r27428 - /trunk/test_suite/system_tests/structure.py -- January 31, 2015 - 15:15

Author: bugman
Date: Sat Jan 31 15:15:17 2015
New Revision: 27428

URL: http://svn.gna.org/viewcvs/relax?rev=27428&view=rev
Log:
Modified the Structure.test_sequence_alignment_central_star_nw70_blosum62 
system test.

Some residues are now deleted so that the sequences are not identical.


Modified:
    trunk/test_suite/system_tests/structure.py

Modified: trunk/test_suite/system_tests/structure.py
URL: 
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/structure.py?rev=27428&r1=27427&r2=27428&view=diff
==============================================================================
--- trunk/test_suite/system_tests/structure.py  (original)
+++ trunk/test_suite/system_tests/structure.py  Sat Jan 31 15:15:17 2015
@@ -4644,7 +4644,7 @@
 
 
     def test_sequence_alignment_central_star_nw70_blosum62(self):
-        """Test of the structure.sequence_alignment user function."""
+        """Test of the structure.sequence_alignment user function using the 
'Central Star', 'NW70', and 'BLOSUM62' options."""
 
         # Path of the structure file.
         path = status.install_path + 
sep+'test_suite'+sep+'shared_data'+sep+'frame_order'+sep+'cam'
@@ -4652,6 +4652,10 @@
         # Load the two rotated structures.
         self.interpreter.structure.read_pdb('1J7P_1st_NH.pdb', dir=path, 
set_model_num=1, set_mol_name='CaM A')
         self.interpreter.structure.read_pdb('1J7P_1st_NH_rot.pdb', dir=path, 
set_model_num=1, set_mol_name='CaM B')
+
+        # Delete some residues.
+        self.interpreter.structure.delete("#CaM B:82")
+        self.interpreter.structure.delete("#CaM A:100-120")
 
         # Perform the alignment.
         self.interpreter.structure.sequence_alignment(pipes=['mf'], 
models=[[1, 1]], molecules=[['CaM A', 'CaM B']], msa_algorithm='Central 
Star', pairwise_algorithm='NW70', matrix='BLOSUM62', gap_open_penalty=10.0, 
gap_extend_penalty=1.0, end_gap_open_penalty=0.5, end_gap_extend_penalty=0.1)
@@ -4672,18 +4676,21 @@
         molecules = ['CaM A', 'CaM B']
         ids = ["Object 'mf'; Model 1; Molecule 'CaM A'", "Object 'mf'; Model 
1; Molecule 'CaM B'"]
         sequences = [
-            
'EEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK**',
-            
'EEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK**'
+            'EEEIREAFRVFDKDGNGYVDEMIREADIDGDGQVNYEEFVQMMTAK**',
+            
'EEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK**'
         ]
         strings = [
-            
'EEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK**',
-            
'EEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK**'
+            
'EEEIREAFRVFDKDGNGY---------------------VDEMIREADIDGDGQVNYEEFVQMMTAK**',
+            
'-EEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK**'
         ]
         gaps = []
         for i in range(len(strings)):
             gaps.append([])
             for j in range(len(strings[0])):
                 gaps[i].append(0)
+        for i in range(18, 39):
+            gaps[0][i] = 1
+        gaps[1][0] = 1
         msa_algorithm = 'Central Star'
         pairwise_algorithm = 'NW70'
         matrix = 'BLOSUM62'