--- /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')