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())
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