> I am quite new to open babel. I have some SDF files of thousands of molecules > and I would like to calculate some of their descriptors.
It depends on what you want. For example: https://open-babel.readthedocs.io/en/latest/Command-line_tools/Rosetta.html obabel benzodiazepine.sdf.gz -otxt --title "" --append atoms -d > The txt format outputs only the title but we set that to nothing and then > append the result. The atoms descriptor counts the number of atoms after the > -d option has removed the hydrogens. https://open-babel.readthedocs.io/en/latest/Command-line_tools/Rosetta.html#calculate-tpsa obabel -:CN2C(=O)N(C)C(=O)C1=C2N=CN1C -osmi --append TPSA Gives a SMILES and then the TPSA descriptor. You can use —append to add various descriptors. Personally, I’d write up a short Python script, but it can be done with the command-line tools as well. Hope that helps, -Geoff ------------------------------------------------------------------------------ Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San Francisco, CA to explore cutting-edge tech and listen to tech luminaries present their vision of the future. This family event has something for everyone, including kids. Get more information and register today. http://sdm.link/attshape _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
