Hi Greg, Thanks so much for taking the time to help! I didn't realize the size limit recommendation for pandas so maybe that's why I don't see much of it. I often work on much larger scale and was investigating moving from KNIME to RDKit on Linux for that reason. The curve is just steep right now :) learning python, pandas, RDKit etc. all at once! I'll start digging/searching for the more traditional straight python ways to do the same.
Thanks again for the info and help! Jason St. Jude Children's Research Hospital On Fri, Jan 4, 2019 at 1:34 AM Greg Landrum <greg.land...@gmail.com> wrote: > Hi Jason, > > This gist shows how to generate fingerprints for the molecules in a pandas > dataframe and then use them to do similarity searches: > https://gist.github.com/greglandrum/045ccf8009fde91fc985864e70ee72a1 > > This is a reasonably efficient way of working with a smallish (<10K) > number of molecules. > > -greg > > > On Thu, Jan 3, 2019 at 7:10 PM Jason Ochoada <jocho...@gmail.com> wrote: > >> Hi Everyone! >> >> I'm a newbie making the shift from RDKit in KNIME to working with the >> full package. I have been working (hacking) my through the tutorials I >> could find pandas, Jupyter, RDKit etc. I'm using RDKit in the anaconda 3 >> environment. I'm struggling to figure out how to do what I imagine is a >> very simple task. I have read in a flat file (Smiles file) and have it in >> a pandas data frame named cpds. It contained SMILES and ID. I have been >> able to add a molecule to the dataframe: >> >> >> PandasTools.AddMoleculeColumnToFrame(cpds,'SMILES','Molecule',includeFingerprints=False) >> print([str(x) for x in cpds.columns]) >> >> But I can't seem to figure out how to create and append a fingerprint. >> I'm open to any options as I'm new and don't have any particular structure >> I like to work in. Of course once I have this I'd like to do similarity >> searches either in RDKit or chemfp etc. someday. >> >> Can you point me to where this might have been done? I've searched and >> searched but I can't seem to find a solution that will work for me. >> >> Thanks, >> Jason Ochoada >> St. Jude Children's Research Hospital >> > _______________________________________________ >> Rdkit-discuss mailing list >> Rdkit-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >> >
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