| Previous changeset 4:4c36f5ad2799 (2020-08-24) Next changeset 6:b17ce46509ad (2020-11-13) |
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Commit message:
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 45fe75a3a8ca80f799c85e194429c4c7f38bb5f6" |
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modified:
extract_rmsd.py |
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| diff -r 4c36f5ad2799 -r dfda5e713926 extract_rmsd.py --- a/extract_rmsd.py Mon Aug 24 16:53:30 2020 -0400 +++ b/extract_rmsd.py Wed Oct 28 21:36:33 2020 +0000 |
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| @@ -2,29 +2,23 @@ import json import MDAnalysis as m -from MDAnalysis.analysis import align, rms -from MDAnalysis.analysis.base import AnalysisFromFunction -from MDAnalysis.coordinates.memory import MemoryReader +from MDAnalysis.analysis import rms import numpy as np -def calc_rmsd(str_files, traj_files, ref_str, str_format, traj_format, - ref_str_format, filepath_out, group, start, end, step, - fitting_atoms): +def calc_rmsd(str_files, traj_files, str_format, traj_format, filepath_out, + group, start, end, step): """ the function will cycle through range 0 to no_t and load all files found. str_files: text file with filepaths for structures, one on each line traj_files: text file with filepaths for trajectories, one on each line - ref_str: reference structure for fitting filepath_in: directory where the files are located filepath_out: pickle file where results (3D matrix) should be saved to group: atoms for which RMSD should be calculated; use the MDAnalysis selection language - fitting_atoms: atoms used for str alignment prior to RMSD calculation; - use the MDAnalysis selection language start: first trajectory frame to calculate RMSD end: last trajectory frame to calculate RMSD @@ -49,22 +43,10 @@ universes = {} for traj in range(no_t): - mobile = m.Universe(str_file_list[traj], traj_file_list[traj], - format=traj_format, topology_format=str_format) - ref = m.Universe(ref_str, topology_format=ref_str_format) - - mobile.trajectory[-1] # set mobile trajectory to last frame - ref.trajectory[0] # set reference trajectory to first frame - - # perform alignment - align.AlignTraj(mobile, ref, select=fitting_atoms, - in_memory=True).run() - - grp = mobile.select_atoms(group) - universes[traj] = m.core.universe.Merge(grp) # create Universe w grp - coordinates = AnalysisFromFunction(lambda ag: ag.positions.copy(), - grp).run().results # write to uv - universes[traj].load_new(coordinates, format=MemoryReader) + # 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") @@ -72,19 +54,14 @@ for traj1 in range(no_t): print("Calculating differences for traj {}".format(traj1)) for traj2 in range(traj1): - - u1 = universes[traj1] - u2 = universes[traj2] - - l1 = u1.select_atoms(group) - l2 = u2.select_atoms(group) - - rmsd = rms.RMSD(l1, l2) - - rmsd.run() - - data[traj1, traj2] = rmsd.rmsd[:, 2] - data[traj2, traj1] = rmsd.rmsd[:, 2] + 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: json.dump(data.tolist(), f, indent=4, sort_keys=True) @@ -99,19 +76,13 @@ help='File containing trajectory filepaths.') parser.add_argument("--strs", help='File containing structure filepaths.') - parser.add_argument("--ref-str", - help='File containing reference structure.') parser.add_argument('--traj-format', required=True, help='Trajectory format.') parser.add_argument("--str-format", help='Structure format.') - parser.add_argument("--ref-str-format", - help='Reference structure format.') parser.add_argument('-o', '--outfile', help="Path to the output JSON file") parser.add_argument('--group', help="Atoms for which RMSD should be" "calculated in MDAnalysis selection language") - parser.add_argument('--fitting', help="Fitting atoms for alignment" - "prior to RMSD calculation") parser.add_argument('--start', type=int, help="First trajectory frame to calculate RMSD") parser.add_argument('--end', type=int, @@ -120,9 +91,9 @@ help="Frame sampling frequency for RMSD calculation") args = parser.parse_args() - calc_rmsd(args.strs, args.trajs, args.ref_str, args.str_format, - args.traj_format, args.ref_str_format, args.outfile, - args.group, args.start, args.end, args.step, args.fitting) + calc_rmsd(args.strs, args.trajs, args.str_format, + args.traj_format, args.outfile, + args.group, args.start, args.end, args.step) if __name__ == "__main__": |