r8551 - /branches/multi_structure/generic_fns/palmer.py -- January 20, 2009 - 16:36

Author: bugman
Date: Tue Jan 20 16:36:43 2009
New Revision: 8551

URL: http://svn.gna.org/viewcvs/relax?rev=8551&view=rev
Log:
Fixes for the create_run() and execute() functions for the new structural 
data design.


Modified:
    branches/multi_structure/generic_fns/palmer.py

Modified: branches/multi_structure/generic_fns/palmer.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/multi_structure/generic_fns/palmer.py?rev=8551&r1=8550&r2=8551&view=diff
==============================================================================
--- branches/multi_structure/generic_fns/palmer.py (original)
+++ branches/multi_structure/generic_fns/palmer.py Tue Jan 20 16:36:43 2009
@@ -495,9 +495,10 @@
     file.write("#! /bin/sh\n")
     file.write(binary + " -i mfin -d mfdata -p mfpar -m mfmodel -o mfout -e 
out")
     if cdp.diff_tensor.type != 'sphere':
-        # Copy the pdb file to the model directory so there are no problems 
with the existance of *.rotate files.
-        system('cp ' + cdp.structure.path[0] + sep + cdp.structure.file[0] + 
' ' + dir)
-        file.write(" -s " + cdp.structure.file[0])
+        # Copy the first pdb file to the model directory so there are no 
problems with the existance of *.rotate files.
+        mol = cdp.structure.structural_data[0].mol[0]
+        system('cp ' + mol.file_path + sep + mol.file_name + ' ' + dir)
+        file.write(" -s " + mol.file_name)
     file.write("\n")
 
 
@@ -552,7 +553,7 @@
 
         # Test if the 'PDB' input file exists.
         if cdp.diff_tensor.type != 'sphere':
-            pdb = cdp.structure.file[0]
+            pdb = cdp.structure.structural_data[0].mol[0].file_name
             if not access(pdb, F_OK):
                 raise RelaxFileError, ('PDB', pdb)
         else: