annotate dihedrals.py @ 8:f55dd7c08112 draft

"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 45fe75a3a8ca80f799c85e194429c4c7f38bb5f6"
author chemteam
date Wed, 28 Oct 2020 21:39:52 +0000
parents 0493024c3318
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
1 #!/usr/bin/env python
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
2
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
3 import argparse
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
4 import csv
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
5 import sys
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
6
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
7 import MDAnalysis as mda
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
8 from MDAnalysis.lib.distances import calc_dihedrals
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
9
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
10 import matplotlib
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
11 import matplotlib.pyplot as plt
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
12
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
13 import numpy as np
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
14
6
0493024c3318 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b"
chemteam
parents: 4
diff changeset
15 matplotlib.use('Agg') # noqa
0493024c3318 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b"
chemteam
parents: 4
diff changeset
16
0
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
17
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
18 def parse_command_line(argv):
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
19 parser = argparse.ArgumentParser()
4
d8178fe9aaff "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
chemteam
parents: 3
diff changeset
20 parser.add_argument('--itraj', help='input traj')
d8178fe9aaff "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
chemteam
parents: 3
diff changeset
21 parser.add_argument('--istr', help='input str')
d8178fe9aaff "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
chemteam
parents: 3
diff changeset
22 parser.add_argument('--itrajext', help='input traj ext')
d8178fe9aaff "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
chemteam
parents: 3
diff changeset
23 parser.add_argument('--istrext', help='input str ext')
0
f95d4348ed7c 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')
f95d4348ed7c 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')
f95d4348ed7c 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')
f95d4348ed7c 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')
f95d4348ed7c 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')
f95d4348ed7c 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')
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
30 parser.add_argument('--isegid3', help='segid 3')
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
31 parser.add_argument('--iresid3', help='resid 3')
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
32 parser.add_argument('--iname3', help='name 3')
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
33 parser.add_argument('--isegid4', help='segid 4')
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
34 parser.add_argument('--iresid4', help='resid 4')
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
35 parser.add_argument('--iname4', help='name 4')
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
36 parser.add_argument('--output', help='output')
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
37 parser.add_argument('--odihedral_plot', help='dihedral plot')
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
38 return parser.parse_args()
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
39
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
40
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
41 args = parse_command_line(sys.argv)
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
42
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
43 atom1 = "(segid %s and resid %s and name %s)" % \
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
44 (args.isegid1, args.iresid1, args.iname1)
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
45 atom2 = "(segid %s and resid %s and name %s)" % \
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
46 (args.isegid2, args.iresid2, args.iname2)
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
47 atom3 = "(segid %s and resid %s and name %s)" % \
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
48 (args.isegid3, args.iresid3, args.iname3)
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
49 atom4 = "(segid %s and resid %s and name %s)" % \
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
50 (args.isegid4, args.iresid4, args.iname4)
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
51
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
52
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
53 def psi(u):
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
54 A = u.select_atoms(atom1).positions
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
55 B = u.select_atoms(atom2).positions
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
56 C = u.select_atoms(atom3).positions
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
57 D = u.select_atoms(atom4).positions
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
58 psi = calc_dihedrals(A, B, C, D)
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
59 return np.rad2deg(psi)
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
60
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
61
4
d8178fe9aaff "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
chemteam
parents: 3
diff changeset
62 u = mda.Universe(args.istr, args.itraj,
d8178fe9aaff "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
chemteam
parents: 3
diff changeset
63 topology_format=args.istrext, format=args.itrajext)
0
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
64 data = np.array([(u.trajectory.frame, psi(u)) for ts in u.trajectory])
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
65 frame, psi = data.T
3
554f60da9c8f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents: 1
diff changeset
66 PSI = np.concatenate(psi, axis=0)
0
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
67
3
554f60da9c8f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents: 1
diff changeset
68 zip(frame, PSI)
0
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
69
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
70 with open(args.output, 'w') as f:
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
71 writer = csv.writer(f, delimiter='\t')
3
554f60da9c8f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents: 1
diff changeset
72 writer.writerows(zip(frame, PSI))
0
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
73
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
74 with open(args.output) as f:
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
75 g = [xtmp.strip() for xtmp in f]
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
76 data = [tuple(map(float, xtmp.split())) for xtmp in g[0:]]
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
77 time = [xtmp[0] for xtmp in data]
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
78 dihedral = [xtmp[1] for xtmp in data]
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
79 plt.plot(time, dihedral)
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
80 plt.xlabel('Frame No.')
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
81 plt.ylabel('Dihedral (degrees)')
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
82 plt.savefig(args.odihedral_plot, format='png')