diff dihedrals.py @ 1:5c38e38dbc35 draft

"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"

--- a/dihedrals.py	Wed Apr 03 15:48:18 2019 -0400
+++ b/dihedrals.py	Mon Oct 07 12:51:36 2019 -0400
@@ -16,8 +16,10 @@
 
 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('--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')
@@ -56,7 +58,8 @@
     return np.rad2deg(psi)
 
 
-u = mda.Universe(args.ipdb, args.idcd, topology_format="PDB", format="DCD")
+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)