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annotate angle.py @ 4:aabf6858f293 draft

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
author chemteam
date Mon, 07 Oct 2019 12:41:24 -0400
parents 935c49339c3b
children fb2b84481239
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24e220d91481 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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1 #!/usr/bin/env python
24e220d91481 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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24e220d91481 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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3 import argparse
24e220d91481 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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4 import csv
24e220d91481 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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5 import sys
24e220d91481 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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6
24e220d91481 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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7 import MDAnalysis as mda
24e220d91481 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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24e220d91481 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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9 import matplotlib
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10 matplotlib.use('Agg') # noqa
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24e220d91481 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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11 import matplotlib.pyplot as plt
24e220d91481 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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24e220d91481 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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13 import numpy as np
24e220d91481 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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14 from numpy.linalg import norm
24e220d91481 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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24e220d91481 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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24e220d91481 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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17 def parse_command_line(argv):
24e220d91481 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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18 parser = argparse.ArgumentParser()
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aabf6858f293 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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19 parser.add_argument('--itraj', help='input traj')
aabf6858f293 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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20 parser.add_argument('--istr', help='input str')
aabf6858f293 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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21 parser.add_argument('--itrajext', help='input traj ext')
aabf6858f293 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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22 parser.add_argument('--istrext', help='input str ext')
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24e220d91481 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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23 parser.add_argument('--isegid1', help='segid 1')
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24 parser.add_argument('--iresid1', help='resid 1')
24e220d91481 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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25 parser.add_argument('--iname1', help='name 1')
24e220d91481 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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26 parser.add_argument('--isegid2', help='segid 2')
24e220d91481 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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27 parser.add_argument('--iresid2', help='resid 2')
24e220d91481 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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28 parser.add_argument('--iname2', help='name 2')
24e220d91481 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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29 parser.add_argument('--isegid3', help='segid 3')
24e220d91481 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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30 parser.add_argument('--iresid3', help='resid 3')
24e220d91481 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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31 parser.add_argument('--iname3', help='name 3')
24e220d91481 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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32 parser.add_argument('--output', help='output')
24e220d91481 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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33 parser.add_argument('--oangle_plot', help='angle plot')
24e220d91481 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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34 return parser.parse_args()
24e220d91481 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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37 args = parse_command_line(sys.argv)
24e220d91481 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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38
24e220d91481 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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39 atom1 = "(segid %s and resid %s and name %s)" % \
24e220d91481 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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40 (args.isegid1, args.iresid1, args.iname1)
24e220d91481 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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41 atom2 = "(segid %s and resid %s and name %s)" % \
24e220d91481 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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42 (args.isegid2, args.iresid2, args.iname2)
24e220d91481 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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43 atom3 = "(segid %s and resid %s and name %s)" % \
24e220d91481 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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44 (args.isegid3, args.iresid3, args.iname3)
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47 def theta(u):
24e220d91481 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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48 A = u.select_atoms(atom1).center_of_geometry()
24e220d91481 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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49 B = u.select_atoms(atom2).center_of_geometry()
24e220d91481 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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50 C = u.select_atoms(atom3).center_of_geometry()
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51 BA = A - B
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52 BC = C - B
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53 theta = np.arccos(np.dot(BA, BC)/(norm(BA)*norm(BC)))
24e220d91481 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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54 return np.rad2deg(theta)
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56
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57 u = mda.Universe(args.istr, args.itraj,
aabf6858f293 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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58 topology_format=args.istrext, format=args.itrajext)
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59 data = np.array([(u.trajectory.frame, theta(u)) for ts in u.trajectory])
24e220d91481 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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60 frame, theta = data.T
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61
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62 with open(args.output, 'w') as f:
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63 writer = csv.writer(f, delimiter='\t')
24e220d91481 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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64 writer.writerows(zip(frame, theta))
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65
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66 with open(args.output) as f:
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67 g = [xtmp.strip() for xtmp in f]
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68 data = [tuple(map(float, xtmp.split())) for xtmp in g[0:]]
24e220d91481 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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69 time = [xtmp[0] for xtmp in data]
24e220d91481 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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70 angle = [xtmp[1] for xtmp in data]
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71 plt.plot(time, angle)
24e220d91481 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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72 plt.xlabel('Frame No.')
24e220d91481 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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73 plt.ylabel('Angle (degrees)')
24e220d91481 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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74 plt.savefig(args.oangle_plot, format='png')