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annotate rdf.py @ 6:aa4090b50e7b draft

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b"
author chemteam
date Wed, 20 May 2020 13:06:33 -0400
parents 312f912de69d
children
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c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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1 #!/usr/bin/env python
c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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3 import argparse
c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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4 import csv
c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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5 import sys
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c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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7 import MDAnalysis as mda
c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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8 from MDAnalysis.analysis.rdf import InterRDF
c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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10 import matplotlib
c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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11 import matplotlib.pyplot as plt
c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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13 import numpy as np
c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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aa4090b50e7b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b"
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15 matplotlib.use('Agg') # noqa
aa4090b50e7b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b"
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c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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18 def parse_command_line(argv):
c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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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')
312f912de69d "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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23 parser.add_argument('--istrext', help='input str ext')
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c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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24 parser.add_argument('--isegid1', help='segid 1')
c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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25 parser.add_argument('--iresid1', help='resid 1')
c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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26 parser.add_argument('--iname1', help='name 1')
c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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27 parser.add_argument('--isegid2', help='segid 2')
c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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28 parser.add_argument('--iresid2', help='resid 2')
c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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29 parser.add_argument('--iname2', help='name 2')
c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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30 parser.add_argument('--inbins', help='Number of bins in the histogram')
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31 parser.add_argument('--istart', help='Starting Point')
c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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32 parser.add_argument('--iend', help='End point')
c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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33 parser.add_argument('--output', help='output')
c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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34 parser.add_argument('--ordf_plot', help='RDF plot')
c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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35 return parser.parse_args()
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c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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38 args = parse_command_line(sys.argv)
c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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40 atom1 = "(segid %s and resid %s and name %s)" % \
c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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41 (args.isegid1, args.iresid1, args.iname1)
c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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42 atom2 = "(segid %s and resid %s and name %s)" % \
c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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43 (args.isegid2, args.iresid2, args.iname2)
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44 bins = int(args.inbins)
c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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45 start = float(args.istart)
c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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46 end = float(args.iend)
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47
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48 u = mda.Universe(args.istr, args.itraj,
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49 topology_format=args.istrext, format=args.itrajext)
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50 x = u.select_atoms(atom1)
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51 y = u.select_atoms(atom2)
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53 rdf = InterRDF(x, y, nbins=bins, range=(start, end))
c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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54 rdf.run()
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55 bins = rdf.bins
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56 bins = np.around(bins, decimals=3)
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57 RDF = rdf.rdf
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58 zip(bins, RDF)
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59
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60 with open(args.output, 'w') as f:
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61 writer = csv.writer(f, delimiter='\t')
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62 writer.writerows(zip(bins, RDF))
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64 with open(args.output) as f:
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65 g = [xtmp.strip() for xtmp in f]
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66 data = [tuple(map(float, xtmp.split())) for xtmp in g[0:]]
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67 time = [xtmp[0] for xtmp in data]
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68 rdf = [xtmp[1] for xtmp in data]
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69 plt.plot(time, rdf)
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70 plt.xlabel(r'r ($\AA$)')
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71 plt.ylabel('g(r)')
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72 plt.savefig(args.ordf_plot, format='png')