David Koes

pharmer doesn't do that. Check out PharmaGist: https://pmc.ncbi.nlm.nih.gov/articles/PMC2447755/

Here is the code from my version of load_query which seems to work: def get_neighbors(points, point, num_neighbors): ''' Naive method for finding the nearest neighbors of a point on a sphere of points Arguments: points -- list of points (numpy arrays) point -- point of interest num_neighbors -- number of neighbors to return Returns: neighbors -- list of neighboring points ''' distances = [ [pt, np.linalg.norm(point - pt)] for pt in points] pts = np.stack(list(map(lambda x: x[0], sorted(distances,...

Based on the N with 4 bonds it looks like you need a newer version of openbabel (e.g., current git version).

I'm not sure I can elaborate beyond the error message much. You have molecules next to each other in the file that have different chemistries but have the same name. This isn't allowed since names are used to uniquely identify molecules.

Doesn't look like brew installed the development (header) files.

Looks like you didn't have openbabel3 installed (or at least it couldn't find it). Glad to hear the precompiled binaries still work.

If you want to do template docking, I recommend generating a large ensemble of conformers for each of your ligands, aligning to the common substructure, and then minimizing with smina rather than docking.

--custom_atoms is what you want. To see the format of the file it is expecting run smina with --print_atom_types. If you are using the default Vina scoring function the number you want to change is the xs_radius.