Mercurial > repos > chemteam > mdanalysis_ramachandran_protein

comparison dihedrals.py @ 0:0f270722aca6 draft

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
author chemteam
date Mon, 24 Aug 2020 16:27:56 -0400
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-1:000000000000 0:0f270722aca6
1 #!/usr/bin/env python
2
3 import argparse
4 import csv
5 import sys
6
7 import MDAnalysis as mda
8 from MDAnalysis.lib.distances import calc_dihedrals
9
10 import matplotlib
11 import matplotlib.pyplot as plt
12
13 import numpy as np
14
15 matplotlib.use('Agg') # noqa
16
17
18 def parse_command_line(argv):
19 parser = argparse.ArgumentParser()
20 parser.add_argument('--itraj', help='input traj')
21 parser.add_argument('--istr', help='input str')
22 parser.add_argument('--itrajext', help='input traj ext')
23 parser.add_argument('--istrext', help='input str ext')
24 parser.add_argument('--isegid1', help='segid 1')
25 parser.add_argument('--iresid1', help='resid 1')
26 parser.add_argument('--iname1', help='name 1')
27 parser.add_argument('--isegid2', help='segid 2')
28 parser.add_argument('--iresid2', help='resid 2')
29 parser.add_argument('--iname2', help='name 2')
30 parser.add_argument('--isegid3', help='segid 3')
31 parser.add_argument('--iresid3', help='resid 3')
32 parser.add_argument('--iname3', help='name 3')
33 parser.add_argument('--isegid4', help='segid 4')
34 parser.add_argument('--iresid4', help='resid 4')
35 parser.add_argument('--iname4', help='name 4')
36 parser.add_argument('--output', help='output')
37 parser.add_argument('--odihedral_plot', help='dihedral plot')
38 return parser.parse_args()
39
40
41 args = parse_command_line(sys.argv)
42
43 atom1 = "(segid %s and resid %s and name %s)" % \
44 (args.isegid1, args.iresid1, args.iname1)
45 atom2 = "(segid %s and resid %s and name %s)" % \
46 (args.isegid2, args.iresid2, args.iname2)
47 atom3 = "(segid %s and resid %s and name %s)" % \
48 (args.isegid3, args.iresid3, args.iname3)
49 atom4 = "(segid %s and resid %s and name %s)" % \
50 (args.isegid4, args.iresid4, args.iname4)
51
52
53 def psi(u):
54 A = u.select_atoms(atom1).positions
55 B = u.select_atoms(atom2).positions
56 C = u.select_atoms(atom3).positions
57 D = u.select_atoms(atom4).positions
58 psi = calc_dihedrals(A, B, C, D)
59 return np.rad2deg(psi)
60
61
62 u = mda.Universe(args.istr, args.itraj,
63 topology_format=args.istrext, format=args.itrajext)
64 data = np.array([(u.trajectory.frame, psi(u)) for ts in u.trajectory])
65 frame, psi = data.T
66 PSI = np.concatenate(psi, axis=0)
67
68 zip(frame, PSI)
69
70 with open(args.output, 'w') as f:
71 writer = csv.writer(f, delimiter='\t')
72 writer.writerows(zip(frame, PSI))
73
74 with open(args.output) as f:
75 g = [xtmp.strip() for xtmp in f]
76 data = [tuple(map(float, xtmp.split())) for xtmp in g[0:]]
77 time = [xtmp[0] for xtmp in data]
78 dihedral = [xtmp[1] for xtmp in data]
79 plt.plot(time, dihedral)
80 plt.xlabel('Frame No.')
81 plt.ylabel('Dihedral (degrees)')
82 plt.savefig(args.odihedral_plot, format='png')