Mercurial > repos > chemteam > mdanalysis_dihedral

annotate distance_single.py @ 5:47dd4e854598 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
author chemteam
date Thu, 06 Feb 2020 19:42:41 -0500
parents
children 0493024c3318
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
5
47dd4e854598 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
1 #!/usr/bin/env python
47dd4e854598 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
2
47dd4e854598 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
3 import argparse
47dd4e854598 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
4 import sys
47dd4e854598 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
5
47dd4e854598 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
6 import MDAnalysis as mda
47dd4e854598 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
7
47dd4e854598 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
8 import matplotlib
47dd4e854598 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
9 matplotlib.use('Agg') # noqa
47dd4e854598 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
10 import matplotlib.pyplot as plt
47dd4e854598 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
11
47dd4e854598 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
12 import numpy as np
47dd4e854598 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
13
47dd4e854598 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
14
47dd4e854598 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
15 def parse_command_line(argv):
47dd4e854598 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
16 parser = argparse.ArgumentParser()
47dd4e854598 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
17 parser.add_argument('--itraj', help='input traj')
47dd4e854598 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
18 parser.add_argument('--istr', help='input str')
47dd4e854598 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
19 parser.add_argument('--itrajext', help='input traj ext')
47dd4e854598 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
20 parser.add_argument('--istrext', help='input str ext')
47dd4e854598 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
21 parser.add_argument('--isegid1', help='segid 1')
47dd4e854598 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
22 parser.add_argument('--iresid1', help='resid 1')
47dd4e854598 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
23 parser.add_argument('--iname1', help='name 1')
47dd4e854598 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
24 parser.add_argument('--isegid2', help='segid 2')
47dd4e854598 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
25 parser.add_argument('--iresid2', help='resid 2')
47dd4e854598 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
26 parser.add_argument('--iname2', help='name 2')
47dd4e854598 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
27 parser.add_argument('--output', help='output')
47dd4e854598 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
28 parser.add_argument('--odistance_plot', help='odistance plot')
47dd4e854598 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
29 parser.add_argument('--header', dest='header', action='store_true')
47dd4e854598 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
30 return parser.parse_args()
47dd4e854598 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
31
47dd4e854598 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
32
47dd4e854598 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
33 args = parse_command_line(sys.argv)
47dd4e854598 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
34
47dd4e854598 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
35 atom1 = "(segid %s and resid %s and name %s)" % \
47dd4e854598 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
36 (args.isegid1, args.iresid1, args.iname1)
47dd4e854598 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
37 atom2 = "(segid %s and resid %s and name %s)" % \
47dd4e854598 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
38 (args.isegid2, args.iresid2, args.iname2)
47dd4e854598 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
39
47dd4e854598 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
40 u = mda.Universe(args.istr, args.itraj,
47dd4e854598 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
41 topology_format=args.istrext, format=args.itrajext)
47dd4e854598 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
42 x = u.select_atoms(atom1)
47dd4e854598 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
43 y = u.select_atoms(atom2)
47dd4e854598 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
44
47dd4e854598 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
45 with open(args.output, 'w') as f:
47dd4e854598 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
46 if args.header:
47dd4e854598 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
47 f.write('Frame\tDistance')
47dd4e854598 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
48 for t in u.trajectory:
47dd4e854598 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
49 r = x.positions - y.positions
47dd4e854598 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
50 d = np.linalg.norm(r)
47dd4e854598 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
51 f.write(str(t.frame) + '\t ')
47dd4e854598 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
52 f.write(str(d) + '\n')
47dd4e854598 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
53
47dd4e854598 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
54 with open(args.output) as f:
47dd4e854598 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
55 g = [xtmp.strip() for xtmp in f]
47dd4e854598 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
56 data = [tuple(map(float, xtmp.split())) for xtmp in g[0:]]
47dd4e854598 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
57 time = [xtmp[0] for xtmp in data]
47dd4e854598 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
58 distance = [xtmp[1] for xtmp in data]
47dd4e854598 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
59 plt.plot(time, distance)
47dd4e854598 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
60 plt.xlabel('Frame No.')
47dd4e854598 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
61 plt.ylabel(r'Distance ($\AA$)')
47dd4e854598 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
62 plt.savefig(args.odistance_plot, format='png')