r2849 - in /1.3: specific_fns/model_free.py test_suite/angles.py test_suite/model_free.py test_suite/sequence.py -- November 15, 2006 - 09:32

Author: bugman
Date: Wed Nov 15 09:31:50 2006
New Revision: 2849

URL: http://svn.gna.org/viewcvs/relax?rev=2849&view=rev
Log:
Because of the previous commit (renaming 'pdb' to 'structure'), much code 
needed updating.

All calls to the functions of 'self.relax.generic.pdb' were replaced with the 
equivalent function in
'self.relax.generic.structure'.  For example all calls to 
'self.relax.generic.pdb.read()' are now
'self.relax.generic.structure.read_pdb'.

All instances of 'self.relax.interpreter._PDB' in the test suite were 
replaced with
'self.relax.interpreter._Structure'.


Modified:
    1.3/specific_fns/model_free.py
    1.3/test_suite/angles.py
    1.3/test_suite/model_free.py
    1.3/test_suite/sequence.py

Modified: 1.3/specific_fns/model_free.py
URL: 
http://svn.gna.org/viewcvs/relax/1.3/specific_fns/model_free.py?rev=2849&r1=2848&r2=2849&view=diff
==============================================================================
--- 1.3/specific_fns/model_free.py (original)
+++ 1.3/specific_fns/model_free.py Wed Nov 15 09:31:50 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: 1.3/test_suite/angles.py
URL: 
http://svn.gna.org/viewcvs/relax/1.3/test_suite/angles.py?rev=2849&r1=2848&r2=2849&view=diff
==============================================================================
--- 1.3/test_suite/angles.py (original)
+++ 1.3/test_suite/angles.py Wed Nov 15 09:31:50 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/data', model=1)
+        self.relax.interpreter._Structure.read_pdb(run, file='test.pdb', 
dir=sys.path[-1] + '/test_suite/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: 1.3/test_suite/model_free.py
URL: 
http://svn.gna.org/viewcvs/relax/1.3/test_suite/model_free.py?rev=2849&r1=2848&r2=2849&view=diff
==============================================================================
--- 1.3/test_suite/model_free.py (original)
+++ 1.3/test_suite/model_free.py Wed Nov 15 09:31:50 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: 1.3/test_suite/sequence.py
URL: 
http://svn.gna.org/viewcvs/relax/1.3/test_suite/sequence.py?rev=2849&r1=2848&r2=2849&view=diff
==============================================================================
--- 1.3/test_suite/sequence.py (original)
+++ 1.3/test_suite/sequence.py Wed Nov 15 09:31:50 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/data', model=1, load_seq=1)
+        self.relax.interpreter._Structure.read_pdb(run, file='test.pdb', 
dir=sys.path[-1] + '/test_suite/data', model=1, load_seq=1)
 
         # Success.
         return 1