def from_xml(self, pipe_node, file_version=None, dir=None):
"""Read a pipe container XML element and place the contents into this pipe.
@param pipe_node: The data pipe XML node.
@type pipe_node: xml.dom.minidom.Element instance
@keyword file_version: The relax XML version of the XML file.
@type file_version: int
@keyword dir: The name of the directory containing the results file (needed for loading external files).
@type dir: str
"""
# Test if empty.
if not self.is_empty():
raise RelaxFromXMLNotEmptyError(self.__class__.__name__)
# Get the global data node, and fill the contents of the pipe.
global_node = pipe_node.getElementsByTagName('global')[0]
xml_to_object(global_node, self, file_version=file_version)
# Backwards compatibility transformations.
self._back_compat_hook(file_version)
# Get the hybrid node (and its sub-node), and recreate the hybrid object.
hybrid_node = pipe_node.getElementsByTagName('hybrid')[0]
pipes_node = hybrid_node.getElementsByTagName('pipes')[0]
setattr(self, 'hybrid_pipes',
node_value_to_python(pipes_node.childNodes[0]))
# Get the experimental information data nodes and, if they exist, fill the contents.
exp_info_nodes = pipe_node.getElementsByTagName('exp_info')
if exp_info_nodes:
# Create the data container.
self.exp_info = ExpInfo()
# Fill its contents.
self.exp_info.from_xml(exp_info_nodes[0],
file_version=file_version)
# Get the diffusion tensor data nodes and, if they exist, fill the contents.
diff_tensor_nodes = pipe_node.getElementsByTagName('diff_tensor')
if diff_tensor_nodes:
# Create the diffusion tensor object.
self.diff_tensor = DiffTensorData()
# Fill its contents.
self.diff_tensor.from_xml(diff_tensor_nodes[0],
file_version=file_version)
# Get the alignment tensor data nodes and, if they exist, fill the contents.
align_tensor_nodes = pipe_node.getElementsByTagName('align_tensors')
if align_tensor_nodes:
# Create the alignment tensor object.
self.align_tensors = AlignTensorList()
# Fill its contents.
self.align_tensors.from_xml(align_tensor_nodes[0],
file_version=file_version)
# Recreate the interatomic data structure (this needs to be before the 'mol' structure as the backward compatibility hooks can create interatomic data containers!).
interatom_nodes = pipe_node.getElementsByTagName('interatomic')
self.interatomic.from_xml(interatom_nodes, file_version=file_version)
# Recreate the molecule, residue, and spin data structure.
mol_nodes = pipe_node.getElementsByTagName('mol')
self.mol.from_xml(mol_nodes, file_version=file_version)
# Get the structural object nodes and, if they exist, fill the contents.
str_nodes = pipe_node.getElementsByTagName('structure')
if str_nodes:
# Create the structural object.
fail = False
self.structure = Internal()
# Fill its contents.
if not fail:
self.structure.from_xml(str_nodes[0],
dir=dir,
file_version=file_version)
def setUp(self):
"""Set 'self.diff_data' to an empty instance of the DiffTensorData class."""
self.diff_data = DiffTensorData()
