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annotate distance_single.py @ 5:d540ea77b909 draft

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
author chemteam
date Thu, 06 Feb 2020 19:43:03 -0500
parents
children aa4090b50e7b
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d540ea77b909 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
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1 #!/usr/bin/env python
d540ea77b909 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
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d540ea77b909 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
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3 import argparse
d540ea77b909 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
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4 import sys
d540ea77b909 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
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d540ea77b909 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
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6 import MDAnalysis as mda
d540ea77b909 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
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d540ea77b909 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
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8 import matplotlib
d540ea77b909 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
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9 matplotlib.use('Agg') # noqa
d540ea77b909 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
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10 import matplotlib.pyplot as plt
d540ea77b909 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
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d540ea77b909 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
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12 import numpy as np
d540ea77b909 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
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d540ea77b909 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
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d540ea77b909 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
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15 def parse_command_line(argv):
d540ea77b909 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
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16 parser = argparse.ArgumentParser()
d540ea77b909 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
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17 parser.add_argument('--itraj', help='input traj')
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18 parser.add_argument('--istr', help='input str')
d540ea77b909 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
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19 parser.add_argument('--itrajext', help='input traj ext')
d540ea77b909 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
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20 parser.add_argument('--istrext', help='input str ext')
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21 parser.add_argument('--isegid1', help='segid 1')
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22 parser.add_argument('--iresid1', help='resid 1')
d540ea77b909 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
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23 parser.add_argument('--iname1', help='name 1')
d540ea77b909 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
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24 parser.add_argument('--isegid2', help='segid 2')
d540ea77b909 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
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25 parser.add_argument('--iresid2', help='resid 2')
d540ea77b909 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
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26 parser.add_argument('--iname2', help='name 2')
d540ea77b909 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
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27 parser.add_argument('--output', help='output')
d540ea77b909 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
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28 parser.add_argument('--odistance_plot', help='odistance plot')
d540ea77b909 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
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29 parser.add_argument('--header', dest='header', action='store_true')
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30 return parser.parse_args()
d540ea77b909 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
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33 args = parse_command_line(sys.argv)
d540ea77b909 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
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d540ea77b909 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
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35 atom1 = "(segid %s and resid %s and name %s)" % \
d540ea77b909 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
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36 (args.isegid1, args.iresid1, args.iname1)
d540ea77b909 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
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37 atom2 = "(segid %s and resid %s and name %s)" % \
d540ea77b909 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
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38 (args.isegid2, args.iresid2, args.iname2)
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d540ea77b909 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
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40 u = mda.Universe(args.istr, args.itraj,
d540ea77b909 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
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41 topology_format=args.istrext, format=args.itrajext)
d540ea77b909 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
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42 x = u.select_atoms(atom1)
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43 y = u.select_atoms(atom2)
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45 with open(args.output, 'w') as f:
d540ea77b909 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
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46 if args.header:
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47 f.write('Frame\tDistance')
d540ea77b909 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
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48 for t in u.trajectory:
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49 r = x.positions - y.positions
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50 d = np.linalg.norm(r)
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51 f.write(str(t.frame) + '\t ')
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52 f.write(str(d) + '\n')
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54 with open(args.output) as f:
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55 g = [xtmp.strip() for xtmp in f]
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56 data = [tuple(map(float, xtmp.split())) for xtmp in g[0:]]
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57 time = [xtmp[0] for xtmp in data]
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58 distance = [xtmp[1] for xtmp in data]
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59 plt.plot(time, distance)
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60 plt.xlabel('Frame No.')
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61 plt.ylabel(r'Distance ($\AA$)')
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62 plt.savefig(args.odistance_plot, format='png')