comparison extract_rmsd.py @ 2:589f8ef21e58 draft default tip

"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f1c3c88c7395f2e84cbc533199406aadb79c5c07"

1:8f6ad93973cb

        if sum(1 for line in f1) != sum(1 for line in f2):
            raise IOError('Number of structure and trajectory files unequal.')

    no_t = len(traj_file_list)

    data = np.zeros((no_t, no_t,
                    int((end - start)/step + ((end - start) % step > 0))))

    # load files
    universes = {}

    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)

    print("All trajs loaded by MDAnalysis")

    # 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
                r = rms.rmsd(A, B)
                data[traj1, traj2, frame] = r
                data[traj2, traj1, frame] = r

    with open(filepath_out, 'w') as f:

    parser.add_argument('--end', type=int,
                        help="Last trajectory frame to calculate RMSD")
    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)

2:589f8ef21e58

        if sum(1 for line in f1) != sum(1 for line in f2):
            raise IOError('Number of structure and trajectory files unequal.')

    no_t = len(traj_file_list)

    # 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.
        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]):
                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

    with open(filepath_out, 'w') as f:

    parser.add_argument('--end', type=int,
                        help="Last trajectory frame to calculate RMSD")
    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)