Mercurial > repos > chemteam > mdanalysis_distance
comparison distance.py @ 0:c33b972fe040 draft
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
| author | chemteam |
|---|---|
| date | Mon, 08 Oct 2018 13:16:12 -0400 |
| parents | |
| children | 2b1434ec8c7e |
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| -1:000000000000 | 0:c33b972fe040 |
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| 1 #!/usr/bin/env python | |
| 2 | |
| 3 import argparse | |
| 4 import sys | |
| 5 | |
| 6 import MDAnalysis as mda | |
| 7 | |
| 8 import matplotlib | |
| 9 import matplotlib.pyplot as plt | |
| 10 | |
| 11 import numpy as np | |
| 12 | |
| 13 matplotlib.use('Agg') | |
| 14 | |
| 15 | |
| 16 def parse_command_line(argv): | |
| 17 parser = argparse.ArgumentParser() | |
| 18 parser.add_argument('--idcd', help='input dcd') | |
| 19 parser.add_argument('--ipdb', help='input pdb') | |
| 20 parser.add_argument('--isegid1', help='segid 1') | |
| 21 parser.add_argument('--iresid1', help='resid 1') | |
| 22 parser.add_argument('--iname1', help='name 1') | |
| 23 parser.add_argument('--isegid2', help='segid 2') | |
| 24 parser.add_argument('--iresid2', help='resid 2') | |
| 25 parser.add_argument('--iname2', help='name 2') | |
| 26 parser.add_argument('--output', help='output') | |
| 27 parser.add_argument('--odistance_plot', help='odistance plot') | |
| 28 return parser.parse_args() | |
| 29 | |
| 30 | |
| 31 args = parse_command_line(sys.argv) | |
| 32 | |
| 33 atom1 = "(segid %s and resid %s and name %s)" % \ | |
| 34 (args.isegid1, args.iresid1, args.iname1) | |
| 35 atom2 = "(segid %s and resid %s and name %s)" % \ | |
| 36 (args.isegid2, args.iresid2, args.iname2) | |
| 37 | |
| 38 u = mda.Universe(args.ipdb, args.idcd, topology_format="PDB", format="DCD") | |
| 39 x = u.select_atoms(atom1) | |
| 40 y = u.select_atoms(atom2) | |
| 41 | |
| 42 with open(args.output, 'w') as f: | |
| 43 for t in u.trajectory: | |
| 44 r = x.positions - y.positions | |
| 45 d = np.linalg.norm(r) | |
| 46 f.write(str(t.frame) + '\t ') | |
| 47 f.write(str(d) + '\n') | |
| 48 | |
| 49 with open(args.output) as f: | |
| 50 g = [xtmp.strip() for xtmp in f] | |
| 51 data = [tuple(map(float, xtmp.split())) for xtmp in g[0:]] | |
| 52 time = [xtmp[0] for xtmp in data] | |
| 53 distance = [xtmp[1] for xtmp in data] | |
| 54 plt.plot(time, distance) | |
| 55 plt.xlabel('Frame No.') | |
| 56 plt.ylabel('Distance ($\AA$)') | |
| 57 plt.savefig(args.odistance_plot, format='png') |