r27421 - /trunk/pipe_control/structure/main.py -- January 31, 2015 - 12:24

Author: bugman
Date: Sat Jan 31 12:24:09 2015
New Revision: 27421

URL: http://svn.gna.org/viewcvs/relax?rev=27421&view=rev
Log:
The residue number based sequence alignment is now executed when assembling 
atomic coordinates.

This is in the assemble_structural_coordinates() function of the 
pipe_control.structure.main module.


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=27421&r1=27420&r2=27421&view=diff
==============================================================================
--- trunk/pipe_control/structure/main.py        (original)
+++ trunk/pipe_control/structure/main.py        Sat Jan 31 12:24:09 2015
@@ -38,7 +38,7 @@
 from lib.plotting.api import correlation_matrix
 from lib.selection import tokenise
 from lib.sequence import write_spin_data
-from lib.sequence_alignment.msa import central_star
+from lib.sequence_alignment.msa import central_star, msa_residue_numbers
 from lib.structure.internal.coordinates import assemble_atomic_coordinates, 
assemble_coord_array, loop_coord_structures
 from lib.structure.internal.displacements import Displacements
 from lib.structure.internal.object import Internal
@@ -152,6 +152,10 @@
         for i in range(len(align.object_ids)):
             print(align.strings[i])
 
+        # Alias the required data structures.
+        strings = align.strings
+        gaps = align.gaps
+
     # Handle sequence alignments - no alignment required.
     elif len(objects) == 1 and same_mol:
         # Printout.
@@ -184,13 +188,13 @@
                 continue
 
             # No residue in the current sequence.
-            if align.gaps[mol_index][i]:
+            if gaps[mol_index][i]:
                 continue
 
             # A gap in one of the other sequences.
             gap = False
             for mol_index2 in range(num_mols):
-                if align.gaps[mol_index2][i]:
+                if gaps[mol_index2][i]:
                     gap = True
 
             # Skip the residue.