def __init__(self):
"""Set up all the PipeContainer data structures."""
# The molecule-residue-spin object.
self.mol = MoleculeList()
# The interatomic data object.
self.interatomic = InteratomList()
# The data pipe type.
self.pipe_type = None
# Hybrid models.
self.hybrid_pipes = []
def __init__(self):
"""Set up all the PipeContainer data structures."""
# The molecule-residue-spin object.
self.mol = MoleculeList()
# The interatomic data object.
self.interatomic = InteratomList()
# The data pipe type.
self.pipe_type = None
# Hybrid models.
self.hybrid_pipes = []
class PipeContainer(Prototype):
"""Class containing all the program data."""
def __init__(self):
"""Set up all the PipeContainer data structures."""
# The molecule-residue-spin object.
self.mol = MoleculeList()
# The interatomic data object.
self.interatomic = InteratomList()
# The data pipe type.
self.pipe_type = None
# Hybrid models.
self.hybrid_pipes = []
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.
"""
# Intro text.
text = "The data pipe storage object.\n"
# Special objects/methods (to avoid the getattr() function call on).
spec_obj = ['exp_info', 'mol', 'interatomic', 'diff_tensor', 'structure']
# Objects.
text = text + "\n"
text = text + "Objects:\n"
for name in dir(self):
# Molecular list.
if name == 'mol':
text = text + " mol: The molecule list (for the storage of the spin system specific data)\n"
# Interatomic data list.
if name == 'interatomic':
text = text + " interatomic: The interatomic data list (for the storage of the inter-spin system data)\n"
# Diffusion tensor.
if name == 'diff_tensor':
text = text + " diff_tensor: The Brownian rotational diffusion tensor data object\n"
# Molecular structure.
if name == 'structure':
text = text + " structure: The 3D molecular data object\n"
# The experimental info data container.
if name == 'exp_info':
text = text + " exp_info: The data container for experimental information\n"
# Skip the PipeContainer methods.
if name in list(self.__class__.__dict__.keys()):
continue
# Skip certain objects.
if match("^_", name) or name in spec_obj:
continue
# Add the object's attribute to the text string.
text = text + " " + name + ": " + repr(getattr(self, name)) + "\n"
# Return the text representation.
return text
def _back_compat_hook(self, file_version=None):
"""Method for converting old data structures to the new ones.
@keyword file_version: The relax XML version of the XML file.
@type file_version: int
"""
# Relaxation data.
self._back_compat_hook_ri_data()
def _back_compat_hook_ri_data(self):
"""Converting the old relaxation data structures to the new ones."""
# Nothing to do.
if not (hasattr(cdp, 'frq_labels') and hasattr(cdp, 'noe_r1_table') and hasattr(cdp, 'remap_table')):
return
# Initialise the new structures.
cdp.ri_ids = []
cdp.ri_type = {}
frq = {} # This will be placed into cdp later as cdp.spectrometer_frq still exists.
# Generate the new structures.
for i in range(cdp.num_ri):
# The ID.
ri_id = "%s_%s" % (cdp.ri_labels[i], cdp.frq_labels[cdp.remap_table[i]])
# Not unique.
if ri_id in cdp.ri_ids:
# Loop until a unique ID is found.
for j in range(100):
# New id.
new_id = "%s_%s" % (ri_id, j)
# Unique.
if not new_id in cdp.ri_ids:
ri_id = new_id
break
# Add the ID.
cdp.ri_ids.append(ri_id)
# The relaxation data type.
cdp.ri_type[ri_id] = cdp.ri_labels[i]
# The frequency data.
frq[ri_id] = cdp.frq[cdp.remap_table[i]]
# Delete the old structures.
del cdp.frq
del cdp.frq_labels
del cdp.noe_r1_table
del cdp.num_frq
del cdp.num_ri
del cdp.remap_table
del cdp.ri_labels
# Set the frequencies.
cdp.frq = frq
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 is_empty(self):
"""Method for testing if the data pipe is empty.
@return: True if the data pipe is empty, False otherwise.
@rtype: bool
"""
# Is the molecule structure data object empty?
if hasattr(self, 'structure'):
return False
# Is the molecule/residue/spin data object empty?
if not self.mol.is_empty():
return False
# Is the interatomic data object empty?
if not self.interatomic.is_empty():
return False
# Tests for the initialised data (the pipe type can be set in an empty data pipe, so this isn't checked).
if self.hybrid_pipes:
return False
# An object has been added to the container.
for name in dir(self):
# Skip the objects initialised in __init__().
if name in ['mol', 'interatomic', 'pipe_type', 'hybrid_pipes']:
continue
# Skip the PipeContainer methods.
if name in list(self.__class__.__dict__.keys()):
continue
# Skip special objects.
if match("^_", name):
continue
# An object has been added.
return False
# The data pipe is empty.
return True
def to_xml(self, doc, element):
"""Create a XML element for the current data pipe.
@param doc: The XML document object.
@type doc: xml.dom.minidom.Document instance
@param element: The XML element to add the pipe XML element to.
@type element: XML element object
"""
# Add all simple python objects within the PipeContainer to the global element.
global_element = doc.createElement('global')
element.appendChild(global_element)
global_element.setAttribute('desc', 'Global data located in the top level of the data pipe')
fill_object_contents(doc, global_element, object=self, blacklist=['align_tensors', 'diff_tensor', 'exp_info', 'interatomic', 'hybrid_pipes', 'mol', 'pipe_type', 'structure'] + list(self.__class__.__dict__.keys()))
# Hybrid info.
self.xml_create_hybrid_element(doc, element)
# Add the experimental information.
if hasattr(self, 'exp_info'):
self.exp_info.to_xml(doc, element)
# Add the diffusion tensor data.
if hasattr(self, 'diff_tensor'):
self.diff_tensor.to_xml(doc, element)
# Add the alignment tensor data.
if hasattr(self, 'align_tensors'):
self.align_tensors.to_xml(doc, element)
# Add the molecule-residue-spin data.
self.mol.to_xml(doc, element)
# Add the interatomic data.
self.interatomic.to_xml(doc, element)
# Add the structural data, if it exists.
if hasattr(self, 'structure'):
self.structure.to_xml(doc, element)
def xml_create_hybrid_element(self, doc, element):
"""Create an XML element for the data pipe hybridisation information.
@param doc: The XML document object.
@type doc: xml.dom.minidom.Document instance
@param element: The element to add the hybridisation info to.
@type element: XML element object
"""
# Create the hybrid element and add it to the higher level element.
hybrid_element = doc.createElement('hybrid')
element.appendChild(hybrid_element)
# Set the hybridisation attributes.
hybrid_element.setAttribute('desc', 'Data pipe hybridisation information')
# Create an element to store the pipes list.
list_element = doc.createElement('pipes')
hybrid_element.appendChild(list_element)
# Add the pipes list.
text_val = doc.createTextNode(str(self.hybrid_pipes))
list_element.appendChild(text_val)
class PipeContainer(Prototype):
"""Class containing all the program data."""
def __init__(self):
"""Set up all the PipeContainer data structures."""
# The molecule-residue-spin object.
self.mol = MoleculeList()
# The interatomic data object.
self.interatomic = InteratomList()
# The data pipe type.
self.pipe_type = None
# Hybrid models.
self.hybrid_pipes = []
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.
"""
# Intro text.
text = "The data pipe storage object.\n"
# Special objects/methods (to avoid the getattr() function call on).
spec_obj = [
'exp_info', 'mol', 'interatomic', 'diff_tensor', 'structure'
]
# Objects.
text = text + "\n"
text = text + "Objects:\n"
for name in dir(self):
# Molecular list.
if name == 'mol':
text = text + " mol: The molecule list (for the storage of the spin system specific data)\n"
# Interatomic data list.
if name == 'interatomic':
text = text + " interatomic: The interatomic data list (for the storage of the inter-spin system data)\n"
# Diffusion tensor.
if name == 'diff_tensor':
text = text + " diff_tensor: The Brownian rotational diffusion tensor data object\n"
# Molecular structure.
if name == 'structure':
text = text + " structure: The 3D molecular data object\n"
# The experimental info data container.
if name == 'exp_info':
text = text + " exp_info: The data container for experimental information\n"
# Skip the PipeContainer methods.
if name in self.__class__.__dict__:
continue
# Skip certain objects.
if match("^_", name) or name in spec_obj:
continue
# Add the object's attribute to the text string.
text = text + " " + name + ": " + repr(getattr(self, name)) + "\n"
# Return the text representation.
return text
def _back_compat_hook(self, file_version=None):
"""Method for converting old data structures to the new ones.
@keyword file_version: The relax XML version of the XML file.
@type file_version: int
"""
# Relaxation data.
self._back_compat_hook_ri_data()
def _back_compat_hook_ri_data(self):
"""Converting the old relaxation data structures to the new ones."""
# Nothing to do.
if not (hasattr(cdp, 'frq_labels') and hasattr(cdp, 'noe_r1_table')
and hasattr(cdp, 'remap_table')):
return
# Initialise the new structures.
cdp.ri_ids = []
cdp.ri_type = {}
frq = {
} # This will be placed into cdp later as cdp.spectrometer_frq still exists.
# Generate the new structures.
for i in range(cdp.num_ri):
# The ID.
ri_id = "%s_%s" % (cdp.ri_labels[i],
cdp.frq_labels[cdp.remap_table[i]])
# Not unique.
if ri_id in cdp.ri_ids:
# Loop until a unique ID is found.
for j in range(100):
# New id.
new_id = "%s_%s" % (ri_id, j)
# Unique.
if not new_id in cdp.ri_ids:
ri_id = new_id
break
# Add the ID.
cdp.ri_ids.append(ri_id)
# The relaxation data type.
cdp.ri_type[ri_id] = cdp.ri_labels[i]
# The frequency data.
frq[ri_id] = cdp.frq[cdp.remap_table[i]]
# Delete the old structures.
del cdp.frq
del cdp.frq_labels
del cdp.noe_r1_table
del cdp.num_frq
del cdp.num_ri
del cdp.remap_table
del cdp.ri_labels
# Set the frequencies.
cdp.frq = frq
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 is_empty(self):
"""Method for testing if the data pipe is empty.
@return: True if the data pipe is empty, False otherwise.
@rtype: bool
"""
# Is the molecule structure data object empty?
if hasattr(self, 'structure'):
return False
# Is the molecule/residue/spin data object empty?
if not self.mol.is_empty():
return False
# Is the interatomic data object empty?
if not self.interatomic.is_empty():
return False
# Tests for the initialised data (the pipe type can be set in an empty data pipe, so this isn't checked).
if self.hybrid_pipes:
return False
# An object has been added to the container.
for name in dir(self):
# Skip the objects initialised in __init__().
if name in ['mol', 'interatomic', 'pipe_type', 'hybrid_pipes']:
continue
# Skip the PipeContainer methods.
if name in self.__class__.__dict__:
continue
# Skip special objects.
if match("^_", name):
continue
# An object has been added.
return False
# The data pipe is empty.
return True
def to_xml(self, doc, element, pipe_type=None):
"""Create a XML element for the current data pipe.
@param doc: The XML document object.
@type doc: xml.dom.minidom.Document instance
@param element: The XML element to add the pipe XML element to.
@type element: XML element object
@keyword pipe_type: The type of the pipe being converted to XML.
@type pipe_type: str
"""
# Add all simple python objects within the PipeContainer to the global element.
global_element = doc.createElement('global')
element.appendChild(global_element)
global_element.setAttribute(
'desc', 'Global data located in the top level of the data pipe')
fill_object_contents(
doc,
global_element,
object=self,
blacklist=[
'align_tensors', 'diff_tensor', 'exp_info', 'interatomic',
'hybrid_pipes', 'mol', 'pipe_type', 'structure'
] + list(self.__class__.__dict__.keys()))
# Hybrid info.
self.xml_create_hybrid_element(doc, element)
# Add the experimental information.
if hasattr(self, 'exp_info'):
self.exp_info.to_xml(doc, element)
# Add the diffusion tensor data.
if hasattr(self, 'diff_tensor'):
self.diff_tensor.to_xml(doc, element)
# Add the alignment tensor data.
if hasattr(self, 'align_tensors'):
self.align_tensors.to_xml(doc, element)
# Add the molecule-residue-spin data.
self.mol.to_xml(doc, element, pipe_type=pipe_type)
# Add the interatomic data.
self.interatomic.to_xml(doc, element, pipe_type=pipe_type)
# Add the structural data, if it exists.
if hasattr(self, 'structure'):
self.structure.to_xml(doc, element)
def xml_create_hybrid_element(self, doc, element):
"""Create an XML element for the data pipe hybridisation information.
@param doc: The XML document object.
@type doc: xml.dom.minidom.Document instance
@param element: The element to add the hybridisation info to.
@type element: XML element object
"""
# Create the hybrid element and add it to the higher level element.
hybrid_element = doc.createElement('hybrid')
element.appendChild(hybrid_element)
# Set the hybridisation attributes.
hybrid_element.setAttribute('desc',
'Data pipe hybridisation information')
# Create an element to store the pipes list.
list_element = doc.createElement('pipes')
hybrid_element.appendChild(list_element)
# Add the pipes list.
text_val = doc.createTextNode(str(self.hybrid_pipes))
list_element.appendChild(text_val)