r9039 - /1.3/generic_fns/noesy.py -- May 06, 2009 - 16:50

Author: bugman
Date: Wed May  6 16:50:13 2009
New Revision: 9039

URL: http://svn.gna.org/viewcvs/relax?rev=9039&view=rev
Log:
Added pseudoatom support to the parse_noe_restraints() function.


Modified:
    1.3/generic_fns/noesy.py

Modified: 1.3/generic_fns/noesy.py
URL: 
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/noesy.py?rev=9039&r1=9038&r2=9039&view=diff
==============================================================================
--- 1.3/generic_fns/noesy.py (original)
+++ 1.3/generic_fns/noesy.py Wed May  6 16:50:13 2009
@@ -156,9 +156,40 @@
 
     # Parse and extract the NOE restraints.
     if format == 'xplor':
-        cdp.noe_restraints = xplor.parse_noe_restraints(lines)
+        noe_restraints = xplor.parse_noe_restraints(lines)
     elif format == 'generic':
-        cdp.noe_restraints = parse_noe_restraints(lines, 
proton1_col=proton1_col, proton2_col=proton2_col, lower_col=lower_col, 
upper_col=upper_col, sep=sep)
+        noe_restraints = parse_noe_restraints(lines, 
proton1_col=proton1_col, proton2_col=proton2_col, lower_col=lower_col, 
upper_col=upper_col, sep=sep)
+
+    # Pseudoatom conversion.
+    for i in range(len(noe_restraints)):
+        # Loop over atom IDs.
+        for j in range(2):
+            # Skip normal atoms.
+            if type(noe_restraints[i][j]) == str:
+                continue
+
+            # Loop over the pseudoatoms.
+            pseudo_name = None
+            for k in range(len(noe_restraints[i][j])):
+                # Get the spin.
+                spin = return_spin(noe_restraints[i][j][k])
+
+                # Check the pseudoatom consistency.
+                if pseudo_name and pseudo_name != spin.pseudo_name:
+                    raise RelaxError, "The pseudoatom names '%s' and '%s' do 
not match." % (pseudo_name, spin.pseudo_name)
+
+                # Set the name.
+                pseudo_name = spin.pseudo_name
+
+            # No pseudoatom.
+            if not pseudo_name:
+                raise RelaxError, "Cannot find the pseudoatom corresponding 
to the atoms in %s." % noe_restraints[i][j]
+
+            # Otherwise, place the pseudoatom name into the NOE restraint 
list.
+            noe_restraints[i][j] = pseudo_name
+
+    # Place the restraints into the current data pipe.
+    cdp.noe_restraints = noe_restraints
 
     # Check for the presence of the spin containers corresponding to the 
atom ids.
     for restraint in cdp.noe_restraints: