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 displacement XML elements to.
@type element: XML element object
"""
# Loop over the starting models.
start_models = sorted(self._translation_vector.keys())
for id_from in start_models:
# Loop over the ending models.
end_models = sorted(self._translation_vector[id_from].keys())
for id_to in end_models:
# Create an XML element for each pair.
pair_element = doc.createElement('pair')
element.appendChild(pair_element)
# Set the attributes.
pair_element.setAttribute('desc', 'The displacement from model %s to model %s' % (id_from, id_to))
pair_element.setAttribute('id_from', id_from)
pair_element.setAttribute('id_to', id_to)
# The objects to store.
obj_names = [
'_translation_vector',
'_translation_distance',
'_rotation_matrix',
'_rotation_axis',
'_rotation_angle'
]
# Store the objects.
for i in range(len(obj_names)):
# Create a new element for this object, and add it to the main element.
sub_elem = doc.createElement(obj_names[i][1:])
pair_element.appendChild(sub_elem)
# Get the sub-object.
subobj = getattr(self, obj_names[i])[id_from][id_to]
# Add the value to the sub element.
object_to_xml(doc, sub_elem, value=subobj)
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 displacement XML elements to.
@type element: XML element object
"""
# Loop over the starting models.
start_models = sorted(self._translation_vector.keys())
for id_from in start_models:
# Loop over the ending models.
end_models = sorted(self._translation_vector[id_from].keys())
for id_to in end_models:
# Create an XML element for each pair.
pair_element = doc.createElement('pair')
element.appendChild(pair_element)
# Set the attributes.
pair_element.setAttribute(
'desc', 'The displacement from model %s to model %s' %
(id_from, id_to))
pair_element.setAttribute('id_from', id_from)
pair_element.setAttribute('id_to', id_to)
# The objects to store.
obj_names = [
'_translation_vector', '_translation_distance',
'_rotation_matrix', '_rotation_axis', '_rotation_angle'
]
# Store the objects.
for i in range(len(obj_names)):
# Create a new element for this object, and add it to the main element.
sub_elem = doc.createElement(obj_names[i][1:])
pair_element.appendChild(sub_elem)
# Get the sub-object.
subobj = getattr(self, obj_names[i])[id_from][id_to]
# Add the value to the sub element.
object_to_xml(doc, sub_elem, value=subobj)
def to_xml(self, doc, element, pipe_type=None):
"""Create XML elements for each spin.
@param doc: The XML document object.
@type doc: xml.dom.minidom.Document instance
@param element: The element to add the spin XML elements to.
@type element: XML element object
@keyword pipe_type: The type of the pipe being converted to XML.
@type pipe_type: str
"""
# The specific analysis API object.
api = specific_analyses.api.return_api(analysis_type=pipe_type)
# Loop over the containers.
for i in range(len(self)):
# Create an XML element for this container and add it to the higher level element.
interatom_element = doc.createElement('interatomic')
element.appendChild(interatom_element)
# Set the spin attributes.
interatom_element.setAttribute('desc',
'Interatomic data container')
interatom_element.setAttribute('spin_id1', str(self[i].spin_id1))
interatom_element.setAttribute('spin_id2', str(self[i].spin_id2))
# Get the specific object names and loop over them to get their descriptions.
object_info = []
try:
for name in api.data_names(error_names=True, sim_names=True):
# Get the description.
if hasattr(api, 'return_data_desc'):
desc = api.return_data_desc(name)
else:
desc = None
# Append the two.
object_info.append([name, desc])
except RelaxImplementError:
pass
# Add the ordered objects.
blacklist = []
for name, desc in object_info:
# Add the name to the blacklist.
blacklist.append(name)
# Skip the object if it is missing from the InteratomContainer.
if not hasattr(self[i], name):
continue
# Create a new element for this object, and add it to the main element.
sub_element = doc.createElement(name)
interatom_element.appendChild(sub_element)
# Add the object description.
if desc:
sub_element.setAttribute('desc', desc)
# Get the object.
object = getattr(self[i], name)
# Convert to XML.
object_to_xml(doc, sub_element, value=object)
# Add all simple python objects within the InteratomContainer to the XML element.
fill_object_contents(doc,
interatom_element,
object=self[i],
blacklist=['spin_id1', 'spin_id2'] +
blacklist +
list(self[i].__class__.__dict__.keys()))
def to_xml(self, doc, element, pipe_type=None):
"""Create XML elements for each spin.
@param doc: The XML document object.
@type doc: xml.dom.minidom.Document instance
@param element: The element to add the spin XML elements to.
@type element: XML element object
@keyword pipe_type: The type of the pipe being converted to XML.
@type pipe_type: str
"""
# The specific analysis API object.
api = specific_analyses.api.return_api(analysis_type=pipe_type)
# Loop over the spins.
for i in range(len(self)):
# Create an XML element for this spin and add it to the higher level element.
spin_element = doc.createElement('spin')
element.appendChild(spin_element)
# Set the spin attributes.
spin_element.setAttribute('desc', 'Spin container')
spin_element.setAttribute('name', str(self[i].name))
spin_element.setAttribute('num', str(self[i].num))
# Get the spin specific object names and loop over them to get their descriptions.
object_info = []
try:
for name in api.data_names(error_names=True, sim_names=True):
# Get the description.
if hasattr(api, 'return_data_desc'):
desc = api.return_data_desc(name)
else:
desc = None
# Append the two.
object_info.append([name, desc])
except RelaxImplementError:
pass
# Add the ordered objects.
blacklist = []
for name, desc in object_info:
# Add the name to the blacklist.
blacklist.append(name)
# Skip the object if it is missing from the SpinContainer.
if not hasattr(self[i], name):
continue
# Create a new element for this object, and add it to the main element.
sub_element = doc.createElement(name)
spin_element.appendChild(sub_element)
# Add the object description.
if desc:
sub_element.setAttribute('desc', desc)
# Get the object.
object = getattr(self[i], name)
# Convert to XML.
object_to_xml(doc, sub_element, value=object)
# Add all simple python objects within the SpinContainer to the XML element.
fill_object_contents(doc, spin_element, object=self[i], blacklist=['name', 'num', 'spin'] + blacklist + list(self[i].__class__.__dict__.keys()))
