Mercurial > repos > chemteam > mdanalysis_hbonds
view dihedrals.py @ 2:d23ef0663267 draft
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
author | chemteam |
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date | Thu, 06 Feb 2020 19:41:49 -0500 |
parents | 5c38e38dbc35 |
children | 5efd0c95f97e |
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#!/usr/bin/env python import argparse import csv import sys import MDAnalysis as mda from MDAnalysis.lib.distances import calc_dihedrals import matplotlib matplotlib.use('Agg') # noqa import matplotlib.pyplot as plt 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('--isegid1', help='segid 1') parser.add_argument('--iresid1', help='resid 1') parser.add_argument('--iname1', help='name 1') parser.add_argument('--isegid2', help='segid 2') parser.add_argument('--iresid2', help='resid 2') parser.add_argument('--iname2', help='name 2') parser.add_argument('--isegid3', help='segid 3') parser.add_argument('--iresid3', help='resid 3') parser.add_argument('--iname3', help='name 3') parser.add_argument('--isegid4', help='segid 4') parser.add_argument('--iresid4', help='resid 4') parser.add_argument('--iname4', help='name 4') parser.add_argument('--output', help='output') parser.add_argument('--odihedral_plot', help='dihedral plot') return parser.parse_args() args = parse_command_line(sys.argv) atom1 = "(segid %s and resid %s and name %s)" % \ (args.isegid1, args.iresid1, args.iname1) atom2 = "(segid %s and resid %s and name %s)" % \ (args.isegid2, args.iresid2, args.iname2) atom3 = "(segid %s and resid %s and name %s)" % \ (args.isegid3, args.iresid3, args.iname3) atom4 = "(segid %s and resid %s and name %s)" % \ (args.isegid4, args.iresid4, args.iname4) def psi(u): A = u.select_atoms(atom1).positions B = u.select_atoms(atom2).positions C = u.select_atoms(atom3).positions D = u.select_atoms(atom4).positions psi = calc_dihedrals(A, B, C, D) return np.rad2deg(psi) u = mda.Universe(args.istr, args.itraj, topology_format=args.istrext, format=args.itrajext) data = np.array([(u.trajectory.frame, psi(u)) for ts in u.trajectory]) frame, psi = data.T PSI = np.concatenate(psi, axis=0) zip(frame, PSI) with open(args.output, 'w') as f: writer = csv.writer(f, delimiter='\t') writer.writerows(zip(frame, PSI)) with open(args.output) as f: g = [xtmp.strip() for xtmp in f] data = [tuple(map(float, xtmp.split())) for xtmp in g[0:]] time = [xtmp[0] for xtmp in data] dihedral = [xtmp[1] for xtmp in data] plt.plot(time, dihedral) plt.xlabel('Frame No.') plt.ylabel('Dihedral (degrees)') plt.savefig(args.odihedral_plot, format='png')