r2905 - in /branches/test_suite: specific_fns/ test_suite/system_tests/ -- December 02, 2006 - 05:52

Author: bugman
Date: Sat Dec  2 05:51:51 2006
New Revision: 2905

URL: http://svn.gna.org/viewcvs/relax?rev=2905&view=rev
Log:
Ported r2849 from the 1.3 line.

The commands used were:
svn merge -r2848:2849 svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3
svn merge -r2848:2849 svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3/test_suite/ 
test_suite/system_tests

The second command fixes the problem of the rearrangement of the test suite 
file layout.


Modified:
    branches/test_suite/specific_fns/model_free.py
    branches/test_suite/test_suite/system_tests/angles.py
    branches/test_suite/test_suite/system_tests/model_free.py
    branches/test_suite/test_suite/system_tests/sequence.py

Modified: branches/test_suite/specific_fns/model_free.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/test_suite/specific_fns/model_free.py?rev=2905&r1=2904&r2=2905&view=diff
==============================================================================
--- branches/test_suite/specific_fns/model_free.py (original)
+++ branches/test_suite/specific_fns/model_free.py Sat Dec  2 05:51:51 2006
@@ -3268,7 +3268,7 @@
 
         # Read the PDB file (if it exists).
         if not pdb == 'None':
-            self.relax.generic.pdb.read(run=self.run, file=pdb, 
model=pdb_model, fail=0, print_flag=print_flag)
+            self.relax.generic.structure.read(run=self.run, file=pdb, 
model=pdb_model, fail=0, print_flag=print_flag)
             return 1
         else:
             return 0
@@ -3461,7 +3461,7 @@
                 raise RelaxError, "The XH unit vector " + 
self.file_line[self.col['xh_vect']] + " is invalid."
 
             # Set the vector.
-            self.relax.generic.pdb.set_vector(run=self.run, 
res=self.res_index, xh_vect=xh_vect)
+            self.relax.generic.structure.set_vector(run=self.run, 
res=self.res_index, xh_vect=xh_vect)
 
 
     def remove_tm(self, run, res_num):

Modified: branches/test_suite/test_suite/system_tests/angles.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/test_suite/test_suite/system_tests/angles.py?rev=2905&r1=2904&r2=2905&view=diff
==============================================================================
--- branches/test_suite/test_suite/system_tests/angles.py (original)
+++ branches/test_suite/test_suite/system_tests/angles.py Sat Dec  2 05:51:51 
2006
@@ -40,10 +40,10 @@
         self.relax.interpreter._Run.create(run, 'mf')
 
         # Read a PDB file.
-        self.relax.interpreter._PDB.read(run, file='test.pdb', 
dir=sys.path[-1] + '/test_suite/system_tests/data', model=1)
+        self.relax.interpreter._Structure.read_pdb(run, file='test.pdb', 
dir=sys.path[-1] + '/test_suite/system_tests/data', model=1)
 
         # Set the NH vector.
-        self.relax.interpreter._PDB.vectors(run, heteronuc='N', proton='H')
+        self.relax.interpreter._Structure.vectors(run, heteronuc='N', 
proton='H')
 
         # Initialise a diffusion tensor.
         self.relax.interpreter._Diffusion_tensor.init(run, (1.698e7, 
1.417e7, 67.174, -83.718), param_types=3)

Modified: branches/test_suite/test_suite/system_tests/model_free.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/test_suite/test_suite/system_tests/model_free.py?rev=2905&r1=2904&r2=2905&view=diff
==============================================================================
--- branches/test_suite/test_suite/system_tests/model_free.py (original)
+++ branches/test_suite/test_suite/system_tests/model_free.py Sat Dec  2 
05:51:51 2006
@@ -281,8 +281,8 @@
         self.relax.interpreter._Sequence.read(self.run, file='noe.500.out', 
dir=path)
 
         # Read the PDF file and set the vectors.
-        self.relax.interpreter._PDB.read(run, file='pdb', dir=path, model=1, 
load_seq=0)
-        self.relax.interpreter._PDB.vectors(run, heteronuc='N', proton='H')
+        self.relax.interpreter._Structure.read_pdb(run, file='pdb', 
dir=path, model=1, load_seq=0)
+        self.relax.interpreter._Structure.vectors(run, heteronuc='N', 
proton='H')
 
         # Read the relaxation data.
         self.relax.interpreter._Relax_data.read(self.run, 'R1', '600', 600.0 
* 1e6, 'r1.600.out', dir=path)

Modified: branches/test_suite/test_suite/system_tests/sequence.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/test_suite/test_suite/system_tests/sequence.py?rev=2905&r1=2904&r2=2905&view=diff
==============================================================================
--- branches/test_suite/test_suite/system_tests/sequence.py (original)
+++ branches/test_suite/test_suite/system_tests/sequence.py Sat Dec  2 
05:51:51 2006
@@ -53,7 +53,7 @@
         self.relax.generic.runs.create(run, 'mf')
 
         # Read the sequence.
-        self.relax.interpreter._PDB.read(run, file='test.pdb', 
dir=sys.path[-1] + '/test_suite/system_tests/data', model=1, load_seq=1)
+        self.relax.interpreter._Structure.read_pdb(run, file='test.pdb', 
dir=sys.path[-1] + '/test_suite/system_tests/data', model=1, load_seq=1)
 
         # Success.
         return 1