r27436 - /trunk/pipe_control/structure/main.py -- February 02, 2015 - 09:20

Author: bugman
Date: Mon Feb  2 09:20:06 2015
New Revision: 27436

URL: http://svn.gna.org/viewcvs/relax?rev=27436&view=rev
Log:
Fix for the internal structural object atomic coordinate assembly function.

This is the pipe_control.structure.main.assemble_structural_coordinates() 
function.  The case of no
sequence alignment being required as only models are being handled is now 
functional.  The strings
and gaps data structures passed into the 
lib.sequence_alignment.msa.msa_residue_skipping() function
for generating the residue skipping data structure are now set to the one 
letter codes and an empty
structure of zeros respectively.


Modified:
    trunk/pipe_control/structure/main.py

Modified: trunk/pipe_control/structure/main.py
URL: 
http://svn.gna.org/viewcvs/relax/trunk/pipe_control/structure/main.py?rev=27436&r1=27435&r2=27436&view=diff
==============================================================================
--- trunk/pipe_control/structure/main.py        (original)
+++ trunk/pipe_control/structure/main.py        Mon Feb  2 09:20:06 2015
@@ -138,10 +138,6 @@
         if mol != molecule_list[0]:
             same_mol = False
 
-    # Init.
-    strings = None
-    gaps = None
-
     # Handle sequence alignments - retrieve the alignment.
     align = None
     if hasattr(ds, 'sequence_alignments'):
@@ -160,6 +156,16 @@
     elif len(objects) == 1 and same_mol:
         # Printout.
         print("\nSequence alignment disabled as only models with identical 
molecule, residue and atomic sequences are being superimposed.")
+
+        # Set the one letter codes to be the alignment strings.
+        strings = one_letter_codes
+
+        # Create an empty gap data structure.
+        gaps = []
+        for mol_index in range(num_mols):
+            gaps.append([])
+            for i in range(len(one_letter_codes[mol_index])):
+                gaps[mol_index].append(0)
 
     # Handle sequence alignments - fall back alignment based on residue 
numbering.
     else: