--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/angle.py	Mon Oct 08 13:16:46 2018 -0400
@@ -0,0 +1,72 @@
+#!/usr/bin/env python
+
+import argparse
+import csv
+import sys
+
+import MDAnalysis as mda
+
+import matplotlib
+import matplotlib.pyplot as plt
+
+import numpy as np
+from numpy.linalg import norm
+
+matplotlib.use('Agg')
+
+
+def parse_command_line(argv):
+    parser = argparse.ArgumentParser()
+    parser.add_argument('--idcd', help='input dcd')
+    parser.add_argument('--ipdb', help='input pdb')
+    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('--output', help='output')
+    parser.add_argument('--oangle_plot', help='angle 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)
+
+
+def theta(u):
+    A = u.select_atoms(atom1).center_of_geometry()
+    B = u.select_atoms(atom2).center_of_geometry()
+    C = u.select_atoms(atom3).center_of_geometry()
+    BA = A - B
+    BC = C - B
+    theta = np.arccos(np.dot(BA, BC)/(norm(BA)*norm(BC)))
+    return np.rad2deg(theta)
+
+
+u = mda.Universe(args.ipdb, args.idcd, topology_format="PDB", format="DCD")
+data = np.array([(u.trajectory.frame, theta(u)) for ts in u.trajectory])
+frame, theta = data.T
+
+with open(args.output, 'w') as f:
+    writer = csv.writer(f, delimiter='\t')
+    writer.writerows(zip(frame, theta))
+
+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]
+    angle = [xtmp[1] for xtmp in data]
+    plt.plot(time, angle)
+    plt.xlabel('Frame No.')
+    plt.ylabel('Angle (degrees)')
+    plt.savefig(args.oangle_plot, format='png')