annotate rdf.py @ 8:8a1a8e2fbad4 draft

"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 45fe75a3a8ca80f799c85e194429c4c7f38bb5f6"
author chemteam
date Wed, 28 Oct 2020 21:39:14 +0000
parents aa4090b50e7b
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
1 #!/usr/bin/env python
c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
2
c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
3 import argparse
c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
4 import csv
c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
5 import sys
c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
6
c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
7 import MDAnalysis as mda
c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
8 from MDAnalysis.analysis.rdf import InterRDF
c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
9
c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
10 import matplotlib
c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
11 import matplotlib.pyplot as plt
c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
12
c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
13 import numpy as np
c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
14
6
aa4090b50e7b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b"
chemteam
parents: 4
diff changeset
15 matplotlib.use('Agg') # noqa
aa4090b50e7b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b"
chemteam
parents: 4
diff changeset
16
0
c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
17
c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
18 def parse_command_line(argv):
c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
19 parser = argparse.ArgumentParser()
4
312f912de69d "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
chemteam
parents: 1
diff changeset
20 parser.add_argument('--itraj', help='input traj')
312f912de69d "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
chemteam
parents: 1
diff changeset
21 parser.add_argument('--istr', help='input str')
312f912de69d "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
chemteam
parents: 1
diff changeset
22 parser.add_argument('--itrajext', help='input traj ext')
312f912de69d "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
chemteam
parents: 1
diff changeset
23 parser.add_argument('--istrext', help='input str ext')
0
c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
24 parser.add_argument('--isegid1', help='segid 1')
c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
25 parser.add_argument('--iresid1', help='resid 1')
c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
26 parser.add_argument('--iname1', help='name 1')
c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
27 parser.add_argument('--isegid2', help='segid 2')
c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
28 parser.add_argument('--iresid2', help='resid 2')
c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
29 parser.add_argument('--iname2', help='name 2')
c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
30 parser.add_argument('--inbins', help='Number of bins in the histogram')
c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
31 parser.add_argument('--istart', help='Starting Point')
c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
32 parser.add_argument('--iend', help='End point')
c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
33 parser.add_argument('--output', help='output')
c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
34 parser.add_argument('--ordf_plot', help='RDF plot')
c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
35 return parser.parse_args()
c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
36
c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
37
c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
38 args = parse_command_line(sys.argv)
c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
39
c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
40 atom1 = "(segid %s and resid %s and name %s)" % \
c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
41 (args.isegid1, args.iresid1, args.iname1)
c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
42 atom2 = "(segid %s and resid %s and name %s)" % \
c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
43 (args.isegid2, args.iresid2, args.iname2)
c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
44 bins = int(args.inbins)
c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
45 start = float(args.istart)
c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
46 end = float(args.iend)
c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
47
4
312f912de69d "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
chemteam
parents: 1
diff changeset
48 u = mda.Universe(args.istr, args.itraj,
312f912de69d "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
chemteam
parents: 1
diff changeset
49 topology_format=args.istrext, format=args.itrajext)
0
c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
50 x = u.select_atoms(atom1)
c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
51 y = u.select_atoms(atom2)
c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
52
c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
53 rdf = InterRDF(x, y, nbins=bins, range=(start, end))
c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
54 rdf.run()
c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
55 bins = rdf.bins
c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
56 bins = np.around(bins, decimals=3)
c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
57 RDF = rdf.rdf
c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
58 zip(bins, RDF)
c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
59
c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
60 with open(args.output, 'w') as f:
c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
61 writer = csv.writer(f, delimiter='\t')
c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
62 writer.writerows(zip(bins, RDF))
c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
63
c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
64 with open(args.output) as f:
c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
65 g = [xtmp.strip() for xtmp in f]
c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
66 data = [tuple(map(float, xtmp.split())) for xtmp in g[0:]]
c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
67 time = [xtmp[0] for xtmp in data]
c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
68 rdf = [xtmp[1] for xtmp in data]
c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
69 plt.plot(time, rdf)
1
2b1434ec8c7e planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 9b44a37fc1a0c338693f54eaf52b582439ca9f0c
chemteam
parents: 0
diff changeset
70 plt.xlabel(r'r ($\AA$)')
0
c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
71 plt.ylabel('g(r)')
c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
72 plt.savefig(args.ordf_plot, format='png')