r9012 - in /branches/ave_noe: ./ generic_fns/structure/main.py test_suite/system_tests/structure.py -- April 15, 2009 - 15:29

Author: bugman
Date: Wed Apr 15 15:29:39 2009
New Revision: 9012

URL: http://svn.gna.org/viewcvs/relax?rev=9012&view=rev
Log:
Merged revisions 9010-9011 via svnmerge from 
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3

........
  r9010 | bugman | 2009-04-15 14:33:53 +0200 (Wed, 15 Apr 2009) | 5 lines
  
  Expanded the test_read_pdb_internal3() and test_read_pdb_scientific3() 
system tests.
  
  Now the reading of atomic positions from different models is tested.
........
  r9011 | bugman | 2009-04-15 15:28:15 +0200 (Wed, 15 Apr 2009) | 6 lines
  
  Removed a test in load_spins() causing a bug.
  
  This test is totally unnecessary as the structures are not created if they 
already exist.  This was
  causing only the position from the first model to be extracted, if ave_pos 
was False.
........

Modified:
    branches/ave_noe/   (props changed)
    branches/ave_noe/generic_fns/structure/main.py
    branches/ave_noe/test_suite/system_tests/structure.py

Propchange: branches/ave_noe/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Wed Apr 15 15:29:39 2009
@@ -1,1 +1,1 @@
-/1.3:1-9003
+/1.3:1-9011

Modified: branches/ave_noe/generic_fns/structure/main.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/ave_noe/generic_fns/structure/main.py?rev=9012&r1=9011&r2=9012&view=diff
==============================================================================
--- branches/ave_noe/generic_fns/structure/main.py (original)
+++ branches/ave_noe/generic_fns/structure/main.py Wed Apr 15 15:29:39 2009
@@ -80,10 +80,6 @@
         if last_model != model_num:
             model_index = model_index + 1
             last_model = model_num
-
-        # Only load one set of spins if combine_models is set.
-        if combine_models and model_index >= 1:
-            break
 
         # Remove the '+' regular expression character from the mol, res, and 
spin names!
         if mol_name and search('\+', mol_name):

Modified: branches/ave_noe/test_suite/system_tests/structure.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/ave_noe/test_suite/system_tests/structure.py?rev=9012&r1=9011&r2=9012&view=diff
==============================================================================
--- branches/ave_noe/test_suite/system_tests/structure.py (original)
+++ branches/ave_noe/test_suite/system_tests/structure.py Wed Apr 15 15:29:39 
2009
@@ -200,14 +200,20 @@
     def test_read_pdb_internal3(self):
         """Load the 'gromacs_phthalic_acid.pdb' PDB file (using the internal 
structural object PDB reader)."""
 
+        # Alias the current data pipe.
+        cdp = pipes.get_pipe()
+
         # Path of the files.
         path = sys.path[-1] + '/test_suite/shared_data/structures'
 
         # Read the PDB.
         
self.relax.interpreter._Structure.read_pdb(file='gromacs_phthalic_acid.pdb', 
dir=path, parser='internal')
 
-        # Try loading a few protons.
-        self.relax.interpreter._Structure.load_spins('@*H*')
+        # Try loading a few protons, without positions averaging across 
models.
+        self.relax.interpreter._Structure.load_spins('@*H*', ave_pos=False)
+
+        # A test.
+        self.assertEqual(len(cdp.mol[0].res[0].spin[0].pos), 2)
 
         # And now all the rest of the atoms.
         self.relax.interpreter._Structure.load_spins()
@@ -443,6 +449,9 @@
     def test_read_pdb_scientific3(self):
         """Load the 'gromacs_phthalic_acid.pdb' PDB file (using the 
Scientific python structural object PDB reader)."""
 
+        # Alias the current data pipe.
+        cdp = pipes.get_pipe()
+
         # Path of the files.
         path = sys.path[-1] + '/test_suite/shared_data/structures'
 
@@ -450,7 +459,10 @@
         
self.relax.interpreter._Structure.read_pdb(file='gromacs_phthalic_acid.pdb', 
dir=path, parser='scientific')
 
         # Try loading a few protons.
-        self.relax.interpreter._Structure.load_spins('@*H*')
+        self.relax.interpreter._Structure.load_spins('@*H*', ave_pos=False)
+
+        # A test.
+        self.assertEqual(len(cdp.mol[0].res[0].spin[0].pos), 2)
 
         # And now all the rest of the atoms.
         self.relax.interpreter._Structure.load_spins()