r14965 - in /1.3/generic_fns/structure: api_base.py internal.py -- November 03, 2011 - 11:17

Author: bugman
Date: Thu Nov  3 11:17:43 2011
New Revision: 14965

URL: http://svn.gna.org/viewcvs/relax?rev=14965&view=rev
Log:
Created the add_model() structural API method.

This is implemented within the internal structural object.


Modified:
    1.3/generic_fns/structure/api_base.py
    1.3/generic_fns/structure/internal.py

Modified: 1.3/generic_fns/structure/api_base.py
URL: 
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/structure/api_base.py?rev=14965&r1=14964&r2=14965&view=diff
==============================================================================
--- 1.3/generic_fns/structure/api_base.py (original)
+++ 1.3/generic_fns/structure/api_base.py Thu Nov  3 11:17:43 2011
@@ -84,6 +84,23 @@
         @type segment_id:       str or None
         @keyword pdb_record:    The optional PDB record name, e.g. 'ATOM' or 
'HETATM'.
         @type pdb_record:       str or None
+        """
+
+        # Raise the error.
+        raise RelaxImplementError
+
+
+    def add_model(self, model=None, coords_from=None):
+        """Add a new model to the store.
+
+        The new model will be constructured with the structural information 
from the other models currently present.  The coords_from argument allows the 
atomic positions to be taken from a certain model.  If this argument is not 
set, then the atomic positions from the first model will be used.
+
+        @keyword model:         The number of the model to create.
+        @type model:            int or None
+        @keyword coords_from:   The model number to take the coordinates 
from.
+        @type coords_from:      int or None
+        @return:                The model container.
+        @rtype:                 ModelContainer instance
         """
 
         # Raise the error.

Modified: 1.3/generic_fns/structure/internal.py
URL: 
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/structure/internal.py?rev=14965&r1=14964&r2=14965&view=diff
==============================================================================
--- 1.3/generic_fns/structure/internal.py (original)
+++ 1.3/generic_fns/structure/internal.py Thu Nov  3 11:17:43 2011
@@ -610,6 +610,46 @@
 
             # Add the atom.
             mol.atom_add(atom_name=atom_name, res_name=res_name, 
res_num=res_num, pos=pos, element=element, atom_num=atom_num, 
chain_id=chain_id, segment_id=segment_id, pdb_record=pdb_record)
+
+
+    def add_model(self, model=None, coords_from=None):
+        """Add a new model to the store.
+
+        The new model will be constructured with the structural information 
from the other models currently present.  The coords_from argument allows the 
atomic positions to be taken from a certain model.  If this argument is not 
set, then the atomic positions from the first model will be used.
+
+        @keyword model:         The number of the model to create.
+        @type model:            int or None
+        @keyword coords_from:   The model number to take the coordinates 
from.
+        @type coords_from:      int or None
+        @return:                The model container.
+        @rtype:                 ModelContainer instance
+        """
+
+        # Check if the model currently exists.
+        if model != None:
+            for i in range(len(self.structural_data)):
+                if model == self.structural_data[i].num:
+                    raise RelaxError("The model '%s' already exists." % 
model)
+
+        # No structural data.
+        new = self.structural_data.is_empty()
+
+        # Add a new model.
+        self.structural_data.add_item(model_num=model)
+
+        # Construct the structural data for the model from the other models.
+        if not new:
+            # The model to duplicate.
+            if coords_from == None:
+                coords_from = self.structural_data[0].num
+
+            # Loop over the atoms.
+            for mol_name, res_num, res_name, atom_num, atom_name, element, 
pos in self.atom_loop(self, model_num=coords_from, mol_name_flag=True, 
res_num_flag=True, res_name_flag=True, atom_num_flag=True, 
atom_name_flag=True, element_flag=True, pos_flag=True):
+                # Add the atom.
+                self.add_atom(self, mol_name=mol_name, atom_name=atom_name, 
res_name=res_name, res_num=res_num, pos=pos, element=element, 
atom_num=atom_num)
+
+        # Return the model.
+        return self.structural_data[-1]
 
 
     def add_molecule(self, name=None, model=None):