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annotate ramachandran_plots.py @ 3:49dac57d004a draft

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planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
author chemteam
date Wed, 03 Apr 2019 15:47:16 -0400
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children 36babbdd7818
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49dac57d004a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
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1 #!/usr/bin/env python
49dac57d004a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
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3 import argparse
49dac57d004a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
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4 import csv
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5 import sys
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6 from collections import namedtuple
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8 import MDAnalysis as mda
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9 from MDAnalysis.lib.distances import calc_dihedrals
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11 import matplotlib
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12 matplotlib.use('Agg') # noqa
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13 import matplotlib.pyplot as plt
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15 import numpy as np
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17 import seaborn as sns
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20 def parse_command_line(argv):
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21 parser = argparse.ArgumentParser()
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22 parser.add_argument('--idcd', help='input dcd')
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23 parser.add_argument('--ipdb', help='input pdb')
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24 parser.add_argument('--isegid1', help='segid 1')
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25 parser.add_argument('--iresid1', help='resid 1')
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26 parser.add_argument('--iname1', help='name 1')
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27 parser.add_argument('--isegid2', help='segid 2')
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28 parser.add_argument('--iresid2', help='resid 2')
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29 parser.add_argument('--iname2', help='name 2')
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30 parser.add_argument('--isegid3', help='segid 3')
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31 parser.add_argument('--iresid3', help='resid 3')
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32 parser.add_argument('--iname3', help='name 3')
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33 parser.add_argument('--isegid4', help='segid 4')
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34 parser.add_argument('--iresid4', help='resid 4')
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35 parser.add_argument('--iname4', help='name 4')
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36 parser.add_argument('--isegid5', help='segid 1')
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37 parser.add_argument('--iresid5', help='resid 1')
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38 parser.add_argument('--iname5', help='name 1')
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39 parser.add_argument('--isegid6', help='segid 2')
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40 parser.add_argument('--iresid6', help='resid 2')
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41 parser.add_argument('--iname6', help='name 2')
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42 parser.add_argument('--isegid7', help='segid 3')
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43 parser.add_argument('--iresid7', help='resid 3')
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44 parser.add_argument('--iname7', help='name 3')
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45 parser.add_argument('--isegid8', help='segid 4')
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46 parser.add_argument('--iresid8', help='resid 4')
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47 parser.add_argument('--iname8', help='name 4')
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48 parser.add_argument('--output', help='output')
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49 parser.add_argument('--oramachandran_plot', help='dihedral plot')
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50 return parser.parse_args()
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51
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53 args = parse_command_line(sys.argv)
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54
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55 Dihedral = namedtuple(
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56 'Dihedral', ['atom1', 'atom2', 'atom3', 'atom4'])
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57
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58 # order of dihedral atom is the crystallographic definition
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59 # (see glycanstructure.org)
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60
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61 # phi
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62 atom1 = "(segid %s and resid %s and name %s)" % \
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63 (args.isegid1, args.iresid1, args.iname1)
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64 atom2 = "(segid %s and resid %s and name %s)" % \
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65 (args.isegid2, args.iresid2, args.iname2)
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66 atom3 = "(segid %s and resid %s and name %s)" % \
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67 (args.isegid3, args.iresid3, args.iname3)
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68 atom4 = "(segid %s and resid %s and name %s)" % \
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69 (args.isegid4, args.iresid4, args.iname4)
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70
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71 dihe_phi = Dihedral(atom1, atom2, atom3, atom4)
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72
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73 # psi
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74 atom1 = "(segid %s and resid %s and name %s)" % \
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75 (args.isegid5, args.iresid5, args.iname5)
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76 atom2 = "(segid %s and resid %s and name %s)" % \
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77 (args.isegid6, args.iresid6, args.iname6)
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78 atom3 = "(segid %s and resid %s and name %s)" % \
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79 (args.isegid7, args.iresid7, args.iname7)
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80 atom4 = "(segid %s and resid %s and name %s)" % \
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81 (args.isegid8, args.iresid8, args.iname8)
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82
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83 dihe_psi = Dihedral(atom1, atom2, atom3, atom4)
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84
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85
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86 def calc_torsion(dihedral):
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87 """atom 1 -4 are valid atom selections. torsion in degrees is returned"""
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88 A = u.select_atoms(dihedral.atom1).positions
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89 B = u.select_atoms(dihedral.atom2).positions
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90 C = u.select_atoms(dihedral.atom3).positions
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91 D = u.select_atoms(dihedral.atom4).positions
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92
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93 dihe = calc_dihedrals(A, B, C, D)
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94 return np.rad2deg(dihe)
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95
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96
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97 u = mda.Universe(args.ipdb, args.idcd, topology_format="PDB", format="DCD")
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98
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99 phi_trajdata = np.array(
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100 [(u.trajectory.frame, calc_torsion(dihe_phi)) for ts in u.trajectory])
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101 psi_trajdata = np.array(
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102 [(u.trajectory.frame, calc_torsion(dihe_psi)) for ts in u.trajectory])
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103
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104 phi_frame, phi_series = phi_trajdata.T
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105 psi_frame, psi_series = psi_trajdata.T
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106
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107 phi_series = np.concatenate(phi_series, axis=0)
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108 psi_series = np.concatenate(psi_series, axis=0)
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109
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110 zip(phi_frame, phi_series, psi_series)
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111
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112 with open(args.output, 'w') as f:
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113 writer = csv.writer(f, delimiter='\t')
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114 writer.writerows(zip(phi_frame, phi_series, psi_series))
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115
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116 with sns.axes_style("white"):
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117 h = sns.jointplot(x=phi_series, y=psi_series, kind="kde", legend=True)
49dac57d004a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
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118 h.set_axis_labels(r'$\Phi$ (degrees)', r'$\Psi$ (degrees)')
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119 h.ax_joint.set_xlim(-180, 180)
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120 h.ax_joint.set_ylim(-180, 180)
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121 plt.savefig(args.oramachandran_plot, format='png')