[Open Babel] Define origin for ECFP2 fingerprints

Is it possible to calculate circular fingerprints around a predefined atom/atom-pair? For example, I'm using a PDB file containing a ligand (LIG) showing a nitrogen atom (e.g. N) that interacts with an oxygen atom of a serine residue (let's call it OG). What I want is to generate a circular finge

[Open Babel] Clustering in OpenBabel

Hi, I would like to run a cluster analysis (i.e. kmeans or Jarvis-Patrick) in a small compound library. Is that possible with OpenBabel? Best wishes, Marcos Vinicius Santana M.Sc Farmacêutico Universidade Federal Fluminense Laboratório de Antibióticos, Bioquímica, Ensino e Modelagem Molecular (LAB

[Open Babel] Substructure search

I posted yesterday about substructure search with Babel. I'm reposting, this time with a git link to my code. My problem is that I want to run a substructure search of 15000 fragments against a dataset of lead compounds. It runs OK for all fragments (I can see the results on the Terminal) but Openb

[Open Babel] Substructure searching with multiple molecules

Hello, I'm using OpenBabel for substructure searching of 15000 fragments against a lead-like dataset. Is there a way to do that using Pybel? On the tutorial it only describes how to do that with one molecule. I tried to iterate over a list of smiles/smarts of my fragments but I get a segmentation e