Dear Niko,
I was exactly looking for this functionality, great work!
A few follow-up questions:
* frame.set_index('_Name') did not work, but there is a name set in the SD
file.
* Is there a way to load in only a specified list of SD tags? (I didn't
find a "names" parameter for LoadSDF)
* frame.head() frame.describe() give a property "ID", which is not present
in my SD file. Where does it come from?
* frame.describe() does not show the basic statistics of the SD file.
The last three points are due to the fact that PandasTools.LoadSDF has
fewer functionalities than PandasTools.read_table?
Cheers & big thanks again,
Paul
>
> 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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