Mercurial > repos > chemteam > mdanalysis_ramachandran_protein

annotate ramachandran_plots.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 #!/usr/bin/env python
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3 import argparse
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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 import matplotlib.pyplot as plt
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13 import matplotlib.ticker as ticker
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16 import numpy as np
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18 import seaborn as sns
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21 import yaml
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23 matplotlib.use('Agg') # noqa
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26 def parse_command_line(argv):
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27 parser = argparse.ArgumentParser()
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28 parser.add_argument('--itraj', help='input traj')
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29 parser.add_argument('--istr', help='input str')
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30 parser.add_argument('--itrajext', help='input traj ext')
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31 parser.add_argument('--istrext', help='input str ext')
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32 parser.add_argument('--iyml', help='input in yml format')
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33 parser.add_argument('--output', help='output')
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34 parser.add_argument('--oramachandran_plot', help='dihedral plot')
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35 return parser.parse_args()
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38 args = parse_command_line(sys.argv)
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39
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40 with open(args.iyml) as file:
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41 params = yaml.load(file, Loader=yaml.FullLoader)
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42
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43 Dihedral = namedtuple(
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44 'Dihedral', ['atom1', 'atom2', 'atom3', 'atom4'])
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46 for k, v in params.items():
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47 for a in ['phi', 'psi']:
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48 assert (a in v), "Key %s is missing in inputs: %s " % (a, k)
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49 atoms = []
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50 for b in ['atom1', 'atom2', 'atom3', 'atom4']:
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51 assert (b in v[a]), "Key %s is missing in inputs: %s %s" % (
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52 b, k, a)
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53 for c in ['segid', 'resid', 'name']:
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54 assert (c in v[a][b]), \
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55 "Key %s is missing in inputs: %s %s %s " % (c, k, a, b)
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56 atoms.append("(segid %s and resid %s and name %s)" %
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57 (v[a][b]['segid'], v[a][b]['resid'], v[a][b]['name']))
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58 print(atoms)
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59 if a == 'phi':
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60 dihe_phi = Dihedral(atoms[0], atoms[1], atoms[2], atoms[3])
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61 if a == 'psi':
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62 dihe_psi = Dihedral(atoms[0], atoms[1], atoms[2], atoms[3])
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63
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64 # order of dihedral atom is the crystallographic definition
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65 # (see glycanstructure.org)
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66
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67 assert(dihe_phi), "phi dihedral doesn't exist"
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68 assert(dihe_psi), "psi dihedral doesn't exist"
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69
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70
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71 def calc_torsion(dihedral):
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72 """atom 1 -4 are valid atom selections. torsion in degrees is returned"""
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73 A = u.select_atoms(dihedral.atom1).positions
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74 B = u.select_atoms(dihedral.atom2).positions
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75 C = u.select_atoms(dihedral.atom3).positions
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76 D = u.select_atoms(dihedral.atom4).positions
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77
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78 dihe = calc_dihedrals(A, B, C, D)
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79 return np.rad2deg(dihe)
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80
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81
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82 u = mda.Universe(args.istr, args.itraj,
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83 topology_format=args.istrext, format=args.itrajext)
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84
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85 phi_trajdata = np.array(
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86 [(u.trajectory.frame, calc_torsion(dihe_phi)) for ts in u.trajectory])
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87 psi_trajdata = np.array(
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88 [(u.trajectory.frame, calc_torsion(dihe_psi)) for ts in u.trajectory])
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89
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90 print(phi_trajdata, psi_trajdata)
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91
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92 phi_frame, phi_series = phi_trajdata.T
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93 psi_frame, psi_series = psi_trajdata.T
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94
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95 phi_series = np.concatenate(phi_series, axis=0)
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96 psi_series = np.concatenate(psi_series, axis=0)
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97
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98 zip(phi_frame, phi_series, psi_series)
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99
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100 with open(args.output, 'w') as f:
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101 writer = csv.writer(f, delimiter='\t')
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102 writer.writerows(zip(phi_frame, phi_series, psi_series))
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103
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104 with sns.axes_style("white"):
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105 h = sns.jointplot(x=phi_series, y=psi_series,
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106 kind="kde", space=0, legend=True)
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107 h.set_axis_labels(r'$\phi$ (degrees)', r'$\psi$ (degrees)')
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108 h.ax_joint.set_xlim(-180, 180)
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109 h.ax_joint.set_ylim(-180, 180)
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110 h.ax_joint.xaxis.set_major_locator(ticker.MultipleLocator(60))
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111 h.ax_joint.yaxis.set_major_locator(ticker.MultipleLocator(60))
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112 plt.savefig(args.oramachandran_plot, format='png', bbox_inches='tight')