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)