Mercurial > repos > chemteam > mdanalysis_dihedral

comparison rdf.py @ 1:cc1d22357daf draft

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planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 9b44a37fc1a0c338693f54eaf52b582439ca9f0c
author chemteam
date Thu, 20 Dec 2018 06:49:06 -0500
parents f95d4348ed7c
children d8178fe9aaff
comparison
equal deleted inserted replaced
0:f95d4348ed7c 1:cc1d22357daf
6 6
7 import MDAnalysis as mda 7 import MDAnalysis as mda
8 from MDAnalysis.analysis.rdf import InterRDF 8 from MDAnalysis.analysis.rdf import InterRDF
9 9
10 import matplotlib 10 import matplotlib
11 matplotlib.use('Agg') # noqa
11 import matplotlib.pyplot as plt 12 import matplotlib.pyplot as plt
12 13
13 import numpy as np 14 import numpy as np
14
15 matplotlib.use('Agg')
16 15
17 16
18 def parse_command_line(argv): 17 def parse_command_line(argv):
19 parser = argparse.ArgumentParser() 18 parser = argparse.ArgumentParser()
20 parser.add_argument('--idcd', help='input dcd') 19 parser.add_argument('--idcd', help='input dcd')
62 g = [xtmp.strip() for xtmp in f] 61 g = [xtmp.strip() for xtmp in f]
63 data = [tuple(map(float, xtmp.split())) for xtmp in g[0:]] 62 data = [tuple(map(float, xtmp.split())) for xtmp in g[0:]]
64 time = [xtmp[0] for xtmp in data] 63 time = [xtmp[0] for xtmp in data]
65 rdf = [xtmp[1] for xtmp in data] 64 rdf = [xtmp[1] for xtmp in data]
66 plt.plot(time, rdf) 65 plt.plot(time, rdf)
67 plt.xlabel('r ($\AA$)') 66 plt.xlabel(r'r ($\AA$)')
68 plt.ylabel('g(r)') 67 plt.ylabel('g(r)')
69 plt.savefig(args.ordf_plot, format='png') 68 plt.savefig(args.ordf_plot, format='png')