diff rdf.py @ 4:36babbdd7818 draft

"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
author chemteam
date Mon, 07 Oct 2019 12:51:57 -0400
parents 0315b541c74d
children 0f17d0720565
line wrap: on
line diff
--- a/rdf.py	Wed Apr 03 15:47:16 2019 -0400
+++ b/rdf.py	Mon Oct 07 12:51:57 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')
@@ -42,7 +44,8 @@
 start = float(args.istart)
 end = float(args.iend)
 
-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)