Mercurial > repos > chemteam > mdanalysis_hbonds
comparison distance_multiple.py @ 2:d23ef0663267 draft
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
author | chemteam |
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date | Thu, 06 Feb 2020 19:41:49 -0500 |
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1:5c38e38dbc35 | 2:d23ef0663267 |
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1 import argparse | |
2 import sys | |
3 | |
4 import MDAnalysis as mda | |
5 from MDAnalysis.analysis import distances | |
6 | |
7 import numpy as np | |
8 | |
9 | |
10 def parse_command_line(argv): | |
11 parser = argparse.ArgumentParser() | |
12 parser.add_argument('--itraj', help='input traj') | |
13 parser.add_argument('--istr', help='input str') | |
14 parser.add_argument('--itrajext', help='input traj ext') | |
15 parser.add_argument('--istrext', help='input str ext') | |
16 parser.add_argument('--list1', help='list 2') | |
17 parser.add_argument('--list2', help='list 2') | |
18 parser.add_argument('--output', help='output') | |
19 parser.add_argument('--header', dest='header', action='store_true') | |
20 return parser.parse_args() | |
21 | |
22 | |
23 args = parse_command_line(sys.argv) | |
24 | |
25 u = mda.Universe(args.istr, args.itraj, | |
26 topology_format=args.istrext, format=args.itrajext) | |
27 | |
28 list1 = np.loadtxt(args.list1, dtype=str, delimiter="\t", ndmin=1) | |
29 list2 = np.loadtxt(args.list2, dtype=str, delimiter="\t", ndmin=1) | |
30 | |
31 sel1 = [u.select_atoms(selection) for selection in list1] | |
32 sel2 = [u.select_atoms(selection) for selection in list2] | |
33 | |
34 d = np.empty((u.trajectory.n_frames, list1.shape[0], list2.shape[0]),) | |
35 | |
36 for ts in u.trajectory: | |
37 c_o_m1 = np.array([selection.center_of_mass() for selection in sel1]) | |
38 c_o_m2 = np.array([selection.center_of_mass() for selection in sel2]) | |
39 distances.distance_array(c_o_m1, c_o_m2, result=d[ts.frame]) | |
40 | |
41 d = np.hstack(( | |
42 np.array(np.reshape(np.arange( | |
43 0, d.shape[0]), (d.shape[0], 1)), dtype=int), # add column w frame | |
44 np.reshape(d, (d.shape[0], d.shape[1] * d.shape[2])) | |
45 )) | |
46 | |
47 if args.header: | |
48 header = 'Frame\t' + '\t'.join( | |
49 ['-'.join(pair) for pair in zip( | |
50 sum([[n, ] * len(list2) for n in list1], []), | |
51 list(list2) * len(list1),)]).replace(' ', '_') | |
52 else: | |
53 header = '' | |
54 | |
55 np.savetxt(args.output, d, header=header, comments='', | |
56 fmt=['%d'] + ['%f'] * (d.shape[1] - 1), delimiter='\t') |