Mercurial > repos > chemteam > mdanalysis_angle

comparison angle.py @ 0:fc7293c6cb6a draft

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planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
author chemteam
date Mon, 08 Oct 2018 13:17:59 -0400
parents
children 4759026f6ff4
comparison
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-1:000000000000 0:fc7293c6cb6a
1 #!/usr/bin/env python
2
3 import argparse
4 import csv
5 import sys
6
7 import MDAnalysis as mda
8
9 import matplotlib
10 import matplotlib.pyplot as plt
11
12 import numpy as np
13 from numpy.linalg import norm
14
15 matplotlib.use('Agg')
16
17
18 def parse_command_line(argv):
19 parser = argparse.ArgumentParser()
20 parser.add_argument('--idcd', help='input dcd')
21 parser.add_argument('--ipdb', help='input pdb')
22 parser.add_argument('--isegid1', help='segid 1')
23 parser.add_argument('--iresid1', help='resid 1')
24 parser.add_argument('--iname1', help='name 1')
25 parser.add_argument('--isegid2', help='segid 2')
26 parser.add_argument('--iresid2', help='resid 2')
27 parser.add_argument('--iname2', help='name 2')
28 parser.add_argument('--isegid3', help='segid 3')
29 parser.add_argument('--iresid3', help='resid 3')
30 parser.add_argument('--iname3', help='name 3')
31 parser.add_argument('--output', help='output')
32 parser.add_argument('--oangle_plot', help='angle plot')
33 return parser.parse_args()
34
35
36 args = parse_command_line(sys.argv)
37
38 atom1 = "(segid %s and resid %s and name %s)" % \
39 (args.isegid1, args.iresid1, args.iname1)
40 atom2 = "(segid %s and resid %s and name %s)" % \
41 (args.isegid2, args.iresid2, args.iname2)
42 atom3 = "(segid %s and resid %s and name %s)" % \
43 (args.isegid3, args.iresid3, args.iname3)
44
45
46 def theta(u):
47 A = u.select_atoms(atom1).center_of_geometry()
48 B = u.select_atoms(atom2).center_of_geometry()
49 C = u.select_atoms(atom3).center_of_geometry()
50 BA = A - B
51 BC = C - B
52 theta = np.arccos(np.dot(BA, BC)/(norm(BA)*norm(BC)))
53 return np.rad2deg(theta)
54
55
56 u = mda.Universe(args.ipdb, args.idcd, topology_format="PDB", format="DCD")
57 data = np.array([(u.trajectory.frame, theta(u)) for ts in u.trajectory])
58 frame, theta = data.T
59
60 with open(args.output, 'w') as f:
61 writer = csv.writer(f, delimiter='\t')
62 writer.writerows(zip(frame, theta))
63
64 with open(args.output) as f:
65 g = [xtmp.strip() for xtmp in f]
66 data = [tuple(map(float, xtmp.split())) for xtmp in g[0:]]
67 time = [xtmp[0] for xtmp in data]
68 angle = [xtmp[1] for xtmp in data]
69 plt.plot(time, angle)
70 plt.xlabel('Frame No.')
71 plt.ylabel('Angle (degrees)')
72 plt.savefig(args.oangle_plot, format='png')