Mercurial > repos > chemteam > mdanalysis_extract_rmsd

comparison rdf.py @ 0:743bd6aa3c7a 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 16:41:41 -0400
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-1:000000000000 0:743bd6aa3c7a
1 #!/usr/bin/env python
2
3 import argparse
4 import csv
5 import sys
6
7 import MDAnalysis as mda
8 from MDAnalysis.analysis.rdf import InterRDF
9
10 import matplotlib
11 import matplotlib.pyplot as plt
12
13 import numpy as np
14
15 matplotlib.use('Agg') # noqa
16
17
18 def parse_command_line(argv):
19 parser = argparse.ArgumentParser()
20 parser.add_argument('--itraj', help='input traj')
21 parser.add_argument('--istr', help='input str')
22 parser.add_argument('--itrajext', help='input traj ext')
23 parser.add_argument('--istrext', help='input str ext')
24 parser.add_argument('--isegid1', help='segid 1')
25 parser.add_argument('--iresid1', help='resid 1')
26 parser.add_argument('--iname1', help='name 1')
27 parser.add_argument('--isegid2', help='segid 2')
28 parser.add_argument('--iresid2', help='resid 2')
29 parser.add_argument('--iname2', help='name 2')
30 parser.add_argument('--inbins', help='Number of bins in the histogram')
31 parser.add_argument('--istart', help='Starting Point')
32 parser.add_argument('--iend', help='End point')
33 parser.add_argument('--output', help='output')
34 parser.add_argument('--ordf_plot', help='RDF plot')
35 return parser.parse_args()
36
37
38 args = parse_command_line(sys.argv)
39
40 atom1 = "(segid %s and resid %s and name %s)" % \
41 (args.isegid1, args.iresid1, args.iname1)
42 atom2 = "(segid %s and resid %s and name %s)" % \
43 (args.isegid2, args.iresid2, args.iname2)
44 bins = int(args.inbins)
45 start = float(args.istart)
46 end = float(args.iend)
47
48 u = mda.Universe(args.istr, args.itraj,
49 topology_format=args.istrext, format=args.itrajext)
50 x = u.select_atoms(atom1)
51 y = u.select_atoms(atom2)
52
53 rdf = InterRDF(x, y, nbins=bins, range=(start, end))
54 rdf.run()
55 bins = rdf.bins
56 bins = np.around(bins, decimals=3)
57 RDF = rdf.rdf
58 zip(bins, RDF)
59
60 with open(args.output, 'w') as f:
61 writer = csv.writer(f, delimiter='\t')
62 writer.writerows(zip(bins, RDF))
63
64 with open(args.output) as f:
65 g = [xtmp.strip() for xtmp in f]
66 data = [tuple(map(float, xtmp.split())) for xtmp in g[0:]]
67 time = [xtmp[0] for xtmp in data]
68 rdf = [xtmp[1] for xtmp in data]
69 plt.plot(time, rdf)
70 plt.xlabel(r'r ($\AA$)')
71 plt.ylabel('g(r)')
72 plt.savefig(args.ordf_plot, format='png')