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annotate end-to-end.py @ 7:ffd6f8d159e1 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 16:14:05 -0400
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ffd6f8d159e1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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1 #!/usr/bin/env python
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3 import argparse
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4 import itertools
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5 import sys
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7 import MDAnalysis as mda
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9 import matplotlib
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10 import matplotlib.pyplot as plt
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12 import numpy as np
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13 import numpy.linalg
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15 matplotlib.use('Agg') # noqa
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18 def parse_command_line(argv):
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19 parser = argparse.ArgumentParser()
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20 parser.add_argument('--itraj', help='input traj')
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21 parser.add_argument('--istr', help='input str')
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22 parser.add_argument('--itrajext', help='input traj ext')
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23 parser.add_argument('--istrext', help='input str ext')
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24 parser.add_argument('--isegid1', help='segid 1')
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25 parser.add_argument('--ilabel', help='plot label')
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26 parser.add_argument('--ititle1', help='plot title')
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27 parser.add_argument('--output1', help='output1 - timeseries')
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28 parser.add_argument('--o_plot', help='End to End plot')
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29 return parser.parse_args()
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32 args = parse_command_line(sys.argv)
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35 u = mda.Universe(args.istr, args.itraj,
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36 topology_format=args.istrext, format=args.itrajext)
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38 ntermatoms = "(segid %s and name N)" % \
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39 (args.isegid1)
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40 ctermatoms = "(segid %s and name C)" % \
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41 (args.isegid1)
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42 # not sure how robust this selection really is
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43 nterm = u.select_atoms(ntermatoms)[0] # first atom named N
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44 cterm = u.select_atoms(ctermatoms)[-1] # takes the last atom named 'C'
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46 enddist = []
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48 for ts in u.trajectory: # iterate through all frames
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49 r = cterm.position - nterm.position # e-to-e vector from atom positions
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50 d = numpy.linalg.norm(r) # end-to-end distance
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51 enddist.append((ts.frame, d))
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53 enddist = np.array(enddist)
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56 color = itertools.cycle(['r', 'b', 'gold'])
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57
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58 fig, axs = plt.subplots(1, 2, sharex=False, sharey=False, tight_layout=True)
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60 params = {
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61 'axes.labelsize': 8,
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62 'legend.fontsize': 10,
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63 'xtick.labelsize': 10,
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64 'ytick.labelsize': 10,
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65 'text.usetex': False,
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66 'figure.figsize': [4.5, 4.5],
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67 'figure.dpi': 300
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68 }
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69 plt.rcParams.update(params)
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70
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71 axs[0].plot(enddist[:, 0], enddist[:, 1], 'r-', lw=2, label=args.ilabel)
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72 axs[0].set_xlabel("number of frames")
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73 axs[0].set_ylabel(r"End to end distance ($\AA$)")
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74 axs[0].legend()
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75
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76 n, bins, patches = axs[1].hist(enddist[:, 1], color=next(
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77 color), label=args.ilabel, alpha=0.5, density=True, stacked=True)
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78
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79 axs[1].legend()
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80 axs[1].set_ylabel('Density Normalised Frequency')
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81 axs[1].set_xlabel(r'End to end distance ($\AA$)')
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82 fig.suptitle(args.ititle1, fontsize=12, fontweight='bold')
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83 fig.subplots_adjust(top=0.45)
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84
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85 print(
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86 " \n".join(
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87 [
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88 'The End to End distance is measured between the following atoms:',
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89 str(nterm),
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90 str(cterm)]))
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91
ffd6f8d159e1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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92 # svg is better but sticking with png for now
ffd6f8d159e1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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93 plt.savefig(args.o_plot, format='png')
ffd6f8d159e1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
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94
ffd6f8d159e1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
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95
ffd6f8d159e1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
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96 np.savetxt(args.output1, enddist, delimiter='\t')