Author: bugman
Date: Thu Jan 8 15:57:58 2009
New Revision: 8333
URL: http://svn.gna.org/viewcvs/relax?rev=8333&view=rev
Log:
Created the ModelList data structure for storing multiple models of the same
molecule.
Modified:
branches/multi_structure/generic_fns/structure/api_base.py
Modified: branches/multi_structure/generic_fns/structure/api_base.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_structure/generic_fns/structure/api_base.py?rev=8333&r1=8332&r2=8333&view=diff
==============================================================================
--- branches/multi_structure/generic_fns/structure/api_base.py (original)
+++ branches/multi_structure/generic_fns/structure/api_base.py Thu Jan 8
15:57:58 2009
@@ -58,7 +58,7 @@
self.model = []
self.file = []
self.path = []
- self.structural_data = []
+ self.structural_data = ModelList()
def add_struct(self, name=None, model=None, file=None, path=None,
str=None, struct_index=None):
@@ -612,3 +612,120 @@
# Raise the error.
raise RelaxImplementError
+
+
+class ModelList(list):
+ """List type data container for the different structural models.
+
+ Here different models are defined as the same molecule but with
different conformations.
+ """
+
+ def __init__(self):
+ """Add the first model container to create an empty but complete
data structure."""
+
+ # Add the initial model container.
+ self.append(ModelContainer())
+
+
+ def __repr__(self):
+ """The string representation of the object.
+
+ Rather than using the standard Python conventions (either the string
representation of the
+ value or the "<...desc...>" notation), a rich-formatted description
of the object is given.
+ """
+
+ text = "Models.\n\n"
+ text = text + "%-8s%-8s" % ("Index", "Model number") + "\n"
+ for i in xrange(len(self)):
+ text = text + "%-8i%-8s" % (i, self[i].num) + "\n"
+ return text
+
+
+ def add_item(self, model_num=None):
+ """Append an empty ModelContainer to the ModelList.
+
+ @keyword model_num: The model number.
+ @type model_num: int
+ """
+
+ # If no model data exists, replace the empty first model with this
model (just a renumbering).
+ if self.is_empty():
+ self[0].num = model_num
+
+ # Otherwise append an empty ModelContainer.
+ else:
+ # Test if the model number already exists.
+ for i in xrange(len(self)):
+ if self[i].num == model_num:
+ raise RelaxError, "The model '" + `model_num` + "'
already exists."
+
+ # Append an empty ModelContainer.
+ self.append(ModelContainer(model_num))
+
+
+ def is_empty(self):
+ """Method for testing if this ModelList object is empty.
+
+ @return: True if this list only has one ModelContainer and the
model name has not
+ been set, False otherwise.
+ @rtype: bool
+ """
+
+ # There is only one ModelContainer and it is empty.
+ if len(self) == 1 and self[0].is_empty():
+ return True
+
+ # Otherwise.
+ return False
+
+
+ def from_xml(self, model_nodes):
+ """Recreate a model list data structure from the XML model nodes.
+
+ @param model_nodes: The model XML nodes.
+ @type model_nodes: xml.dom.minicompat.NodeList instance
+ """
+
+ # Test if empty.
+ if not self.is_empty():
+ raise RelaxFromXMLNotEmptyError, self.__class__.__name__
+
+ # Loop over the models.
+ for model_node in model_nodes:
+ # Get the model details and add the model to the ModelList
structure.
+ num = eval(model_node.getAttribute('num'))
+ if num == 'None':
+ num = None
+ self.add_item(model_num=num)
+
+ # Get the structure nodes.
+ struct_nodes = model_node.getElementsByTagName('struct')
+
+ # Recreate the structure data structures for the current model.
+ self[-1].struct.from_xml(struct_nodes)
+
+
+ def to_xml(self, doc, element):
+ """Create XML elements for each model.
+
+ @param doc: The XML document object.
+ @type doc: xml.dom.minidom.Document instance
+ @param element: The element to add the model XML elements to.
+ @type element: XML element object
+ """
+
+ # Loop over the models.
+ for i in xrange(len(self)):
+ # Create an XML element for this model and add it to the higher
level element.
+ model_element = doc.createElement('model')
+ element.appendChild(model_element)
+
+ # Set the model attributes.
+ model_element.setAttribute('desc', 'Model container')
+ model_element.setAttribute('num', str(self[i].num))
+
+ # Add all simple python objects within the ModelContainer to the
XML element.
+ fill_object_contents(doc, model_element, object=self[i],
blacklist=['num', 'struct'] + self[i].__class__.__dict__.keys())
+
+ # Add the structure data.
+ self[i].struct.to_xml(doc, model_element)
r8333 - /branches/multi_structure/generic_fns/structure/api_base.py