Mercurial > repos > chemteam > mdanalysis_ramachandran_plot

comparison extract_rmsd.py @ 4:70a2d548e62c 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 16:23:14 -0400
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children af9f01ca6a5c
comparison
equal deleted inserted replaced
3:8bd0e29927da 4:70a2d548e62c
1 import argparse
2 import json
3
4 import MDAnalysis as m
5 from MDAnalysis.analysis import align, rms
6 from MDAnalysis.analysis.base import AnalysisFromFunction
7 from MDAnalysis.coordinates.memory import MemoryReader
8
9 import numpy as np
10
11
12 def calc_rmsd(str_files, traj_files, ref_str, str_format, traj_format,
13 ref_str_format, filepath_out, group, start, end, step,
14 fitting_atoms):
15 """
16 the function will cycle through range 0 to no_t and load all files found.
17
18 str_files: text file with filepaths for structures, one on each line
19 traj_files: text file with filepaths for trajectories, one on each line
20 ref_str: reference structure for fitting
21 filepath_in: directory where the files are located
22 filepath_out: pickle file where results (3D matrix) should be saved to
23
24 group: atoms for which RMSD should be calculated;
25 use the MDAnalysis selection language
26 fitting_atoms: atoms used for str alignment prior to RMSD calculation;
27 use the MDAnalysis selection language
28
29 start: first trajectory frame to calculate RMSD
30 end: last trajectory frame to calculate RMSD
31 step: how frequently frames are sampled between start and end; obviously,
32 the larger the step, the quicker the script finishes
33 """
34
35 # open list of files
36 with open(str_files) as f1, open(traj_files) as f2:
37 str_file_list = f1.read().strip().split('\n')
38 traj_file_list = f2.read().strip().split('\n')
39
40 if sum(1 for line in f1) != sum(1 for line in f2):
41 raise IOError('Number of structure and trajectory files unequal.')
42
43 no_t = len(traj_file_list)
44
45 data = np.zeros((no_t, no_t,
46 int((end - start)/step + ((end - start) % step > 0))))
47
48 # load files
49 universes = {}
50
51 for traj in range(no_t):
52 mobile = m.Universe(str_file_list[traj], traj_file_list[traj],
53 format=traj_format, topology_format=str_format)
54 ref = m.Universe(ref_str, topology_format=ref_str_format)
55
56 mobile.trajectory[-1] # set mobile trajectory to last frame
57 ref.trajectory[0] # set reference trajectory to first frame
58
59 # perform alignment
60 align.AlignTraj(mobile, ref, select=fitting_atoms,
61 in_memory=True).run()
62
63 grp = mobile.select_atoms(group)
64 universes[traj] = m.core.universe.Merge(grp) # create Universe w grp
65 coordinates = AnalysisFromFunction(lambda ag: ag.positions.copy(),
66 grp).run().results # write to uv
67 universes[traj].load_new(coordinates, format=MemoryReader)
68
69 print("All trajs loaded by MDAnalysis")
70
71 # calculate differences
72 for traj1 in range(no_t):
73 print("Calculating differences for traj {}".format(traj1))
74 for traj2 in range(traj1):
75
76 u1 = universes[traj1]
77 u2 = universes[traj2]
78
79 l1 = u1.select_atoms(group)
80 l2 = u2.select_atoms(group)
81
82 rmsd = rms.RMSD(l1, l2)
83
84 rmsd.run()
85
86 data[traj1, traj2] = rmsd.rmsd[:, 2]
87 data[traj2, traj1] = rmsd.rmsd[:, 2]
88
89 with open(filepath_out, 'w') as f:
90 json.dump(data.tolist(), f, indent=4, sort_keys=True)
91
92 print("Done!")
93 return
94
95
96 def main():
97 parser = argparse.ArgumentParser()
98 parser.add_argument('--trajs', required=True,
99 help='File containing trajectory filepaths.')
100 parser.add_argument("--strs",
101 help='File containing structure filepaths.')
102 parser.add_argument("--ref-str",
103 help='File containing reference structure.')
104 parser.add_argument('--traj-format', required=True,
105 help='Trajectory format.')
106 parser.add_argument("--str-format", help='Structure format.')
107 parser.add_argument("--ref-str-format",
108 help='Reference structure format.')
109 parser.add_argument('-o', '--outfile',
110 help="Path to the output JSON file")
111 parser.add_argument('--group', help="Atoms for which RMSD should be"
112 "calculated in MDAnalysis selection language")
113 parser.add_argument('--fitting', help="Fitting atoms for alignment"
114 "prior to RMSD calculation")
115 parser.add_argument('--start', type=int,
116 help="First trajectory frame to calculate RMSD")
117 parser.add_argument('--end', type=int,
118 help="Last trajectory frame to calculate RMSD")
119 parser.add_argument('--step', type=int,
120 help="Frame sampling frequency for RMSD calculation")
121 args = parser.parse_args()
122
123 calc_rmsd(args.strs, args.trajs, args.ref_str, args.str_format,
124 args.traj_format, args.ref_str_format, args.outfile,
125 args.group, args.start, args.end, args.step, args.fitting)
126
127
128 if __name__ == "__main__":
129 main()