r27432 - /trunk/test_suite/system_tests/scripts/n_state_model/structure_align.py -- January 31, 2015 - 17:54

Author: bugman
Date: Sat Jan 31 17:54:04 2015
New Revision: 27432

URL: http://svn.gna.org/viewcvs/relax?rev=27432&view=rev
Log:
Updated the Structure.test_align_CaM_BLOSUM62 system test script.

The MSA algorithm and pairwise alignment algorithms are now specified in the
structure.sequence_alignment user function calls.


Modified:
    trunk/test_suite/system_tests/scripts/n_state_model/structure_align.py

Modified: 
trunk/test_suite/system_tests/scripts/n_state_model/structure_align.py
URL: 
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/scripts/n_state_model/structure_align.py?rev=27432&r1=27431&r2=27432&view=diff
==============================================================================
--- trunk/test_suite/system_tests/scripts/n_state_model/structure_align.py    
  (original)
+++ trunk/test_suite/system_tests/scripts/n_state_model/structure_align.py    
  Sat Jan 31 17:54:04 2015
@@ -17,11 +17,11 @@
     structure.read_pdb('%s.pdb' % code, dir=status.install_path + 
sep+'test_suite'+sep+'shared_data'+sep+'structures')
 
 # First align then superimpose the N-domains - aligning 1OSA onto 1J70 to 
act as a scaffold.
-structure.sequence_alignment(pipes=['1J7O', '1OSA'], matrix='BLOSUM62', 
gap_open_penalty=10.0, gap_extend_penalty=1.0, end_gap_open_penalty=0.0, 
end_gap_extend_penalty=0.0)
+structure.sequence_alignment(pipes=['1J7O', '1OSA'], msa_algorithm='Central 
Star', pairwise_algorithm='NW70', matrix='BLOSUM62', gap_open_penalty=10.0, 
gap_extend_penalty=1.0, end_gap_open_penalty=0.0, end_gap_extend_penalty=0.0)
 structure.superimpose(pipes=['1J7O', '1OSA'], atom_id='@N,C,CA,O', 
method='fit to first')
 
 # Then align then superimpose the C-domains - aligning 1J7P onto the 1OSA 
scaffold.
-structure.sequence_alignment(pipes=['1OSA', '1J7P'], matrix='BLOSUM62', 
gap_open_penalty=10.0, gap_extend_penalty=1.0, end_gap_open_penalty=0.0, 
end_gap_extend_penalty=0.0)
+structure.sequence_alignment(pipes=['1OSA', '1J7P'], msa_algorithm='Central 
Star', pairwise_algorithm='NW70', matrix='BLOSUM62', gap_open_penalty=10.0, 
gap_extend_penalty=1.0, end_gap_open_penalty=0.0, end_gap_extend_penalty=0.0)
 structure.superimpose(pipes=['1OSA', '1J7P'], atom_id='@N,C,CA,O', 
method='fit to first')
 
 # Write out the result.