r27430 - /trunk/test_suite/system_tests/structure.py -- January 31, 2015 - 17:26

Author: bugman
Date: Sat Jan 31 17:26:57 2015
New Revision: 27430

URL: http://svn.gna.org/viewcvs/relax?rev=27430&view=rev
Log:
Corrections and simplifications for the 
Structure.test_sequence_alignment_residue_number system test.


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=27430&r1=27429&r2=27430&view=diff
==============================================================================
--- trunk/test_suite/system_tests/structure.py  (original)
+++ trunk/test_suite/system_tests/structure.py  Sat Jan 31 17:26:57 2015
@@ -4732,6 +4732,7 @@
         # Delete some residues.
         self.interpreter.structure.delete("#CaM B:82")
         self.interpreter.structure.delete("#CaM A:100-120")
+        self.interpreter.structure.delete(":CA")
 
         # Perform the alignment.
         self.interpreter.structure.sequence_alignment(pipes=['mf'], 
models=[[1, 1]], molecules=[['CaM A', 'CaM B']], msa_algorithm='residue 
number')
@@ -4752,12 +4753,12 @@
         molecules = ['CaM A', 'CaM B']
         ids = ["Object 'mf'; Model 1; Molecule 'CaM A'", "Object 'mf'; Model 
1; Molecule 'CaM B'"]
         sequences = [
-            'EEEIREAFRVFDKDGNGYVDEMIREADIDGDGQVNYEEFVQMMTAK**',
-            
'EEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK**'
+            'EEEIREAFRVFDKDGNGYVDEMIREADIDGDGQVNYEEFVQMMTAK',
+            
'EEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK'
         ]
         strings = [
-            
'EEEIREAFRVFDKDGNGY---------------------VDEMIREADIDGDGQVNYEEFVQMMTAK**',
-            
'-EEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK**'
+            
'EEEIREAFRVFDKDGNGY---------------------VDEMIREADIDGDGQVNYEEFVQMMTAK',
+            
'-EEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK'
         ]
         gaps = []
         for i in range(len(strings)):
@@ -4767,13 +4768,13 @@
         for i in range(18, 39):
             gaps[0][i] = 1
         gaps[1][0] = 1
-        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
+        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
 
         # Check the data.
         for i in range(2):