Mercurial > repos > chemteam > mdanalysis_angle

annotate dihedrals.py @ 4:e7d0075052c9 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 12:51:05 -0400
parents ad135cf42274
children 7c5fd4117a07
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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
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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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8 from MDAnalysis.lib.distances import calc_dihedrals
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10 import matplotlib
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11 matplotlib.use('Agg') # noqa
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12 import matplotlib.pyplot as plt
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fc7293c6cb6a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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14 import numpy as np
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):
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18 parser = argparse.ArgumentParser()
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19 parser.add_argument('--itraj', help='input traj')
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20 parser.add_argument('--istr', help='input str')
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21 parser.add_argument('--itrajext', help='input traj ext')
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22 parser.add_argument('--istrext', help='input str ext')
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23 parser.add_argument('--isegid1', help='segid 1')
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24 parser.add_argument('--iresid1', help='resid 1')
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25 parser.add_argument('--iname1', help='name 1')
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26 parser.add_argument('--isegid2', help='segid 2')
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27 parser.add_argument('--iresid2', help='resid 2')
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28 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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29 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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30 parser.add_argument('--iresid3', help='resid 3')
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31 parser.add_argument('--iname3', help='name 3')
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32 parser.add_argument('--isegid4', help='segid 4')
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33 parser.add_argument('--iresid4', help='resid 4')
fc7293c6cb6a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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34 parser.add_argument('--iname4', help='name 4')
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35 parser.add_argument('--output', help='output')
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36 parser.add_argument('--odihedral_plot', help='dihedral plot')
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37 return parser.parse_args()
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40 args = parse_command_line(sys.argv)
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42 atom1 = "(segid %s and resid %s and name %s)" % \
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43 (args.isegid1, args.iresid1, args.iname1)
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44 atom2 = "(segid %s and resid %s and name %s)" % \
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45 (args.isegid2, args.iresid2, args.iname2)
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46 atom3 = "(segid %s and resid %s and name %s)" % \
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47 (args.isegid3, args.iresid3, args.iname3)
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48 atom4 = "(segid %s and resid %s and name %s)" % \
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49 (args.isegid4, args.iresid4, args.iname4)
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52 def psi(u):
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53 A = u.select_atoms(atom1).positions
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54 B = u.select_atoms(atom2).positions
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55 C = u.select_atoms(atom3).positions
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56 D = u.select_atoms(atom4).positions
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57 psi = calc_dihedrals(A, B, C, D)
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58 return np.rad2deg(psi)
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60
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61 u = mda.Universe(args.istr, args.itraj,
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62 topology_format=args.istrext, format=args.itrajext)
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63 data = np.array([(u.trajectory.frame, psi(u)) for ts in u.trajectory])
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64 frame, psi = data.T
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65 PSI = np.concatenate(psi, axis=0)
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66
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67 zip(frame, PSI)
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69 with open(args.output, 'w') as f:
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70 writer = csv.writer(f, delimiter='\t')
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71 writer.writerows(zip(frame, PSI))
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72
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73 with open(args.output) as f:
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74 g = [xtmp.strip() for xtmp in f]
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75 data = [tuple(map(float, xtmp.split())) for xtmp in g[0:]]
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76 time = [xtmp[0] for xtmp in data]
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77 dihedral = [xtmp[1] for xtmp in data]
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78 plt.plot(time, dihedral)
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79 plt.xlabel('Frame No.')
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80 plt.ylabel('Dihedral (degrees)')
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81 plt.savefig(args.odihedral_plot, format='png')