r8528 - /branches/multi_structure/generic_fns/structure/scientific.py -- January 19, 2009 - 14:33

Author: bugman
Date: Mon Jan 19 14:33:03 2009
New Revision: 8528

URL: http://svn.gna.org/viewcvs/relax?rev=8528&view=rev
Log:
Fixes for the Scientific python MolContainer usage.

Now all molecules are stored in the MolContainer object to allow for the 
to_xml() method, which has
now been added.  The MolContainer is no longer a list type.  These changes 
will break things!


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

Modified: branches/multi_structure/generic_fns/structure/scientific.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/multi_structure/generic_fns/structure/scientific.py?rev=8528&r1=8527&r2=8528&view=diff
==============================================================================
--- branches/multi_structure/generic_fns/structure/scientific.py (original)
+++ branches/multi_structure/generic_fns/structure/scientific.py Mon Jan 19 
14:33:03 2009
@@ -37,6 +37,7 @@
 
 # relax module imports.
 from api_base import Base_struct_API
+from data.relax_xml import fill_object_contents, xml_to_object
 from generic_fns import pipes, relax_re
 from generic_fns.mol_res_spin import Selection, parse_token, tokenise
 from relax_errors import RelaxError, RelaxPdbLoadError
@@ -567,7 +568,8 @@
             if hasattr(model, 'peptide_chains'):
                 for mol in model.peptide_chains:
                     mol.mol_type = 'protein'
-                    mol_conts[-1].append(mol)
+                    mol_conts[-1].append(MolContainer())
+                    mol_conts[-1][-1].data = mol
                     mol_conts[-1][-1].mol_type = 'protein'
                     self.target_mol_name(set=set_mol_name, 
target=new_mol_name, index=mol_index, mol_num=mol_index+1, file=file)
                     mol_index = mol_index + 1
@@ -575,7 +577,8 @@
             # Then the nucleotide chains (generating the molecule names and 
incrementing the molecule index).
             if hasattr(model, 'nucleotide_chains'):
                 for mol in model.nucleotide_chains:
-                    mol_conts[-1].append(mol)
+                    mol_conts[-1].append(MolContainer())
+                    mol_conts[-1][-1].data = mol
                     mol_conts[-1][-1].mol_type = 'nucleic acid'
                     self.target_mol_name(set=set_mol_name, 
target=new_mol_name, index=mol_index, mol_num=mol_index+1, file=file)
                     mol_index = mol_index + 1
@@ -605,5 +608,26 @@
         return True
 
 
-class MolContainer(list):
+class MolContainer:
     """The empty list-type container for the non-protein and non-RNA 
molecular information."""
+
+
+    def to_xml(self, doc, element):
+        """Create XML elements for the contents of this molecule container.
+
+        @param doc:     The XML document object.
+        @type doc:      xml.dom.minidom.Document instance
+        @param element: The element to add the molecule XML elements to.
+        @type element:  XML element object
+        """
+
+        # Create an XML element for this molecule and add it to the higher 
level element.
+        mol_element = doc.createElement('mol')
+        element.appendChild(mol_element)
+
+        # Set the molecule attributes.
+        mol_element.setAttribute('desc', 'Molecule container')
+        mol_element.setAttribute('name', str(self.mol_name))
+
+        # Add all simple python objects within the MolContainer to the XML 
element.
+        fill_object_contents(doc, mol_element, object=self, 
blacklist=['data'] + self.__class__.__dict__.keys())