--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/distance_multiple.py	Thu Feb 06 19:43:03 2020 -0500
@@ -0,0 +1,56 @@
+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')