Author: bugman
Date: Sat Jan 31 17:59:44 2015
New Revision: 27434
URL: http://svn.gna.org/viewcvs/relax?rev=27434&view=rev
Log:
The structure.sequence_alignment user function now sets some arguments to None
before storage.
This is for all arguments not used in the sequence alignment. For example the
residue number based
alignment does not use the gap penalties, pairwise alignment algorithm or the
substitution matrices.
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=27434&r1=27433&r2=27434&view=diff
==============================================================================
--- trunk/pipe_control/structure/main.py (original)
+++ trunk/pipe_control/structure/main.py Sat Jan 31 17:59:44 2015
@@ -1256,6 +1256,15 @@
if not hasattr(ds, 'sequence_alignments'):
ds.sequence_alignments = Sequence_alignments()
+ # Set some unused arguments to None for storage.
+ if msa_algorithm == 'residue number':
+ pairwise_algorithm = None
+ matrix = None
+ gap_open_penalty = None
+ gap_extend_penalty = None
+ end_gap_open_penalty = None
+ end_gap_extend_penalty = None
+
# Store the alignment.
ds.sequence_alignments.add(object_ids=object_id_list, models=model_list,
molecules=molecule_list, sequences=one_letter_codes, strings=strings,
gaps=gaps, msa_algorithm=msa_algorithm, pairwise_algorithm=pairwise_algorithm,
matrix=matrix, gap_open_penalty=gap_open_penalty,
gap_extend_penalty=gap_extend_penalty,
end_gap_open_penalty=end_gap_open_penalty,
end_gap_extend_penalty=end_gap_extend_penalty)
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