| Previous changeset 0:743bd6aa3c7a (2020-08-24) Next changeset 2:589f8ef21e58 (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 extract_rmsd.xml |
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| diff -r 743bd6aa3c7a -r 8f6ad93973cb extract_rmsd.py --- a/extract_rmsd.py Mon Aug 24 16:41:41 2020 -0400 +++ b/extract_rmsd.py Wed Oct 28 21:41:04 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__": |
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| diff -r 743bd6aa3c7a -r 8f6ad93973cb extract_rmsd.xml --- a/extract_rmsd.xml Mon Aug 24 16:41:41 2020 -0400 +++ b/extract_rmsd.xml Wed Oct 28 21:41:04 2020 +0000 |
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| @@ -2,7 +2,7 @@ <description>from MD ensemble with MDAnalysis</description> <macros> <import>macros.xml</import> - <token name="@GALAXY_VERSION@">0</token> + <token name="@GALAXY_VERSION@">1</token> </macros> <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ @@ -16,13 +16,10 @@ python '$__tool_directory__/extract_rmsd.py' --trajs trajs.txt --strs strs.txt - --ref-str '$refstr' --traj-format '$trajs[0].ext' --str-format '$strs[0].ext' - --ref-str-format '${refstr.ext}' --outfile '$output' --group '$group' - --fitting '$fitting' --start '$start' --end '$end' --step '$step' @@ -31,9 +28,7 @@ <inputs> <param type="data_collection" name="strs" label="Input structures" format="pdb,gro"/> <param type="data_collection" name="trajs" label="Input trajectories" format="xtc,dcd,trr"/> - <param name="refstr" type="data" format="pdb,gro" label="Reference structure" help="Structure for aligning all trajectories against."/> <param name='group' type='text' label='Group for RMSD calculation' /> - <param name='fitting' type='text' label='Group for alignment prior to RMSD calculation' /> <param name="start" type="integer" min="0" value="0" label="First trajectory frame for RMSD calculation" /> <param name="end" type="integer" min="0" value="0" label="End trajectory frame for RMSD calculation" /> <param name="step" type="integer" min="1" value="1" label="Frequency of trajectory frame sampling for RMSD calculation" /> @@ -56,8 +51,6 @@ </collection> </param> - <param name="refstr" ftype="pdb" value="test.pdb" /> - <param name="fitting" value="protein" /> <param name="group" value="resname BGLC" /> <param name="start" value="0" /> <param name="end" value="15" /> @@ -65,7 +58,7 @@ <output name="output"> <assert_contents> <has_text text="0.0" n="20"/> - <has_size value="1588" /> + <has_size value="1126" /> <has_n_lines n="74" /> </assert_contents> </output> @@ -81,6 +74,8 @@ - calculates RMSD differences for a selected group of atoms between all possible pairs of trajectories at all time points - returns RMSD data as a three-dimensional tensor. +Note: in an older version of this tool trajectories were aligned to a reference group prior to RMSD calculation. This is no longer supported; you should perform alignment yourself using a more efficient tool such as 'Modify/convert GROMACS trajectories'. + _____ |