Mercurial > repos > chemteam > mdanalysis_distance
comparison distance_multiple.py @ 5:d540ea77b909 draft
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
| author | chemteam |
|---|---|
| date | Thu, 06 Feb 2020 19:43:03 -0500 |
| parents | |
| children |
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| 4:312f912de69d | 5:d540ea77b909 |
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| 1 import argparse | |
| 2 import sys | |
| 3 | |
| 4 import MDAnalysis as mda | |
| 5 from MDAnalysis.analysis import distances | |
| 6 | |
| 7 import numpy as np | |
| 8 | |
| 9 | |
| 10 def parse_command_line(argv): | |
| 11 parser = argparse.ArgumentParser() | |
| 12 parser.add_argument('--itraj', help='input traj') | |
| 13 parser.add_argument('--istr', help='input str') | |
| 14 parser.add_argument('--itrajext', help='input traj ext') | |
| 15 parser.add_argument('--istrext', help='input str ext') | |
| 16 parser.add_argument('--list1', help='list 2') | |
| 17 parser.add_argument('--list2', help='list 2') | |
| 18 parser.add_argument('--output', help='output') | |
| 19 parser.add_argument('--header', dest='header', action='store_true') | |
| 20 return parser.parse_args() | |
| 21 | |
| 22 | |
| 23 args = parse_command_line(sys.argv) | |
| 24 | |
| 25 u = mda.Universe(args.istr, args.itraj, | |
| 26 topology_format=args.istrext, format=args.itrajext) | |
| 27 | |
| 28 list1 = np.loadtxt(args.list1, dtype=str, delimiter="\t", ndmin=1) | |
| 29 list2 = np.loadtxt(args.list2, dtype=str, delimiter="\t", ndmin=1) | |
| 30 | |
| 31 sel1 = [u.select_atoms(selection) for selection in list1] | |
| 32 sel2 = [u.select_atoms(selection) for selection in list2] | |
| 33 | |
| 34 d = np.empty((u.trajectory.n_frames, list1.shape[0], list2.shape[0]),) | |
| 35 | |
| 36 for ts in u.trajectory: | |
| 37 c_o_m1 = np.array([selection.center_of_mass() for selection in sel1]) | |
| 38 c_o_m2 = np.array([selection.center_of_mass() for selection in sel2]) | |
| 39 distances.distance_array(c_o_m1, c_o_m2, result=d[ts.frame]) | |
| 40 | |
| 41 d = np.hstack(( | |
| 42 np.array(np.reshape(np.arange( | |
| 43 0, d.shape[0]), (d.shape[0], 1)), dtype=int), # add column w frame | |
| 44 np.reshape(d, (d.shape[0], d.shape[1] * d.shape[2])) | |
| 45 )) | |
| 46 | |
| 47 if args.header: | |
| 48 header = 'Frame\t' + '\t'.join( | |
| 49 ['-'.join(pair) for pair in zip( | |
| 50 sum([[n, ] * len(list2) for n in list1], []), | |
| 51 list(list2) * len(list1),)]).replace(' ', '_') | |
| 52 else: | |
| 53 header = '' | |
| 54 | |
| 55 np.savetxt(args.output, d, header=header, comments='', | |
| 56 fmt=['%d'] + ['%f'] * (d.shape[1] - 1), delimiter='\t') |