r8406 - /branches/multi_structure/generic_fns/structure/internal.py -- January 12, 2009 - 14:13

Author: bugman
Date: Mon Jan 12 14:13:02 2009
New Revision: 8406

URL: http://svn.gna.org/viewcvs/relax?rev=8406&view=rev
Log:
Shifted __fill_object_from_pdb() from the Internal class to MolContainer.


Modified:
    branches/multi_structure/generic_fns/structure/internal.py

Modified: branches/multi_structure/generic_fns/structure/internal.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/multi_structure/generic_fns/structure/internal.py?rev=8406&r1=8405&r2=8406&view=diff
==============================================================================
--- branches/multi_structure/generic_fns/structure/internal.py (original)
+++ branches/multi_structure/generic_fns/structure/internal.py Mon Jan 12 
14:13:02 2009
@@ -192,42 +192,6 @@
 
         # Return the information.
         return bonded_num, bonded_name, element, pos, attached_name, None
-
-
-    def __fill_object_from_pdb(self, records, model_index, mol_index):
-        """Method for generating a complete Structure_container object from 
the given PDB records.
-
-        @param records:         A list of structural PDB records.
-        @type records:          list of str
-        @param model_index:     The model index.
-        @type model_index:      int
-        @param mol_index:       The molecule index.
-        @type mol_index:        int
-        """
-
-        # Loop over the records.
-        for record in records:
-            # Parse the record.
-            record = self.__parse_pdb_record(record)
-
-            # Nothing to do.
-            if not record:
-                continue
-
-            # Add the atom.
-            if record[0] == 'ATOM' or record[0] == 'HETATM':
-                self.atom_add(pdb_record=record[0], atom_num=record[1], 
atom_name=record[2], res_name=record[4], chain_id=record[5], 
res_num=record[6], pos=[record[8], record[9], record[10]], 
segment_id=record[13], element=record[14], model_index=model_index, 
mol_index=mol_index)
-
-            # Connect atoms.
-            if record[0] == 'CONECT':
-                # Loop over the atoms of the record.
-                for i in xrange(len(record)-2):
-                    # Skip if there is no record.
-                    if record[i+2] == None:
-                        continue
-
-                    # Make the connection.
-                    self.atom_connect(index1=self.__atom_index(record[1], 
struct_index), index2=self.__atom_index(record[i+2], struct_index), 
struct_index=struct_index)
 
 
     def __find_bonded_atoms(self, index, struct_index, radius=1.2):
@@ -1009,7 +973,7 @@
                 self.structural_data[-1].mol.add_item(mol_name=new_mol_name, 
mol_cont=mol)
 
                 # Fill the molecular data object.
-                self.__fill_object_from_pdb(mol_records, 
model_index=len(self.structural_data), 
mol_index=len(self.structural_data[-1].mol))
+                
self.structural_data[-1].mol[-1].__fill_object_from_pdb(mol_records)
 
                 # Increment the molecule index.
                 mol_index = mol_index + 1
@@ -1450,3 +1414,35 @@
 
         # The z coordinate (array of float).
         self.z = []
+
+
+    def __fill_object_from_pdb(self, records):
+        """Method for generating a complete Structure_container object from 
the given PDB records.
+
+        @param records:         A list of structural PDB records.
+        @type records:          list of str
+        """
+
+        # Loop over the records.
+        for record in records:
+            # Parse the record.
+            record = self.__parse_pdb_record(record)
+
+            # Nothing to do.
+            if not record:
+                continue
+
+            # Add the atom.
+            if record[0] == 'ATOM' or record[0] == 'HETATM':
+                self.atom_add(pdb_record=record[0], atom_num=record[1], 
atom_name=record[2], res_name=record[4], chain_id=record[5], 
res_num=record[6], pos=[record[8], record[9], record[10]], 
segment_id=record[13], element=record[14])
+
+            # Connect atoms.
+            if record[0] == 'CONECT':
+                # Loop over the atoms of the record.
+                for i in xrange(len(record)-2):
+                    # Skip if there is no record.
+                    if record[i+2] == None:
+                        continue
+
+                    # Make the connection.
+                    self.atom_connect(index1=self.__atom_index(record[1], 
struct_index), index2=self.__atom_index(record[i+2], struct_index))