Mercurial > repos > chemteam > mdanalysis_dihedral

comparison rdf.py @ 0:f95d4348ed7c draft

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planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
author chemteam
date Mon, 08 Oct 2018 13:16:46 -0400
parents
children cc1d22357daf
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-1:000000000000 0:f95d4348ed7c
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')
16
17
18 def parse_command_line(argv):
19 parser = argparse.ArgumentParser()
20 parser.add_argument('--idcd', help='input dcd')
21 parser.add_argument('--ipdb', help='input pdb')
22 parser.add_argument('--isegid1', help='segid 1')
23 parser.add_argument('--iresid1', help='resid 1')
24 parser.add_argument('--iname1', help='name 1')
25 parser.add_argument('--isegid2', help='segid 2')
26 parser.add_argument('--iresid2', help='resid 2')
27 parser.add_argument('--iname2', help='name 2')
28 parser.add_argument('--inbins', help='Number of bins in the histogram')
29 parser.add_argument('--istart', help='Starting Point')
30 parser.add_argument('--iend', help='End point')
31 parser.add_argument('--output', help='output')
32 parser.add_argument('--ordf_plot', help='RDF plot')
33 return parser.parse_args()
34
35
36 args = parse_command_line(sys.argv)
37
38 atom1 = "(segid %s and resid %s and name %s)" % \
39 (args.isegid1, args.iresid1, args.iname1)
40 atom2 = "(segid %s and resid %s and name %s)" % \
41 (args.isegid2, args.iresid2, args.iname2)
42 bins = int(args.inbins)
43 start = float(args.istart)
44 end = float(args.iend)
45
46 u = mda.Universe(args.ipdb, args.idcd, topology_format="PDB", format="DCD")
47 x = u.select_atoms(atom1)
48 y = u.select_atoms(atom2)
49
50 rdf = InterRDF(x, y, nbins=bins, range=(start, end))
51 rdf.run()
52 bins = rdf.bins
53 bins = np.around(bins, decimals=3)
54 RDF = rdf.rdf
55 zip(bins, RDF)
56
57 with open(args.output, 'w') as f:
58 writer = csv.writer(f, delimiter='\t')
59 writer.writerows(zip(bins, RDF))
60
61 with open(args.output) as f:
62 g = [xtmp.strip() for xtmp in f]
63 data = [tuple(map(float, xtmp.split())) for xtmp in g[0:]]
64 time = [xtmp[0] for xtmp in data]
65 rdf = [xtmp[1] for xtmp in data]
66 plt.plot(time, rdf)
67 plt.xlabel('r ($\AA$)')
68 plt.ylabel('g(r)')
69 plt.savefig(args.ordf_plot, format='png')