r17133 - in /branches/interatomic: generic_fns/diffusion_tensor.py test_suite/system_tests/scripts/bmrb_rw.py -- July 02, 2012 - 18:08

Author: bugman
Date: Mon Jul  2 18:08:29 2012
New Revision: 17133

URL: http://svn.gna.org/viewcvs/relax?rev=17133&view=rev
Log:
More BMRB function conversions for the interatomic data design.


Modified:
    branches/interatomic/generic_fns/diffusion_tensor.py
    branches/interatomic/test_suite/system_tests/scripts/bmrb_rw.py

Modified: branches/interatomic/generic_fns/diffusion_tensor.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/interatomic/generic_fns/diffusion_tensor.py?rev=17133&r1=17132&r2=17133&view=diff
==============================================================================
--- branches/interatomic/generic_fns/diffusion_tensor.py (original)
+++ branches/interatomic/generic_fns/diffusion_tensor.py Mon Jul  2 18:08:29 
2012
@@ -37,7 +37,8 @@
 from data.diff_tensor import DiffTensorData
 from generic_fns import pipes
 from generic_fns.angles import fold_spherical_angles
-from generic_fns.mol_res_spin import get_molecule_names, spin_loop
+from generic_fns.interatomic import return_interatom_list
+from generic_fns.mol_res_spin import get_molecule_names, return_spin, 
spin_loop
 from maths_fns.coord_transform import cartesian_to_spherical
 from maths_fns.rotation_matrix import R_to_euler_zyz
 from physical_constants import element_from_isotope, number_from_isotope
@@ -175,7 +176,7 @@
             raise RelaxError("For the BMRB, the residue of spin '%s' must be 
named." % spin_id)
         if spin.name == None:
             raise RelaxError("For the BMRB, the spin '%s' must be named." % 
spin_id)
-        if spin.heteronuc_type == None:
+        if not hasattr(spin, 'isotope') or spin.isotope == None:
             raise RelaxError("For the BMRB, the spin isotope type of '%s' 
must be specified." % spin_id)
 
         # The molecule/residue/spin info.
@@ -184,23 +185,32 @@
         res_name_list.append(str(res_name))
         atom_name_list.append(str(spin.name))
 
+        # Interatomic info.
+        interatoms = return_interatom_list(spin_id)
+        if len(interatoms) == 0:
+            raise RelaxError("No interatomic interactions are defined for 
the spin '%s'." % spin_id)
+        if len(interatoms) > 1:
+            raise RelaxError("The BMRB only handles a signal interatomic 
interaction for the spin '%s'." % spin_id)
+
+        # Get the attached spin.
+        spin_attached = return_spin(interatoms[0].spin_id1)
+        if id(spin_attached) == id(spin):
+            spin_attached = return_spin(interatoms[0].spin_id2)
+
         # The attached atom info.
-        if hasattr(spin, 'attached_atom'):
-            attached_atom_name_list.append(str(spin.attached_atom))
-        elif hasattr(spin, 'attached_proton'):
-            attached_atom_name_list.append(str(spin.attached_proton))
+        if hasattr(spin_attached, 'name'):
+            attached_atom_name_list.append(str(spin_attached.name))
         else:
             attached_atom_name_list.append(None)
-
-        if hasattr(spin, 'proton_type'):
-            
attached_element_list.append(element_from_isotope(spin.proton_type))
-            
attached_isotope_list.append(str(number_from_isotope(spin.proton_type)))
+        if hasattr(spin_attached, 'isotope'):
+            
attached_element_list.append(element_from_isotope(spin_attached.isotope))
+            
attached_isotope_list.append(str(number_from_isotope(spin_attached.isotope)))
         else:
             attached_element_list.append(None)
             attached_isotope_list.append(None)
 
         # Other info.
-        isotope_list.append(int(string.strip(spin.heteronuc_type, 
string.ascii_letters)))
+        isotope_list.append(int(string.strip(spin.isotope, 
string.ascii_letters)))
         element_list.append(spin.element)
 
     # Convert the molecule names into the entity IDs.

Modified: branches/interatomic/test_suite/system_tests/scripts/bmrb_rw.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/interatomic/test_suite/system_tests/scripts/bmrb_rw.py?rev=17133&r1=17132&r2=17133&view=diff
==============================================================================
--- branches/interatomic/test_suite/system_tests/scripts/bmrb_rw.py (original)
+++ branches/interatomic/test_suite/system_tests/scripts/bmrb_rw.py Mon Jul  
2 18:08:29 2012
@@ -24,15 +24,21 @@
 
 # Play with the data.
 self._execute_uf(uf_name='deselect.all')
-self._execute_uf(uf_name='spin.copy', spin_from=':9', spin_to=':9@NE')
-self._execute_uf(uf_name='select.spin', spin_id=':9')
-self._execute_uf(uf_name='select.spin', spin_id=':10')
-self._execute_uf(uf_name='select.spin', spin_id=':11')
-self._execute_uf(uf_name='spin.name', name='N', force=False)
-self._execute_uf(uf_name='spin.element', element='N', force=False)
+self._execute_uf(uf_name='select.spin', spin_id=':9@N')
+self._execute_uf(uf_name='select.spin', spin_id=':10@N')
+self._execute_uf(uf_name='select.spin', spin_id=':11@N')
+self._execute_uf(uf_name='spin.name', name='N', spin_id='@N', force=False)
+self._execute_uf(uf_name='spin.element', element='N', spin_id='@N*', 
force=False)
 self._execute_uf(uf_name='molecule.name', name='OMP')
 self._execute_uf(uf_name='molecule.type', type='protein')
 self._execute_uf(uf_name='bmrb.thiol_state', state='reduced')
+
+# Set up a second spin type.
+self._execute_uf(uf_name='spin.copy', spin_from=':9@N', spin_to=':9@NE1')
+self._execute_uf(uf_name='spin.create', res_num=9, spin_name='HE1')
+self._execute_uf(uf_name='spin.element', element='H', spin_id=':9@HE1')
+self._execute_uf(uf_name='spin.isotope', isotope='1H', spin_id=':9@HE1')
+self._execute_uf(uf_name='dipole_pair.define', spin_id1=':9@NE1', 
spin_id2=':9@HE1')
 
 # Display the data (as a test).
 self._execute_uf(uf_name='relax_data.display', ri_id='R1_800')