Mercurial > repos > chemteam > mdanalysis_distance
view distance_multiple.py @ 7:ffd6f8d159e1 draft
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
author | chemteam |
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date | Mon, 24 Aug 2020 16:14:05 -0400 |
parents | d540ea77b909 |
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import argparse import sys import MDAnalysis as mda from MDAnalysis.analysis import distances import numpy as np def parse_command_line(argv): parser = argparse.ArgumentParser() parser.add_argument('--itraj', help='input traj') parser.add_argument('--istr', help='input str') parser.add_argument('--itrajext', help='input traj ext') parser.add_argument('--istrext', help='input str ext') parser.add_argument('--list1', help='list 2') parser.add_argument('--list2', help='list 2') parser.add_argument('--output', help='output') parser.add_argument('--header', dest='header', action='store_true') return parser.parse_args() args = parse_command_line(sys.argv) u = mda.Universe(args.istr, args.itraj, topology_format=args.istrext, format=args.itrajext) list1 = np.loadtxt(args.list1, dtype=str, delimiter="\t", ndmin=1) list2 = np.loadtxt(args.list2, dtype=str, delimiter="\t", ndmin=1) sel1 = [u.select_atoms(selection) for selection in list1] sel2 = [u.select_atoms(selection) for selection in list2] d = np.empty((u.trajectory.n_frames, list1.shape[0], list2.shape[0]),) for ts in u.trajectory: c_o_m1 = np.array([selection.center_of_mass() for selection in sel1]) c_o_m2 = np.array([selection.center_of_mass() for selection in sel2]) distances.distance_array(c_o_m1, c_o_m2, result=d[ts.frame]) d = np.hstack(( np.array(np.reshape(np.arange( 0, d.shape[0]), (d.shape[0], 1)), dtype=int), # add column w frame np.reshape(d, (d.shape[0], d.shape[1] * d.shape[2])) )) if args.header: header = 'Frame\t' + '\t'.join( ['-'.join(pair) for pair in zip( sum([[n, ] * len(list2) for n in list1], []), list(list2) * len(list1),)]).replace(' ', '_') else: header = '' np.savetxt(args.output, d, header=header, comments='', fmt=['%d'] + ['%f'] * (d.shape[1] - 1), delimiter='\t')