David Koes

Merge branch 'master' of ssh://git.code.sf.net/p/smina/code

fix ad4_scoring hbond coefficient

This seems to be an honest-to-goodness bug. Surprisingly, I can't find the commit where it was fixed in gnina - it seems like it has been correct from the beginning. I will update smina.

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.