annotate rdf.py @ 3:49dac57d004a draft

planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
author chemteam
date Wed, 03 Apr 2019 15:47:16 -0400
parents 0315b541c74d
children 36babbdd7818
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
9bb57bd1fdc8 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
1 #!/usr/bin/env python
9bb57bd1fdc8 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
2
9bb57bd1fdc8 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
3 import argparse
9bb57bd1fdc8 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
4 import csv
9bb57bd1fdc8 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
5 import sys
9bb57bd1fdc8 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
6
9bb57bd1fdc8 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
7 import MDAnalysis as mda
9bb57bd1fdc8 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
8 from MDAnalysis.analysis.rdf import InterRDF
9bb57bd1fdc8 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
9
9bb57bd1fdc8 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
10 import matplotlib
1
0315b541c74d planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 9b44a37fc1a0c338693f54eaf52b582439ca9f0c
chemteam
parents: 0
diff changeset
11 matplotlib.use('Agg') # noqa
0
9bb57bd1fdc8 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
12 import matplotlib.pyplot as plt
9bb57bd1fdc8 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
13
9bb57bd1fdc8 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
14 import numpy as np
9bb57bd1fdc8 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
15
9bb57bd1fdc8 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
16
9bb57bd1fdc8 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
17 def parse_command_line(argv):
9bb57bd1fdc8 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
18 parser = argparse.ArgumentParser()
9bb57bd1fdc8 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
19 parser.add_argument('--idcd', help='input dcd')
9bb57bd1fdc8 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
20 parser.add_argument('--ipdb', help='input pdb')
9bb57bd1fdc8 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
21 parser.add_argument('--isegid1', help='segid 1')
9bb57bd1fdc8 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
22 parser.add_argument('--iresid1', help='resid 1')
9bb57bd1fdc8 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
23 parser.add_argument('--iname1', help='name 1')
9bb57bd1fdc8 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
24 parser.add_argument('--isegid2', help='segid 2')
9bb57bd1fdc8 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
25 parser.add_argument('--iresid2', help='resid 2')
9bb57bd1fdc8 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
26 parser.add_argument('--iname2', help='name 2')
9bb57bd1fdc8 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
27 parser.add_argument('--inbins', help='Number of bins in the histogram')
9bb57bd1fdc8 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
28 parser.add_argument('--istart', help='Starting Point')
9bb57bd1fdc8 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
29 parser.add_argument('--iend', help='End point')
9bb57bd1fdc8 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
30 parser.add_argument('--output', help='output')
9bb57bd1fdc8 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
31 parser.add_argument('--ordf_plot', help='RDF plot')
9bb57bd1fdc8 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
32 return parser.parse_args()
9bb57bd1fdc8 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
33
9bb57bd1fdc8 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
34
9bb57bd1fdc8 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
35 args = parse_command_line(sys.argv)
9bb57bd1fdc8 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
36
9bb57bd1fdc8 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
37 atom1 = "(segid %s and resid %s and name %s)" % \
9bb57bd1fdc8 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
38 (args.isegid1, args.iresid1, args.iname1)
9bb57bd1fdc8 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
39 atom2 = "(segid %s and resid %s and name %s)" % \
9bb57bd1fdc8 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
40 (args.isegid2, args.iresid2, args.iname2)
9bb57bd1fdc8 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
41 bins = int(args.inbins)
9bb57bd1fdc8 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
42 start = float(args.istart)
9bb57bd1fdc8 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
43 end = float(args.iend)
9bb57bd1fdc8 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
44
9bb57bd1fdc8 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
45 u = mda.Universe(args.ipdb, args.idcd, topology_format="PDB", format="DCD")
9bb57bd1fdc8 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
46 x = u.select_atoms(atom1)
9bb57bd1fdc8 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
47 y = u.select_atoms(atom2)
9bb57bd1fdc8 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
48
9bb57bd1fdc8 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
49 rdf = InterRDF(x, y, nbins=bins, range=(start, end))
9bb57bd1fdc8 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
50 rdf.run()
9bb57bd1fdc8 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
51 bins = rdf.bins
9bb57bd1fdc8 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
52 bins = np.around(bins, decimals=3)
9bb57bd1fdc8 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
53 RDF = rdf.rdf
9bb57bd1fdc8 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
54 zip(bins, RDF)
9bb57bd1fdc8 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
55
9bb57bd1fdc8 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
56 with open(args.output, 'w') as f:
9bb57bd1fdc8 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
57 writer = csv.writer(f, delimiter='\t')
9bb57bd1fdc8 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
58 writer.writerows(zip(bins, RDF))
9bb57bd1fdc8 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
59
9bb57bd1fdc8 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
60 with open(args.output) as f:
9bb57bd1fdc8 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
61 g = [xtmp.strip() for xtmp in f]
9bb57bd1fdc8 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
62 data = [tuple(map(float, xtmp.split())) for xtmp in g[0:]]
9bb57bd1fdc8 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
63 time = [xtmp[0] for xtmp in data]
9bb57bd1fdc8 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
64 rdf = [xtmp[1] for xtmp in data]
9bb57bd1fdc8 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
65 plt.plot(time, rdf)
1
0315b541c74d planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 9b44a37fc1a0c338693f54eaf52b582439ca9f0c
chemteam
parents: 0
diff changeset
66 plt.xlabel(r'r ($\AA$)')
0
9bb57bd1fdc8 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
67 plt.ylabel('g(r)')
9bb57bd1fdc8 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
68 plt.savefig(args.ordf_plot, format='png')