Mercurial > repos > chemteam > mdanalysis_angle

annotate angle.py @ 2:4c93f7541218 draft

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planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 8e1fece3eaef36823e90f5d10f8bb8b809544c55
author chemteam
date Sun, 13 Jan 2019 03:24:24 -0500
parents 4759026f6ff4
children e7d0075052c9
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fc7293c6cb6a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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1 #!/usr/bin/env python
fc7293c6cb6a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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fc7293c6cb6a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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3 import argparse
fc7293c6cb6a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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4 import csv
fc7293c6cb6a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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5 import sys
fc7293c6cb6a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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fc7293c6cb6a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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7 import MDAnalysis as mda
fc7293c6cb6a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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fc7293c6cb6a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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9 import matplotlib
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10 matplotlib.use('Agg') # noqa
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fc7293c6cb6a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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11 import matplotlib.pyplot as plt
fc7293c6cb6a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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fc7293c6cb6a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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13 import numpy as np
fc7293c6cb6a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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14 from numpy.linalg import norm
fc7293c6cb6a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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fc7293c6cb6a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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fc7293c6cb6a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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17 def parse_command_line(argv):
fc7293c6cb6a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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18 parser = argparse.ArgumentParser()
fc7293c6cb6a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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19 parser.add_argument('--idcd', help='input dcd')
fc7293c6cb6a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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20 parser.add_argument('--ipdb', help='input pdb')
fc7293c6cb6a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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21 parser.add_argument('--isegid1', help='segid 1')
fc7293c6cb6a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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22 parser.add_argument('--iresid1', help='resid 1')
fc7293c6cb6a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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23 parser.add_argument('--iname1', help='name 1')
fc7293c6cb6a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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24 parser.add_argument('--isegid2', help='segid 2')
fc7293c6cb6a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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25 parser.add_argument('--iresid2', help='resid 2')
fc7293c6cb6a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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26 parser.add_argument('--iname2', help='name 2')
fc7293c6cb6a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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27 parser.add_argument('--isegid3', help='segid 3')
fc7293c6cb6a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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28 parser.add_argument('--iresid3', help='resid 3')
fc7293c6cb6a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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29 parser.add_argument('--iname3', help='name 3')
fc7293c6cb6a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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30 parser.add_argument('--output', help='output')
fc7293c6cb6a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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31 parser.add_argument('--oangle_plot', help='angle plot')
fc7293c6cb6a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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32 return parser.parse_args()
fc7293c6cb6a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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35 args = parse_command_line(sys.argv)
fc7293c6cb6a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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37 atom1 = "(segid %s and resid %s and name %s)" % \
fc7293c6cb6a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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38 (args.isegid1, args.iresid1, args.iname1)
fc7293c6cb6a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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39 atom2 = "(segid %s and resid %s and name %s)" % \
fc7293c6cb6a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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40 (args.isegid2, args.iresid2, args.iname2)
fc7293c6cb6a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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41 atom3 = "(segid %s and resid %s and name %s)" % \
fc7293c6cb6a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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42 (args.isegid3, args.iresid3, args.iname3)
fc7293c6cb6a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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45 def theta(u):
fc7293c6cb6a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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46 A = u.select_atoms(atom1).center_of_geometry()
fc7293c6cb6a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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47 B = u.select_atoms(atom2).center_of_geometry()
fc7293c6cb6a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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48 C = u.select_atoms(atom3).center_of_geometry()
fc7293c6cb6a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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49 BA = A - B
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50 BC = C - B
fc7293c6cb6a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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51 theta = np.arccos(np.dot(BA, BC)/(norm(BA)*norm(BC)))
fc7293c6cb6a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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52 return np.rad2deg(theta)
fc7293c6cb6a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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53
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55 u = mda.Universe(args.ipdb, args.idcd, topology_format="PDB", format="DCD")
fc7293c6cb6a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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56 data = np.array([(u.trajectory.frame, theta(u)) for ts in u.trajectory])
fc7293c6cb6a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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57 frame, theta = data.T
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58
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59 with open(args.output, 'w') as f:
fc7293c6cb6a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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60 writer = csv.writer(f, delimiter='\t')
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61 writer.writerows(zip(frame, theta))
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62
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63 with open(args.output) as f:
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64 g = [xtmp.strip() for xtmp in f]
fc7293c6cb6a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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65 data = [tuple(map(float, xtmp.split())) for xtmp in g[0:]]
fc7293c6cb6a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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66 time = [xtmp[0] for xtmp in data]
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67 angle = [xtmp[1] for xtmp in data]
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68 plt.plot(time, angle)
fc7293c6cb6a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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69 plt.xlabel('Frame No.')
fc7293c6cb6a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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70 plt.ylabel('Angle (degrees)')
fc7293c6cb6a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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71 plt.savefig(args.oangle_plot, format='png')