diff distance.py @ 4:312f912de69d draft

"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
author chemteam
date Mon, 07 Oct 2019 12:52:40 -0400
parents 2b1434ec8c7e
children
line wrap: on
line diff
--- a/distance.py	Wed Apr 03 15:46:56 2019 -0400
+++ b/distance.py	Mon Oct 07 12:52:40 2019 -0400
@@ -14,8 +14,10 @@
 
 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')
@@ -34,7 +36,8 @@
 atom2 = "(segid %s and resid %s and name %s)" % \
     (args.isegid2, args.iresid2, args.iname2)
 
-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)
 x = u.select_atoms(atom1)
 y = u.select_atoms(atom2)