Mercurial > repos > chemteam > mdanalysis_ramachandran_plot
comparison ramachandran_plots.py @ 0:d710c7f00ae6 draft
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
author | chemteam |
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date | Wed, 03 Apr 2019 15:46:32 -0400 |
parents | |
children | ce0728b92289 |
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-1:000000000000 | 0:d710c7f00ae6 |
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1 #!/usr/bin/env python | |
2 | |
3 import argparse | |
4 import csv | |
5 import sys | |
6 from collections import namedtuple | |
7 | |
8 import MDAnalysis as mda | |
9 from MDAnalysis.lib.distances import calc_dihedrals | |
10 | |
11 import matplotlib | |
12 matplotlib.use('Agg') # noqa | |
13 import matplotlib.pyplot as plt | |
14 | |
15 import numpy as np | |
16 | |
17 import seaborn as sns | |
18 | |
19 | |
20 def parse_command_line(argv): | |
21 parser = argparse.ArgumentParser() | |
22 parser.add_argument('--idcd', help='input dcd') | |
23 parser.add_argument('--ipdb', help='input pdb') | |
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('--isegid5', help='segid 1') | |
37 parser.add_argument('--iresid5', help='resid 1') | |
38 parser.add_argument('--iname5', help='name 1') | |
39 parser.add_argument('--isegid6', help='segid 2') | |
40 parser.add_argument('--iresid6', help='resid 2') | |
41 parser.add_argument('--iname6', help='name 2') | |
42 parser.add_argument('--isegid7', help='segid 3') | |
43 parser.add_argument('--iresid7', help='resid 3') | |
44 parser.add_argument('--iname7', help='name 3') | |
45 parser.add_argument('--isegid8', help='segid 4') | |
46 parser.add_argument('--iresid8', help='resid 4') | |
47 parser.add_argument('--iname8', help='name 4') | |
48 parser.add_argument('--output', help='output') | |
49 parser.add_argument('--oramachandran_plot', help='dihedral plot') | |
50 return parser.parse_args() | |
51 | |
52 | |
53 args = parse_command_line(sys.argv) | |
54 | |
55 Dihedral = namedtuple( | |
56 'Dihedral', ['atom1', 'atom2', 'atom3', 'atom4']) | |
57 | |
58 # order of dihedral atom is the crystallographic definition | |
59 # (see glycanstructure.org) | |
60 | |
61 # phi | |
62 atom1 = "(segid %s and resid %s and name %s)" % \ | |
63 (args.isegid1, args.iresid1, args.iname1) | |
64 atom2 = "(segid %s and resid %s and name %s)" % \ | |
65 (args.isegid2, args.iresid2, args.iname2) | |
66 atom3 = "(segid %s and resid %s and name %s)" % \ | |
67 (args.isegid3, args.iresid3, args.iname3) | |
68 atom4 = "(segid %s and resid %s and name %s)" % \ | |
69 (args.isegid4, args.iresid4, args.iname4) | |
70 | |
71 dihe_phi = Dihedral(atom1, atom2, atom3, atom4) | |
72 | |
73 # psi | |
74 atom1 = "(segid %s and resid %s and name %s)" % \ | |
75 (args.isegid5, args.iresid5, args.iname5) | |
76 atom2 = "(segid %s and resid %s and name %s)" % \ | |
77 (args.isegid6, args.iresid6, args.iname6) | |
78 atom3 = "(segid %s and resid %s and name %s)" % \ | |
79 (args.isegid7, args.iresid7, args.iname7) | |
80 atom4 = "(segid %s and resid %s and name %s)" % \ | |
81 (args.isegid8, args.iresid8, args.iname8) | |
82 | |
83 dihe_psi = Dihedral(atom1, atom2, atom3, atom4) | |
84 | |
85 | |
86 def calc_torsion(dihedral): | |
87 """atom 1 -4 are valid atom selections. torsion in degrees is returned""" | |
88 A = u.select_atoms(dihedral.atom1).positions | |
89 B = u.select_atoms(dihedral.atom2).positions | |
90 C = u.select_atoms(dihedral.atom3).positions | |
91 D = u.select_atoms(dihedral.atom4).positions | |
92 | |
93 dihe = calc_dihedrals(A, B, C, D) | |
94 return np.rad2deg(dihe) | |
95 | |
96 | |
97 u = mda.Universe(args.ipdb, args.idcd, topology_format="PDB", format="DCD") | |
98 | |
99 phi_trajdata = np.array( | |
100 [(u.trajectory.frame, calc_torsion(dihe_phi)) for ts in u.trajectory]) | |
101 psi_trajdata = np.array( | |
102 [(u.trajectory.frame, calc_torsion(dihe_psi)) for ts in u.trajectory]) | |
103 | |
104 phi_frame, phi_series = phi_trajdata.T | |
105 psi_frame, psi_series = psi_trajdata.T | |
106 | |
107 phi_series = np.concatenate(phi_series, axis=0) | |
108 psi_series = np.concatenate(psi_series, axis=0) | |
109 | |
110 zip(phi_frame, phi_series, psi_series) | |
111 | |
112 with open(args.output, 'w') as f: | |
113 writer = csv.writer(f, delimiter='\t') | |
114 writer.writerows(zip(phi_frame, phi_series, psi_series)) | |
115 | |
116 with sns.axes_style("white"): | |
117 h = sns.jointplot(x=phi_series, y=psi_series, kind="kde", legend=True) | |
118 h.set_axis_labels(r'$\Phi$ (degrees)', r'$\Psi$ (degrees)') | |
119 h.ax_joint.set_xlim(-180, 180) | |
120 h.ax_joint.set_ylim(-180, 180) | |
121 plt.savefig(args.oramachandran_plot, format='png') |