r14915 - /1.3/generic_fns/structure/api_base.py -- October 25, 2011 - 16:24

Author: bugman
Date: Tue Oct 25 16:24:30 2011
New Revision: 14915

URL: http://svn.gna.org/viewcvs/relax?rev=14915&view=rev
Log:
The structural model displacement data structure is now restored from the XML 
save files.

There are a few fixes for the to_xml() methods as well.


Modified:
    1.3/generic_fns/structure/api_base.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=14915&r1=14914&r2=14915&view=diff
==============================================================================
--- 1.3/generic_fns/structure/api_base.py (original)
+++ 1.3/generic_fns/structure/api_base.py Tue Oct 25 16:24:30 2011
@@ -38,8 +38,8 @@
 from warnings import warn
 
 # relax module import.
-from data.relax_xml import fill_object_contents, xml_to_object
-from float import floatAsByteArray
+from data.relax_xml import fill_object_contents, node_value_to_python, 
xml_to_object
+from float import floatAsByteArray, packBytesAsPyFloat
 from maths_fns.rotation_matrix import R_to_axis_angle
 from relax_errors import RelaxError, RelaxFileError, 
RelaxFromXMLNotEmptyError, RelaxImplementError
 from relax_io import file_root
@@ -224,6 +224,15 @@
         model_nodes = str_node.getElementsByTagName('model')
         self.structural_data.from_xml(model_nodes, id=id)
 
+        # The displacement structure.
+        disp_nodes = str_node.getElementsByTagName('displacements')
+        if len(disp_nodes):
+            # Initialise the object.
+            self.displacements = Displacements()
+
+            # Recreate the molecule data structures for the current model.
+            self.displacements.from_xml(disp_nodes[0])
+
 
     def get_model(self, model):
         """Return or create the model.
@@ -544,7 +553,7 @@
         if hasattr(self, 'displacements'):
             # Create an XML element.
             disp_element = doc.createElement('displacements')
-            element.appendChild(disp_element)
+            str_element.appendChild(disp_element)
 
             # Set the attributes.
             disp_element.setAttribute('desc', 'The rotational and 
translational displacements between models')
@@ -954,6 +963,62 @@
         self._rotation_angle[model_from][model_to] = angle
 
 
+    def from_xml(self, str_node, dir=None, id=None):
+        """Recreate the structural object from the XML structural object 
node.
+
+        @param str_node:    The structural object XML node.
+        @type str_node:     xml.dom.minicompat.Element instance
+        @keyword dir:       The name of the directory containing the results 
file.
+        @type dir:          str
+        @keyword id:        The specific structural object ID string.  This 
can be 'scientific',
+                            'internal', etc.
+        @type id:           str
+        """
+
+        # Get the pairs of displacements.
+        pair_nodes = str_node.getElementsByTagName('pair')
+
+        # Loop over the pairs.
+        for pair_node in pair_nodes:
+            # Get the two models.
+            model_from = int(pair_node.getAttribute('model_from'))
+            model_to = int(pair_node.getAttribute('model_to'))
+
+            # Initialise structures if necessary.
+            if not self._translation_vector.has_key(model_from):
+                self._translation_vector[model_from] = {}
+            if not self._translation_distance.has_key(model_from):
+                self._translation_distance[model_from] = {}
+            if not self._rotation_matrix.has_key(model_from):
+                self._rotation_matrix[model_from] = {}
+            if not self._rotation_axis.has_key(model_from):
+                self._rotation_axis[model_from] = {}
+            if not self._rotation_angle.has_key(model_from):
+                self._rotation_angle[model_from] = {}
+
+            # Loop over the nodes of the element
+            for node in pair_node.childNodes:
+                # Skip empty nodes.
+                if node.localName == None:
+                    continue
+
+                # The name of the python object to recreate.
+                name = '_%s' % node.localName
+
+                # IEEE-754 floats (for full precision restoration).
+                ieee_array = node.getAttribute('ieee_754_byte_array')
+                if ieee_array:
+                    val = packBytesAsPyFloat(eval(ieee_array))
+
+                # Get the node contents.
+                else:
+                    val = node_value_to_python(node.childNodes[0])
+
+                # Store the value.
+                obj = getattr(self, name)
+                obj[model_from][model_to] = val
+
+
     def to_xml(self, doc, element):
         """Create XML elements for each model.
 
@@ -962,9 +1027,6 @@
         @param element: The element to add the displacement XML elements to.
         @type element:  XML element object
         """
-
-        # Init a global index.
-        index = 0
 
         # Loop over the starting models.
         start_models = self._translation_vector.keys()
@@ -975,7 +1037,7 @@
             end_models.sort()
             for model_to in end_models:
                 # Create an XML element for each pair.
-                pair_element = doc.createElement('set_%s' % index)
+                pair_element = doc.createElement('pair')
                 element.appendChild(pair_element)
 
                 # Set the attributes.
@@ -1009,9 +1071,6 @@
                     text_val = doc.createTextNode(repr(subobj))
                     sub_elem.appendChild(text_val)
 
-                # Increment the index.
-                index += 1
-
 
 
 class ModelList(list):