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annotate dihedrals.py @ 1:560e55dd269c 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 06:45:47 -0500
parents b8e2e0e7a238
children 90865413242d
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b8e2e0e7a238 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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1 #!/usr/bin/env python
b8e2e0e7a238 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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3 import argparse
b8e2e0e7a238 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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4 import csv
b8e2e0e7a238 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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5 import sys
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7 import MDAnalysis as mda
b8e2e0e7a238 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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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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14 import numpy as np
b8e2e0e7a238 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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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('--idcd', help='input dcd')
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20 parser.add_argument('--ipdb', help='input pdb')
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21 parser.add_argument('--isegid1', help='segid 1')
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22 parser.add_argument('--iresid1', help='resid 1')
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23 parser.add_argument('--iname1', help='name 1')
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24 parser.add_argument('--isegid2', help='segid 2')
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25 parser.add_argument('--iresid2', help='resid 2')
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26 parser.add_argument('--iname2', help='name 2')
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27 parser.add_argument('--isegid3', help='segid 3')
b8e2e0e7a238 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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28 parser.add_argument('--iresid3', help='resid 3')
b8e2e0e7a238 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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29 parser.add_argument('--iname3', help='name 3')
b8e2e0e7a238 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
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30 parser.add_argument('--isegid4', help='segid 4')
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31 parser.add_argument('--iresid4', help='resid 4')
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32 parser.add_argument('--iname4', help='name 4')
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33 parser.add_argument('--output', help='output')
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34 parser.add_argument('--odihedral_plot', help='dihedral plot')
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35 return parser.parse_args()
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38 args = parse_command_line(sys.argv)
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40 atom1 = "(segid %s and resid %s and name %s)" % \
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41 (args.isegid1, args.iresid1, args.iname1)
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42 atom2 = "(segid %s and resid %s and name %s)" % \
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43 (args.isegid2, args.iresid2, args.iname2)
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44 atom3 = "(segid %s and resid %s and name %s)" % \
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45 (args.isegid3, args.iresid3, args.iname3)
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46 atom4 = "(segid %s and resid %s and name %s)" % \
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47 (args.isegid4, args.iresid4, args.iname4)
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50 def psi(u):
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51 A = u.select_atoms(atom1).positions
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52 B = u.select_atoms(atom2).positions
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53 C = u.select_atoms(atom3).positions
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54 D = u.select_atoms(atom4).positions
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55 psi = calc_dihedrals(A, B, C, D)
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56 return np.rad2deg(psi)
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59 u = mda.Universe(args.ipdb, args.idcd, topology_format="PDB", format="DCD")
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60 data = np.array([(u.trajectory.frame, psi(u)) for ts in u.trajectory])
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61 frame, psi = data.T
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63 zip(frame, psi)
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64
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65 with open(args.output, 'w') as f:
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66 writer = csv.writer(f, delimiter='\t')
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67 writer.writerows(zip(frame, psi))
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68
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69 with open(args.output) as f:
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70 g = [xtmp.strip() for xtmp in f]
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71 data = [tuple(map(float, xtmp.split())) for xtmp in g[0:]]
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72 time = [xtmp[0] for xtmp in data]
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73 dihedral = [xtmp[1] for xtmp in data]
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74 plt.plot(time, dihedral)
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75 plt.xlabel('Frame No.')
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76 plt.ylabel('Dihedral (degrees)')
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77 plt.savefig(args.odihedral_plot, format='png')