Mercurial > repos > chemteam > mdanalysis_hbonds
changeset 6:b17ce46509ad draft default tip
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f1c3c88c7395f2e84cbc533199406aadb79c5c07"
| author | chemteam |
|---|---|
| date | Fri, 13 Nov 2020 19:39:59 +0000 |
| parents | dfda5e713926 |
| children | |
| files | extract_rmsd.py |
| diffstat | 1 files changed, 12 insertions(+), 13 deletions(-) [+] |
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--- a/extract_rmsd.py Wed Oct 28 21:36:33 2020 +0000 +++ b/extract_rmsd.py Fri Nov 13 19:39:59 2020 +0000 @@ -36,29 +36,29 @@ no_t = len(traj_file_list) - data = np.zeros((no_t, no_t, - int((end - start)/step + ((end - start) % step > 0)))) - - # load files - universes = {} + # hard to find array size before loading files + universe_coordinate_data = [] for traj in range(no_t): # We no longer align here, users should do this themselves. - universes[traj] = m.Universe(str_file_list[traj], traj_file_list[traj], - format=traj_format, - topology_format=str_format) + u = m.Universe(str_file_list[traj], traj_file_list[traj], + format=traj_format, topology_format=str_format) + u.transfer_to_memory() + grp = u.select_atoms(group).universe + coordinates = grp.trajectory.coordinate_array[start:end:step] + universe_coordinate_data.append(coordinates) + universe_coordinate_data = np.array(universe_coordinate_data) print("All trajs loaded by MDAnalysis") + data = np.zeros((no_t, no_t, universe_coordinate_data.shape[1])) # calculate differences for traj1 in range(no_t): print("Calculating differences for traj {}".format(traj1)) for traj2 in range(traj1): for frame in range(data.shape[2]): - universes[traj1].trajectory[frame] - universes[traj2].trajectory[frame] - A = universes[traj1].select_atoms(group).positions - B = universes[traj2].select_atoms(group).positions + A = universe_coordinate_data[traj1, frame] + B = universe_coordinate_data[traj2, frame] r = rms.rmsd(A, B) data[traj1, traj2, frame] = r data[traj2, traj1, frame] = r @@ -90,7 +90,6 @@ parser.add_argument('--step', type=int, help="Frame sampling frequency for RMSD calculation") args = parser.parse_args() - calc_rmsd(args.strs, args.trajs, args.str_format, args.traj_format, args.outfile, args.group, args.start, args.end, args.step)