Mercurial > repos > chemteam > mdanalysis_dihedral

annotate angle.py @ 3:554f60da9c8f 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 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
author chemteam
date Wed, 03 Apr 2019 15:47:36 -0400
parents cc1d22357daf
children d8178fe9aaff
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
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
9 import matplotlib
1
cc1d22357daf planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 9b44a37fc1a0c338693f54eaf52b582439ca9f0c
chemteam
parents: 0
diff changeset
10 matplotlib.use('Agg') # noqa
0
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 from numpy.linalg import norm
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
15
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
16
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
17 def parse_command_line(argv):
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
18 parser = argparse.ArgumentParser()
f95d4348ed7c 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')
f95d4348ed7c 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')
f95d4348ed7c 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')
f95d4348ed7c 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')
f95d4348ed7c 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')
f95d4348ed7c 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')
f95d4348ed7c 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')
f95d4348ed7c 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')
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
27 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
28 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
29 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
30 parser.add_argument('--output', help='output')
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
31 parser.add_argument('--oangle_plot', help='angle plot')
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
32 return parser.parse_args()
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
33
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
34
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
35 args = parse_command_line(sys.argv)
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
36
f95d4348ed7c 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)" % \
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
38 (args.isegid1, args.iresid1, args.iname1)
f95d4348ed7c 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)" % \
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
40 (args.isegid2, args.iresid2, args.iname2)
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
41 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
42 (args.isegid3, args.iresid3, args.iname3)
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
43
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
44
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
45 def theta(u):
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
46 A = u.select_atoms(atom1).center_of_geometry()
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
47 B = u.select_atoms(atom2).center_of_geometry()
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
48 C = u.select_atoms(atom3).center_of_geometry()
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
49 BA = A - B
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
50 BC = C - B
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
51 theta = np.arccos(np.dot(BA, BC)/(norm(BA)*norm(BC)))
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
52 return np.rad2deg(theta)
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
53
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
54
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
55 u = mda.Universe(args.ipdb, args.idcd, topology_format="PDB", format="DCD")
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
56 data = np.array([(u.trajectory.frame, theta(u)) for ts in u.trajectory])
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
57 frame, theta = data.T
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
58
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
59 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
60 writer = csv.writer(f, delimiter='\t')
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
61 writer.writerows(zip(frame, theta))
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
62
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
63 with open(args.output) as f:
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
64 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
65 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
66 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
67 angle = [xtmp[1] for xtmp in data]
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
68 plt.plot(time, angle)
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
69 plt.xlabel('Frame No.')
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
70 plt.ylabel('Angle (degrees)')
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
parents:
diff changeset
71 plt.savefig(args.oangle_plot, format='png')