Mercurial > repos > chemteam > mdanalysis_ramachandran_protein
diff end-to-end.py @ 0:0f270722aca6 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 16:27:56 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/end-to-end.py Mon Aug 24 16:27:56 2020 -0400 @@ -0,0 +1,96 @@ +#!/usr/bin/env python + +import argparse +import itertools +import sys + +import MDAnalysis as mda + +import matplotlib +import matplotlib.pyplot as plt + +import numpy as np +import numpy.linalg + +matplotlib.use('Agg') # noqa + + +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('--ilabel', help='plot label') + parser.add_argument('--ititle1', help='plot title') + parser.add_argument('--output1', help='output1 - timeseries') + parser.add_argument('--o_plot', help='End to End plot') + return parser.parse_args() + + +args = parse_command_line(sys.argv) + + +u = mda.Universe(args.istr, args.itraj, + topology_format=args.istrext, format=args.itrajext) + +ntermatoms = "(segid %s and name N)" % \ + (args.isegid1) +ctermatoms = "(segid %s and name C)" % \ + (args.isegid1) +# not sure how robust this selection really is +nterm = u.select_atoms(ntermatoms)[0] # first atom named N +cterm = u.select_atoms(ctermatoms)[-1] # takes the last atom named 'C' + +enddist = [] + +for ts in u.trajectory: # iterate through all frames + r = cterm.position - nterm.position # e-to-e vector from atom positions + d = numpy.linalg.norm(r) # end-to-end distance + enddist.append((ts.frame, d)) + +enddist = np.array(enddist) + + +color = itertools.cycle(['r', 'b', 'gold']) + +fig, axs = plt.subplots(1, 2, sharex=False, sharey=False, tight_layout=True) + +params = { + 'axes.labelsize': 8, + 'legend.fontsize': 10, + 'xtick.labelsize': 10, + 'ytick.labelsize': 10, + 'text.usetex': False, + 'figure.figsize': [4.5, 4.5], + 'figure.dpi': 300 +} +plt.rcParams.update(params) + +axs[0].plot(enddist[:, 0], enddist[:, 1], 'r-', lw=2, label=args.ilabel) +axs[0].set_xlabel("number of frames") +axs[0].set_ylabel(r"End to end distance ($\AA$)") +axs[0].legend() + +n, bins, patches = axs[1].hist(enddist[:, 1], color=next( + color), label=args.ilabel, alpha=0.5, density=True, stacked=True) + +axs[1].legend() +axs[1].set_ylabel('Density Normalised Frequency') +axs[1].set_xlabel(r'End to end distance ($\AA$)') +fig.suptitle(args.ititle1, fontsize=12, fontweight='bold') +fig.subplots_adjust(top=0.45) + +print( + " \n".join( + [ + 'The End to End distance is measured between the following atoms:', + str(nterm), + str(cterm)])) + +# svg is better but sticking with png for now +plt.savefig(args.o_plot, format='png') + + +np.savetxt(args.output1, enddist, delimiter='\t')