.com wrote:
> Dear RDKitters,
>
> I was wondering if anyone has looked into the Pandas data frame with
> respect to read in a SD file similar to this syntax:
>
> data =
> pd.read_table(open('whatever.smi','r'),header=None,names=['smiles','cas','mutagenic'])
>
> Ideally, "names" would be automatically set according to the SD tags.
>
>
> Cheers & Thanks,
> Paul
>
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