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annotate distance_single.py @ 0:78aa3659fcd1 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 16:47:23 -0400
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78aa3659fcd1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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1 #!/usr/bin/env python
78aa3659fcd1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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78aa3659fcd1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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3 import argparse
78aa3659fcd1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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4 import sys
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78aa3659fcd1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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6 import MDAnalysis as mda
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78aa3659fcd1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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8 import matplotlib
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9 import matplotlib.pyplot as plt
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78aa3659fcd1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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11 import numpy as np
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78aa3659fcd1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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13 matplotlib.use('Agg') # noqa
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78aa3659fcd1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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78aa3659fcd1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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16 def parse_command_line(argv):
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17 parser = argparse.ArgumentParser()
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18 parser.add_argument('--itraj', help='input traj')
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19 parser.add_argument('--istr', help='input str')
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20 parser.add_argument('--itrajext', help='input traj ext')
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21 parser.add_argument('--istrext', help='input str ext')
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22 parser.add_argument('--isegid1', help='segid 1')
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23 parser.add_argument('--iresid1', help='resid 1')
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24 parser.add_argument('--iname1', help='name 1')
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25 parser.add_argument('--isegid2', help='segid 2')
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26 parser.add_argument('--iresid2', help='resid 2')
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27 parser.add_argument('--iname2', help='name 2')
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28 parser.add_argument('--output', help='output')
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29 parser.add_argument('--odistance_plot', help='odistance plot')
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30 parser.add_argument('--header', dest='header', action='store_true')
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31 return parser.parse_args()
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34 args = parse_command_line(sys.argv)
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36 atom1 = "(segid %s and resid %s and name %s)" % \
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37 (args.isegid1, args.iresid1, args.iname1)
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38 atom2 = "(segid %s and resid %s and name %s)" % \
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39 (args.isegid2, args.iresid2, args.iname2)
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41 u = mda.Universe(args.istr, args.itraj,
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42 topology_format=args.istrext, format=args.itrajext)
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43 x = u.select_atoms(atom1)
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44 y = u.select_atoms(atom2)
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46 with open(args.output, 'w') as f:
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47 if args.header:
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48 f.write('Frame\tDistance')
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49 for t in u.trajectory:
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50 r = x.positions - y.positions
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51 d = np.linalg.norm(r)
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52 f.write(str(t.frame) + '\t ')
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53 f.write(str(d) + '\n')
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54
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55 with open(args.output) as f:
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56 g = [xtmp.strip() for xtmp in f]
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57 data = [tuple(map(float, xtmp.split())) for xtmp in g[0:]]
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58 time = [xtmp[0] for xtmp in data]
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59 distance = [xtmp[1] for xtmp in data]
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60 plt.plot(time, distance)
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61 plt.xlabel('Frame No.')
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62 plt.ylabel(r'Distance ($\AA$)')
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63 plt.savefig(args.odistance_plot, format='png')