annotate distance_single.py @ 3:8bd0e29927da draft

"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b"
author chemteam
date Wed, 20 May 2020 13:03:30 -0400
parents b348dfa55e0a
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
b348dfa55e0a "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
1 #!/usr/bin/env python
b348dfa55e0a "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
2
b348dfa55e0a "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
3 import argparse
b348dfa55e0a "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
4 import sys
b348dfa55e0a "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
5
b348dfa55e0a "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
6 import MDAnalysis as mda
b348dfa55e0a "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
7
b348dfa55e0a "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
8 import matplotlib
b348dfa55e0a "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
9 import matplotlib.pyplot as plt
b348dfa55e0a "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
10
b348dfa55e0a "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
11 import numpy as np
b348dfa55e0a "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
12
3
8bd0e29927da "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b"
chemteam
parents: 2
diff changeset
13 matplotlib.use('Agg') # noqa
8bd0e29927da "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b"
chemteam
parents: 2
diff changeset
14
2
b348dfa55e0a "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
15
b348dfa55e0a "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
16 def parse_command_line(argv):
b348dfa55e0a "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
17 parser = argparse.ArgumentParser()
b348dfa55e0a "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
18 parser.add_argument('--itraj', help='input traj')
b348dfa55e0a "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
19 parser.add_argument('--istr', help='input str')
b348dfa55e0a "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
20 parser.add_argument('--itrajext', help='input traj ext')
b348dfa55e0a "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
21 parser.add_argument('--istrext', help='input str ext')
b348dfa55e0a "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
22 parser.add_argument('--isegid1', help='segid 1')
b348dfa55e0a "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
23 parser.add_argument('--iresid1', help='resid 1')
b348dfa55e0a "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
24 parser.add_argument('--iname1', help='name 1')
b348dfa55e0a "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
25 parser.add_argument('--isegid2', help='segid 2')
b348dfa55e0a "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
26 parser.add_argument('--iresid2', help='resid 2')
b348dfa55e0a "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
27 parser.add_argument('--iname2', help='name 2')
b348dfa55e0a "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
28 parser.add_argument('--output', help='output')
b348dfa55e0a "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
29 parser.add_argument('--odistance_plot', help='odistance plot')
b348dfa55e0a "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
30 parser.add_argument('--header', dest='header', action='store_true')
b348dfa55e0a "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
31 return parser.parse_args()
b348dfa55e0a "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
32
b348dfa55e0a "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
33
b348dfa55e0a "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
34 args = parse_command_line(sys.argv)
b348dfa55e0a "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
35
b348dfa55e0a "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
36 atom1 = "(segid %s and resid %s and name %s)" % \
b348dfa55e0a "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
37 (args.isegid1, args.iresid1, args.iname1)
b348dfa55e0a "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
38 atom2 = "(segid %s and resid %s and name %s)" % \
b348dfa55e0a "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
39 (args.isegid2, args.iresid2, args.iname2)
b348dfa55e0a "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
40
b348dfa55e0a "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
41 u = mda.Universe(args.istr, args.itraj,
b348dfa55e0a "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
42 topology_format=args.istrext, format=args.itrajext)
b348dfa55e0a "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
43 x = u.select_atoms(atom1)
b348dfa55e0a "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
44 y = u.select_atoms(atom2)
b348dfa55e0a "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
45
b348dfa55e0a "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
46 with open(args.output, 'w') as f:
b348dfa55e0a "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
47 if args.header:
b348dfa55e0a "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
48 f.write('Frame\tDistance')
b348dfa55e0a "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
49 for t in u.trajectory:
b348dfa55e0a "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
50 r = x.positions - y.positions
b348dfa55e0a "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
51 d = np.linalg.norm(r)
b348dfa55e0a "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
52 f.write(str(t.frame) + '\t ')
b348dfa55e0a "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
53 f.write(str(d) + '\n')
b348dfa55e0a "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
54
b348dfa55e0a "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
55 with open(args.output) as f:
b348dfa55e0a "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
56 g = [xtmp.strip() for xtmp in f]
b348dfa55e0a "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
57 data = [tuple(map(float, xtmp.split())) for xtmp in g[0:]]
b348dfa55e0a "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
58 time = [xtmp[0] for xtmp in data]
b348dfa55e0a "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
59 distance = [xtmp[1] for xtmp in data]
b348dfa55e0a "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
60 plt.plot(time, distance)
b348dfa55e0a "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
61 plt.xlabel('Frame No.')
b348dfa55e0a "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
62 plt.ylabel(r'Distance ($\AA$)')
b348dfa55e0a "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
chemteam
parents:
diff changeset
63 plt.savefig(args.odistance_plot, format='png')