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annotate distance.py @ 0:1abbf9ca75fa draft

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planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
author chemteam
date Mon, 08 Oct 2018 12:42:19 -0400
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children 8845c77d62f2
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1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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1 #!/usr/bin/env python
1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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3 import argparse
1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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4 import sys
1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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6 import MDAnalysis as mda
1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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8 import matplotlib
1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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9 import matplotlib.pyplot as plt
1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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11 import numpy as np
1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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13 matplotlib.use('Agg')
1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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16 def parse_command_line(argv):
1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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17 parser = argparse.ArgumentParser()
1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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18 parser.add_argument('--idcd', help='input dcd')
1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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19 parser.add_argument('--ipdb', help='input pdb')
1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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20 parser.add_argument('--isegid1', help='segid 1')
1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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21 parser.add_argument('--iresid1', help='resid 1')
1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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22 parser.add_argument('--iname1', help='name 1')
1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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23 parser.add_argument('--isegid2', help='segid 2')
1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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24 parser.add_argument('--iresid2', help='resid 2')
1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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25 parser.add_argument('--iname2', help='name 2')
1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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26 parser.add_argument('--output', help='output')
1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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27 parser.add_argument('--odistance_plot', help='odistance plot')
1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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28 return parser.parse_args()
1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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31 args = parse_command_line(sys.argv)
1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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33 atom1 = "(segid %s and resid %s and name %s)" % \
1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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34 (args.isegid1, args.iresid1, args.iname1)
1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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35 atom2 = "(segid %s and resid %s and name %s)" % \
1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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36 (args.isegid2, args.iresid2, args.iname2)
1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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38 u = mda.Universe(args.ipdb, args.idcd, topology_format="PDB", format="DCD")
1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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39 x = u.select_atoms(atom1)
1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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40 y = u.select_atoms(atom2)
1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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41
1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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42 with open(args.output, 'w') as f:
1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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43 for t in u.trajectory:
1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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44 r = x.positions - y.positions
1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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45 d = np.linalg.norm(r)
1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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46 f.write(str(t.frame) + '\t ')
1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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47 f.write(str(d) + '\n')
1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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48
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49 with open(args.output) as f:
1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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50 g = [xtmp.strip() for xtmp in f]
1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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51 data = [tuple(map(float, xtmp.split())) for xtmp in g[0:]]
1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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52 time = [xtmp[0] for xtmp in data]
1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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53 distance = [xtmp[1] for xtmp in data]
1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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54 plt.plot(time, distance)
1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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55 plt.xlabel('Frame No.')
1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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56 plt.ylabel('Distance ($\AA$)')
1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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57 plt.savefig(args.odistance_plot, format='png')