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:
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