Mercurial > repos > chemteam > mdanalysis_endtoend

annotate extract_rmsd.py @ 0:78aa3659fcd1 draft

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
author chemteam
date Mon, 24 Aug 2020 16:47:23 -0400
parents
children ce9dc91ff87f
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78aa3659fcd1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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1 import argparse
78aa3659fcd1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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2 import json
78aa3659fcd1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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78aa3659fcd1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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4 import MDAnalysis as m
78aa3659fcd1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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5 from MDAnalysis.analysis import align, rms
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6 from MDAnalysis.analysis.base import AnalysisFromFunction
78aa3659fcd1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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7 from MDAnalysis.coordinates.memory import MemoryReader
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9 import numpy as np
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12 def calc_rmsd(str_files, traj_files, ref_str, str_format, traj_format,
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13 ref_str_format, filepath_out, group, start, end, step,
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14 fitting_atoms):
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15 """
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16 the function will cycle through range 0 to no_t and load all files found.
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18 str_files: text file with filepaths for structures, one on each line
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19 traj_files: text file with filepaths for trajectories, one on each line
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20 ref_str: reference structure for fitting
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21 filepath_in: directory where the files are located
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22 filepath_out: pickle file where results (3D matrix) should be saved to
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24 group: atoms for which RMSD should be calculated;
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25 use the MDAnalysis selection language
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26 fitting_atoms: atoms used for str alignment prior to RMSD calculation;
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27 use the MDAnalysis selection language
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29 start: first trajectory frame to calculate RMSD
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30 end: last trajectory frame to calculate RMSD
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31 step: how frequently frames are sampled between start and end; obviously,
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32 the larger the step, the quicker the script finishes
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33 """
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35 # open list of files
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36 with open(str_files) as f1, open(traj_files) as f2:
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37 str_file_list = f1.read().strip().split('\n')
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38 traj_file_list = f2.read().strip().split('\n')
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39
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40 if sum(1 for line in f1) != sum(1 for line in f2):
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41 raise IOError('Number of structure and trajectory files unequal.')
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43 no_t = len(traj_file_list)
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45 data = np.zeros((no_t, no_t,
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46 int((end - start)/step + ((end - start) % step > 0))))
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48 # load files
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49 universes = {}
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51 for traj in range(no_t):
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52 mobile = m.Universe(str_file_list[traj], traj_file_list[traj],
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53 format=traj_format, topology_format=str_format)
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54 ref = m.Universe(ref_str, topology_format=ref_str_format)
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56 mobile.trajectory[-1] # set mobile trajectory to last frame
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57 ref.trajectory[0] # set reference trajectory to first frame
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59 # perform alignment
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60 align.AlignTraj(mobile, ref, select=fitting_atoms,
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61 in_memory=True).run()
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63 grp = mobile.select_atoms(group)
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64 universes[traj] = m.core.universe.Merge(grp) # create Universe w grp
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65 coordinates = AnalysisFromFunction(lambda ag: ag.positions.copy(),
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66 grp).run().results # write to uv
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67 universes[traj].load_new(coordinates, format=MemoryReader)
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68
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69 print("All trajs loaded by MDAnalysis")
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70
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71 # calculate differences
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72 for traj1 in range(no_t):
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73 print("Calculating differences for traj {}".format(traj1))
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74 for traj2 in range(traj1):
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75
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76 u1 = universes[traj1]
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77 u2 = universes[traj2]
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79 l1 = u1.select_atoms(group)
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80 l2 = u2.select_atoms(group)
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81
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82 rmsd = rms.RMSD(l1, l2)
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84 rmsd.run()
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85
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86 data[traj1, traj2] = rmsd.rmsd[:, 2]
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87 data[traj2, traj1] = rmsd.rmsd[:, 2]
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88
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89 with open(filepath_out, 'w') as f:
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90 json.dump(data.tolist(), f, indent=4, sort_keys=True)
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91
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92 print("Done!")
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93 return
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94
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95
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96 def main():
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97 parser = argparse.ArgumentParser()
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98 parser.add_argument('--trajs', required=True,
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99 help='File containing trajectory filepaths.')
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100 parser.add_argument("--strs",
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101 help='File containing structure filepaths.')
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102 parser.add_argument("--ref-str",
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103 help='File containing reference structure.')
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104 parser.add_argument('--traj-format', required=True,
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105 help='Trajectory format.')
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106 parser.add_argument("--str-format", help='Structure format.')
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107 parser.add_argument("--ref-str-format",
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108 help='Reference structure format.')
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109 parser.add_argument('-o', '--outfile',
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110 help="Path to the output JSON file")
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111 parser.add_argument('--group', help="Atoms for which RMSD should be"
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112 "calculated in MDAnalysis selection language")
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113 parser.add_argument('--fitting', help="Fitting atoms for alignment"
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114 "prior to RMSD calculation")
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115 parser.add_argument('--start', type=int,
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116 help="First trajectory frame to calculate RMSD")
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117 parser.add_argument('--end', type=int,
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118 help="Last trajectory frame to calculate RMSD")
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119 parser.add_argument('--step', type=int,
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120 help="Frame sampling frequency for RMSD calculation")
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121 args = parser.parse_args()
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122
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123 calc_rmsd(args.strs, args.trajs, args.ref_str, args.str_format,
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124 args.traj_format, args.ref_str_format, args.outfile,
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125 args.group, args.start, args.end, args.step, args.fitting)
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126
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127
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128 if __name__ == "__main__":
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129 main()