r27422 - /trunk/lib/structure/internal/object.py -- January 31, 2015 - 12:41

Author: bugman
Date: Sat Jan 31 12:41:37 2015
New Revision: 27422

URL: http://svn.gna.org/viewcvs/relax?rev=27422&view=rev
Log:
Modified the internal structural object one_letter_codes() method.

This now validates the models to make sure all models match, and the method 
requires the selection
object so that residue subsets can be handled.


Modified:
    trunk/lib/structure/internal/object.py

Modified: trunk/lib/structure/internal/object.py
URL: 
http://svn.gna.org/viewcvs/relax/trunk/lib/structure/internal/object.py?rev=27422&r1=27421&r2=27422&view=diff
==============================================================================
--- trunk/lib/structure/internal/object.py      (original)
+++ trunk/lib/structure/internal/object.py      Sat Jan 31 12:41:37 2015
@@ -2295,11 +2295,13 @@
         return len(self.structural_data[0].mol)
 
 
-    def one_letter_codes(self, mol_name=None):
+    def one_letter_codes(self, mol_name=None, selection=None):
         """Generate and return the one letter code sequence for the given 
molecule.
 
         @keyword mol_name:  The name of the molecule to return the one 
letter codes for.
         @type mol_name:     str
+        @keyword selection: The internal structural selection object.  This 
is obtained by calling the selection() method with the atom ID string.
+        @type selection:    lib.structure.internal.Internal_selection 
instance
         @return:            The one letter code sequence for the given 
molecule.
         @rtype:             str
         """
@@ -2307,11 +2309,17 @@
         # Initialise.
         codes = ''
 
+        # Validate the models.
+        self.validate_models(verbosity=0)
+
         # Use the first model.
         model = self.structural_data[0]
 
+        # Residue numbers.
+        res_nums = []
+
         # Loop over the molecules.
-        for mol_index in range(len(model.mol)):
+        for mol_index, i in selection.loop():
             # Alias.
             mol = model.mol[mol_index]
 
@@ -2319,9 +2327,13 @@
             if mol_name and mol_name != mol.mol_name:
                 continue
 
-            # Loop over the residues.
-            for res_name, res_num in mol.loop_residues():
-                codes += aa_codes_three_to_one(res_name)
+            # Not a new residue.
+            if mol.res_num[i] in res_nums:
+                continue
+
+            # Convert to the one letter code and store the residue number.
+            codes += aa_codes_three_to_one(mol.res_name[i])
+            res_nums.append(mol.res_num[i])
             
         # Return the codes.
         return codes