| Previous changeset 1:8f6ad93973cb (2020-10-28) |
|
Commit message:
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f1c3c88c7395f2e84cbc533199406aadb79c5c07" |
|
modified:
extract_rmsd.py extract_rmsd.xml |
| b |
| diff -r 8f6ad93973cb -r 589f8ef21e58 extract_rmsd.py --- a/extract_rmsd.py Wed Oct 28 21:41:04 2020 +0000 +++ b/extract_rmsd.py Fri Nov 13 19:44:09 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) |
| b |
| diff -r 8f6ad93973cb -r 589f8ef21e58 extract_rmsd.xml --- a/extract_rmsd.xml Wed Oct 28 21:41:04 2020 +0000 +++ b/extract_rmsd.xml Fri Nov 13 19:44:09 2020 +0000 |
| [ |
| @@ -2,7 +2,7 @@ <description>from MD ensemble with MDAnalysis</description> <macros> <import>macros.xml</import> - <token name="@GALAXY_VERSION@">1</token> + <token name="@GALAXY_VERSION@">2</token> </macros> <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ @@ -57,7 +57,7 @@ <param name="step" value="1" /> <output name="output"> <assert_contents> - <has_text text="0.0" n="20"/> + <has_text text="0.0" n="60"/> <has_size value="1126" /> <has_n_lines n="74" /> </assert_contents> @@ -101,4 +101,4 @@ ]]></help> <expand macro="citations" /> -</tool> \ No newline at end of file +</tool> |