class Relax_data_store(dict):
"""The relax data storage object."""
# The current data pipe.
current_pipe = None
builtins.cdp = None
# Class variable for storing the class instance.
instance = None
def __new__(self, *args, **kargs):
"""Replacement function for implementing the singleton design pattern."""
# First initialisation.
if self.instance is None:
# Create a new instance.
self.instance = dict.__new__(self, *args, **kargs)
# Add some initial structures.
self.instance.pipe_bundles = {}
self.instance.relax_gui = Gui()
# Already initialised, so return the instance.
return self.instance
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 relax data storage object.\n"
# The data pipes.
text = text + "\n"
text = text + "Data pipes:\n"
pipes = sorted(self.instance.keys())
if pipes:
for pipe in pipes:
text = text + " %s\n" % repr(pipe)
else:
text = text + " None\n"
# Data store objects.
text = text + "\n"
text = text + "Data store objects:\n"
names = sorted(self.__class__.__dict__.keys())
for name in names:
# The object.
obj = getattr(self, name)
# The text.
if obj == None or isinstance(obj, str):
text = text + " %s %s: %s\n" % (name, type(obj), obj)
else:
text = text + " %s %s: %s\n" % (name, type(obj), obj.__doc__.split('\n')[0])
# dict methods.
text = text + "\n"
text = text + "Inherited dictionary methods:\n"
for name in dir(dict):
# Skip special methods.
if search("^_", name):
continue
# Skip overwritten methods.
if name in self.__class__.__dict__:
continue
# The object.
obj = getattr(self, name)
# The text.
text = text + " %s %s: %s\n" % (name, type(obj), obj.__doc__.split('\n')[0])
# All other objects.
text = text + "\n"
text = text + "All other objects:\n"
for name in dir(self):
# Skip special methods.
if search("^_", name):
continue
# Skip overwritten methods.
if name in self.__class__.__dict__:
continue
# Skip dictionary methods.
if name in dir(dict):
continue
# The object.
obj = getattr(self, name)
# The text.
text = text + " %s %s: %s\n" % (name, type(obj), obj)
# Return the text.
return text
def __reset__(self):
"""Delete all the data from the relax data storage object.
This method is to make the current single instance of the Data object identical to a newly
created instance of Data, hence resetting the relax program state.
"""
# Loop over the keys of self.__dict__ and delete the corresponding object.
keys = list(self.__dict__.keys())
for key in keys:
# Delete the object.
del self.__dict__[key]
# Remove all items from the dictionary.
self.instance.clear()
# Reset the current data pipe.
builtins.cdp = None
# Recreate the pipe bundle object.
self.instance.pipe_bundles = {}
# Re-add the GUI object.
self.instance.relax_gui = Gui()
# Signal the change.
status.observers.reset.notify()
status.observers.pipe_alteration.notify()
def _back_compat_hook(self, file_version=None, pipes=None):
"""Method for converting the old data structures to the new ones.
@keyword file_version: The relax XML version of the XML file.
@type file_version: int
@keyword pipes: The list of new pipe names to update.
@type pipes: list of str
"""
# Loop over the new data pipes.
for pipe_name in pipes:
# The data pipe object.
dp = self[pipe_name]
# Convert the molecule-residue-spin data.
for mol in dp.mol:
# Loop over the residues.
for res in mol.res:
# Loop over the spins.
for spin in res.spin:
# The list of objects to remove at the end.
eliminate = []
# The current spin ID.
spin_id = pipe_control.mol_res_spin.generate_spin_id_unique(pipe_cont=dp, mol=mol, res=res, spin=spin)
# Rename the old peak intensity data structures.
if hasattr(spin, 'intensities'):
spin.peak_intensity = spin.intensities
eliminate.append('intensities')
if hasattr(spin, 'intensity_err'):
spin.peak_intensity_err = spin.intensity_err
eliminate.append('intensity_err')
if hasattr(spin, 'intensity_sim'):
spin.peak_intensity_sim = spin.intensity_sim
eliminate.append('intensity_sim')
if hasattr(spin, 'sim_intensity'):
spin.peak_intensity_sim = spin.sim_intensity
eliminate.append('sim_intensity')
if hasattr(spin, 'intensity_bc'):
spin.peak_intensity_bc = spin.intensity_bc
eliminate.append('intensity_bc')
# Convert proton spins (the 'heteronuc_type' variable indicates a pre-interatomic container design state).
if hasattr(spin, 'heteronuc_type') and hasattr(spin, 'element') and spin.element == 'H':
# Rename the nuclear isotope.
spin.isotope = spin.proton_type
# Append the old structures to be eliminated.
eliminate.append('proton_type')
# Convert heteronuclear spins (the 'heteronuc_type' variable indicates a pre-interatomic container design state).
elif hasattr(spin, 'heteronuc_type'):
# Rename the nuclear isotope.
spin.isotope = spin.heteronuc_type
# Name the spin if needed.
if spin.name == None:
if search('N', spin.isotope):
pipe_control.mol_res_spin.name_spin(spin_id=spin_id, name='N', pipe=pipe_name)
elif search('C', spin.isotope):
pipe_control.mol_res_spin.name_spin(spin_id=spin_id, name='C', pipe=pipe_name)
# An attached proton - convert into a spin container.
if (hasattr(spin, 'attached_proton') and spin.attached_proton != None) or (hasattr(spin, 'proton_type') and spin.proton_type != None):
# The proton name.
if hasattr(spin, 'attached_proton') and spin.attached_proton != None:
proton_name = spin.attached_proton
else:
proton_name = 'H'
# The two spin IDs (newly regenerated due to the above renaming).
spin_id1 = pipe_control.mol_res_spin.generate_spin_id_unique(pipe_cont=dp, mol=mol, res=res, spin=spin)
spin_id2 = pipe_control.mol_res_spin.generate_spin_id_unique(pipe_cont=dp, mol=mol, res=res, spin_name=proton_name)
# Fetch the proton spin if it exists.
h_spin = pipe_control.mol_res_spin.return_spin(spin_id2, pipe=pipe_name)
if h_spin:
spin_id2 = pipe_control.mol_res_spin.generate_spin_id_unique(pipe_cont=dp, mol=mol, res=res, spin_name=proton_name, spin_num=h_spin.num)
# Create a new spin container for the proton if needed.
if not h_spin:
h_spin = pipe_control.mol_res_spin.create_spin(mol_name=mol.name, res_num=res.num, res_name=res.name, spin_name=proton_name, pipe=pipe_name)
h_spin.select = False
# Set up a dipole interaction between the two spins if needed.
if not hasattr(h_spin, 'element'):
pipe_control.mol_res_spin.set_spin_element(spin_id=spin_id2, element='H', pipe=pipe_name)
if not hasattr(h_spin, 'isotope'):
pipe_control.mol_res_spin.set_spin_isotope(spin_id=spin_id2, isotope='1H', pipe=pipe_name)
pipe_control.interatomic.define(spin_id1, spin_id2, verbose=False, pipe=pipe_name)
# Get the interatomic data container.
interatom = pipe_control.interatomic.return_interatom(spin_id1=spin_id1, spin_id2=spin_id2, pipe=pipe_name)
# Set the interatomic distance.
if hasattr(spin, 'r'):
interatom.r = spin.r
# Set the interatomic unit vectors.
if hasattr(spin, 'xh_vect'):
interatom.vector = spin.xh_vect
# Set the RDC values.
if hasattr(spin, 'rdc'):
interatom.rdc = spin.rdc
if hasattr(spin, 'rdc_err'):
interatom.rdc_err = spin.rdc_err
if hasattr(spin, 'rdc_sim'):
interatom.rdc_sim = spin.rdc_sim
if hasattr(spin, 'rdc_bc'):
interatom.rdc_bc = spin.rdc_bc
# Append the old structures to be eliminated.
eliminate += ['heteronuc_type', 'proton_type', 'attached_proton', 'r', 'r_err', 'r_sim', 'rdc', 'rdc_err', 'rdc_sim', 'rdc_bc', 'xh_vect']
# Delete the old structures.
for name in eliminate:
if hasattr(spin, name):
delattr(spin, name)
# Conversions for the interatomic data containers.
if hasattr(dp, 'interatomic'):
for interatom in dp.interatomic:
# RDC data.
if hasattr(interatom, 'rdc') and not hasattr(interatom, 'rdc_data_types'):
# Initialise.
interatom.rdc_data_types = {}
# Add the data type, assumed to be 'D', for each alignment ID.
for id in dp.rdc_ids:
interatom.rdc_data_types[id] = 'D'
# Convert the alignment tensors.
if hasattr(dp, 'align_tensors'):
for i in range(len(dp.align_tensors)):
# Fix for the addition of the alignment ID structure as opposed to the tensor name or tag.
if not hasattr(dp.align_tensors[i], 'align_id'):
dp.align_tensors[i].set('align_id', dp.align_tensors[i].name)
# Convert spectrometer frequency information.
if hasattr(dp, 'frq'):
# Convert to the new structure.
dp.spectrometer_frq = dp.frq
del dp.frq
# Build the new frequency list structure.
dp.spectrometer_frq_list = []
for frq in list(dp.spectrometer_frq.values()):
if frq not in dp.spectrometer_frq_list:
dp.spectrometer_frq_list.append(frq)
# And finally count the elements and sort the list.
dp.spectrometer_frq_count = len(dp.spectrometer_frq_list)
dp.spectrometer_frq_list.sort()
# Convert the Sobol' integration information.
if hasattr(dp, 'num_int_pts'):
# Convert to the new structure.
dp.sobol_max_points = dp.num_int_pts
del dp.num_int_pts
# Add the oversampling variable.
cdp.sobol_oversample = 1
# PCS Q factor conversions.
if hasattr(dp, 'q_factors_pcs'):
dp.q_factors_pcs_norm_squared_sum = dp.q_factors_pcs
del dp.q_factors_pcs
if hasattr(dp, 'q_pcs'):
dp.q_pcs_norm_squared_sum = dp.q_pcs
del dp.q_pcs
# RDC Q factor conversions.
if hasattr(dp, 'q_factors_rdc'):
dp.q_factors_rdc_norm_tensor_size = dp.q_factors_rdc
del dp.q_factors_rdc
if hasattr(dp, 'q_rdc'):
dp.q_rdc_norm_tensor_size = dp.q_rdc
del dp.q_rdc
if hasattr(dp, 'q_factors_rdc_norm2'):
dp.q_factors_rdc_norm_squared_sum = dp.q_factors_rdc_norm2
del dp.q_factors_rdc_norm2
if hasattr(dp, 'q_rdc_norm2'):
dp.q_rdc_norm_squared_sum = dp.q_rdc_norm2
del dp.q_rdc_norm2
def add(self, pipe_name, pipe_type, bundle=None, switch=True):
"""Method for adding a new data pipe container to the dictionary.
This method should be used rather than importing the PipeContainer class and using the statement 'D[pipe] = PipeContainer()', where D is the relax data storage object and pipe is the name of the data pipe.
@param pipe_name: The name of the new data pipe.
@type pipe_name: str
@param pipe_type: The data pipe type.
@type pipe_type: str
@keyword bundle: The optional data pipe bundle to associate the data pipe with.
@type bundle: str or None
@keyword switch: A flag which if True will cause the new data pipe to be set to the current data pipe.
@type switch: bool
"""
# Test if the pipe already exists.
if pipe_name in self.instance:
raise RelaxPipeError(pipe_name)
# Create a new container.
self[pipe_name] = PipeContainer()
# Add the data pipe type string to the container.
self[pipe_name].pipe_type = pipe_type
# The pipe bundle.
if bundle:
# A new bundle.
if bundle not in self.pipe_bundles:
self.pipe_bundles[bundle] = []
# Add the pipe to the bundle.
self.pipe_bundles[bundle].append(pipe_name)
# Change the current data pipe.
if switch:
# Set the current data pipe.
self.instance.current_pipe = pipe_name
builtins.cdp = self[pipe_name]
# Signal the switch.
status.observers.pipe_alteration.notify()
def is_empty(self, verbosity=False):
"""Method for testing if the relax data store is empty.
@keyword verbosity: A flag which if True will cause messages to be printed to STDERR.
@type verbosity: bool
@return: True if the data store is empty, False otherwise.
@rtype: bool
"""
# No pipes should exist.
if len(self):
if verbosity:
stderr.write("The relax data store contains the data pipes %s.\n" % sorted(self.keys()))
return False
# Objects which should be in here.
blacklist = [
'pipe_bundles',
'relax_gui'
]
# An object has been added to the data store.
for name in dir(self):
# Skip the data store methods.
if name in self.__class__.__dict__:
continue
# Skip the dict methods.
if name in dict.__dict__:
continue
# Skip special objects.
if search("^__", name):
continue
# Blacklisted objects to skip.
if name in blacklist:
continue
# An object has been added.
if verbosity:
stderr.write("The relax data store contains the object %s.\n" % name)
return False
# The data store is empty.
return True
def from_xml(self, file, dir=None, pipe_to=None, verbosity=1):
"""Parse a XML document representation of a data pipe, and load it into the relax data store.
@param file: The open file object.
@type file: file
@keyword dir: The name of the directory containing the results file (needed for loading external files).
@type dir: str
@keyword pipe_to: The data pipe to load the XML data pipe into (the file must only contain one data pipe).
@type pipe_to: str
@keyword verbosity: A flag specifying the amount of information to print. The higher the value, the greater the verbosity.
@type verbosity: int
@raises RelaxError: If pipe_to is given and the file contains multiple pipe elements; or if the data pipes in the XML file already exist in the relax data store; or if the data pipe type is invalid; or if the target data pipe is not empty.
@raises RelaxNoPipeError: If pipe_to is given but the data pipe does not exist.
@raises RelaxError: If the data pipes in the XML file already exist in the relax data store, or if the data pipe type is invalid.
@raises RelaxPipeError: If the data pipes of the XML file are already present in the relax data store.
"""
# Create the XML document from the file.
doc = xml.dom.minidom.parse(file)
# Get the relax node.
relax_node = doc.childNodes[0]
# Get the relax version of the XML file.
file_version = relax_node.getAttribute('file_version')
if file_version == '':
file_version = 1
else:
file_version = int(file_version)
# Get the pipe nodes.
pipe_nodes = relax_node.getElementsByTagName('pipe')
# Structure for the names of the new pipes.
pipes = []
# Target loading to a specific pipe (for pipe results reading).
if pipe_to:
# Check if there are multiple pipes in the XML file.
if len(pipe_nodes) > 1:
raise RelaxError("The pipe_to target pipe argument '%s' cannot be given as the file contains multiple pipe elements." % pipe_to)
# The pipe type.
pipe_type = pipe_nodes[0].getAttribute('type')
# Check that the pipe already exists.
if not pipe_to in self:
raise RelaxNoPipeError(pipe_to)
# Check if the pipe type matches.
if pipe_type != self[pipe_to].pipe_type:
raise RelaxError("The XML file pipe type '%s' does not match the pipe type '%s'" % (pipe_type, self[pipe_to].pipe_type))
# Check if the pipe is empty.
if not self[pipe_to].is_empty():
raise RelaxError("The data pipe '%s' is not empty." % pipe_to)
# Load the data.
self[pipe_to].from_xml(pipe_nodes[0], dir=dir, file_version=file_version)
# Store the pipe name.
pipes.append(pipe_to)
# Load the state.
else:
# Get the GUI nodes.
gui_nodes = relax_node.getElementsByTagName('relax_gui')
if gui_nodes:
self.relax_gui.from_xml(gui_nodes[0], file_version=file_version)
# Get the sequence alignment nodes.
seq_align_nodes = relax_node.getElementsByTagName('sequence_alignments')
if seq_align_nodes:
# Initialise the object.
self.sequence_alignments = Sequence_alignments()
# Populate it.
self.sequence_alignments.from_xml(seq_align_nodes[0], file_version=file_version)
# Recreate all the data store data structures.
xml_to_object(relax_node, self, file_version=file_version, blacklist=['pipe', 'relax_gui', 'sequence_alignments'])
# Checks.
for pipe_node in pipe_nodes:
# The pipe name and type.
pipe_name = str(pipe_node.getAttribute('name'))
pipe_type = pipe_node.getAttribute('type')
# Existence check.
if pipe_name in self:
raise RelaxPipeError(pipe_name)
# Valid type check.
if not pipe_type in pipe_control.pipes.VALID_TYPES:
raise RelaxError("The data pipe type '%s' is invalid and must be one of the strings in the list %s." % (pipe_type, pipe_control.pipes.VALID_TYPES))
# Load the data pipes.
for pipe_node in pipe_nodes:
# The pipe name and type.
pipe_name = str(pipe_node.getAttribute('name'))
pipe_type = pipe_node.getAttribute('type')
# Add the data pipe.
switch = False
if self.current_pipe == None:
switch = True
self.add(pipe_name, pipe_type, switch=switch)
# Fill the pipe.
self[pipe_name].from_xml(pipe_node, file_version=file_version, dir=dir)
# Store the pipe name.
pipes.append(pipe_name)
# Set the current pipe.
if self.current_pipe in self:
builtins.cdp = self[self.current_pipe]
# Finally update the molecule, residue, and spin metadata for each data pipe.
for pipe in pipes:
pipe_control.mol_res_spin.metadata_update(pipe=pipe)
# Backwards compatibility transformations.
self._back_compat_hook(file_version, pipes=pipes)
def to_xml(self, file, pipes=None):
"""Create a XML document representation of the current data pipe.
This method creates the top level XML document including all the information needed
about relax, calls the PipeContainer.xml_write() method to fill in the document contents,
and writes the XML into the file object.
@param file: The open file object.
@type file: file
@param pipes: The name of the pipe, or list of pipes to place in the XML file.
@type pipes: str or list of str
"""
# The pipes to include in the XML file.
all = False
if not pipes:
all = True
pipes = list(self.keys())
elif isinstance(pipes, str):
pipes = [pipes]
# Sort the pipes.
pipes.sort()
# Create the XML document object.
xmldoc = xml.dom.minidom.Document()
# Create the top level element, including the relax URL.
top_element = xmldoc.createElementNS('http://www.nmr-relax.com', 'relax')
top_element.setAttribute("xmlns", "http://www.nmr-relax.com")
# Append the element.
xmldoc.appendChild(top_element)
# Set the relax version number, and add a creation time.
top_element.setAttribute('version', version.version)
top_element.setAttribute('time', asctime())
top_element.setAttribute('file_version', "2")
if version.repo_revision:
top_element.setAttribute('revision', version.repo_revision)
if version.repo_url:
top_element.setAttribute('url', version.repo_url)
# Add all objects in the data store base object to the XML element.
if all:
blacklist = list(self.__class__.__dict__.keys()) + list(dict.__dict__.keys())
for name in dir(self):
# Skip blacklisted objects.
if name in blacklist:
continue
# Skip special objects.
if search('^_', name):
continue
# Execute any to_xml() methods, and add that object to the blacklist.
obj = getattr(self, name)
if hasattr(obj, 'to_xml'):
obj.to_xml(xmldoc, top_element)
blacklist = blacklist + [name]
# Remove the current data pipe from the blacklist!
blacklist.remove('current_pipe')
# Add all simple python objects within the store.
fill_object_contents(xmldoc, top_element, object=self, blacklist=blacklist)
# Loop over the pipes.
for pipe in pipes:
# Create the pipe XML element and add it to the top level XML element.
pipe_element = xmldoc.createElement('pipe')
top_element.appendChild(pipe_element)
# Set the data pipe attributes.
pipe_element.setAttribute('desc', 'The contents of a relax data pipe')
pipe_element.setAttribute('name', pipe)
pipe_element.setAttribute('type', self[pipe].pipe_type)
# Fill the data pipe XML element.
self[pipe].to_xml(xmldoc, pipe_element, pipe_type=self[pipe].pipe_type)
# Write out the XML file.
file.write(xmldoc.toprettyxml(indent=' '))
def from_xml(self, file, dir=None, pipe_to=None, verbosity=1):
"""Parse a XML document representation of a data pipe, and load it into the relax data store.
@param file: The open file object.
@type file: file
@keyword dir: The name of the directory containing the results file (needed for loading external files).
@type dir: str
@keyword pipe_to: The data pipe to load the XML data pipe into (the file must only contain one data pipe).
@type pipe_to: str
@keyword verbosity: A flag specifying the amount of information to print. The higher the value, the greater the verbosity.
@type verbosity: int
@raises RelaxError: If pipe_to is given and the file contains multiple pipe elements; or if the data pipes in the XML file already exist in the relax data store; or if the data pipe type is invalid; or if the target data pipe is not empty.
@raises RelaxNoPipeError: If pipe_to is given but the data pipe does not exist.
@raises RelaxError: If the data pipes in the XML file already exist in the relax data store, or if the data pipe type is invalid.
@raises RelaxPipeError: If the data pipes of the XML file are already present in the relax data store.
"""
# Create the XML document from the file.
doc = xml.dom.minidom.parse(file)
# Get the relax node.
relax_node = doc.childNodes[0]
# Get the relax version of the XML file.
file_version = relax_node.getAttribute('file_version')
if file_version == '':
file_version = 1
else:
file_version = int(file_version)
# Get the pipe nodes.
pipe_nodes = relax_node.getElementsByTagName('pipe')
# Structure for the names of the new pipes.
pipes = []
# Target loading to a specific pipe (for pipe results reading).
if pipe_to:
# Check if there are multiple pipes in the XML file.
if len(pipe_nodes) > 1:
raise RelaxError("The pipe_to target pipe argument '%s' cannot be given as the file contains multiple pipe elements." % pipe_to)
# The pipe type.
pipe_type = pipe_nodes[0].getAttribute('type')
# Check that the pipe already exists.
if not pipe_to in self:
raise RelaxNoPipeError(pipe_to)
# Check if the pipe type matches.
if pipe_type != self[pipe_to].pipe_type:
raise RelaxError("The XML file pipe type '%s' does not match the pipe type '%s'" % (pipe_type, self[pipe_to].pipe_type))
# Check if the pipe is empty.
if not self[pipe_to].is_empty():
raise RelaxError("The data pipe '%s' is not empty." % pipe_to)
# Load the data.
self[pipe_to].from_xml(pipe_nodes[0], dir=dir, file_version=file_version)
# Store the pipe name.
pipes.append(pipe_to)
# Load the state.
else:
# Get the GUI nodes.
gui_nodes = relax_node.getElementsByTagName('relax_gui')
if gui_nodes:
self.relax_gui.from_xml(gui_nodes[0], file_version=file_version)
# Get the sequence alignment nodes.
seq_align_nodes = relax_node.getElementsByTagName('sequence_alignments')
if seq_align_nodes:
# Initialise the object.
self.sequence_alignments = Sequence_alignments()
# Populate it.
self.sequence_alignments.from_xml(seq_align_nodes[0], file_version=file_version)
# Recreate all the data store data structures.
xml_to_object(relax_node, self, file_version=file_version, blacklist=['pipe', 'relax_gui', 'sequence_alignments'])
# Checks.
for pipe_node in pipe_nodes:
# The pipe name and type.
pipe_name = str(pipe_node.getAttribute('name'))
pipe_type = pipe_node.getAttribute('type')
# Existence check.
if pipe_name in self:
raise RelaxPipeError(pipe_name)
# Valid type check.
if not pipe_type in pipe_control.pipes.VALID_TYPES:
raise RelaxError("The data pipe type '%s' is invalid and must be one of the strings in the list %s." % (pipe_type, pipe_control.pipes.VALID_TYPES))
# Load the data pipes.
for pipe_node in pipe_nodes:
# The pipe name and type.
pipe_name = str(pipe_node.getAttribute('name'))
pipe_type = pipe_node.getAttribute('type')
# Add the data pipe.
switch = False
if self.current_pipe == None:
switch = True
self.add(pipe_name, pipe_type, switch=switch)
# Fill the pipe.
self[pipe_name].from_xml(pipe_node, file_version=file_version, dir=dir)
# Store the pipe name.
pipes.append(pipe_name)
# Set the current pipe.
if self.current_pipe in self:
builtins.cdp = self[self.current_pipe]
# Finally update the molecule, residue, and spin metadata for each data pipe.
for pipe in pipes:
pipe_control.mol_res_spin.metadata_update(pipe=pipe)
# Backwards compatibility transformations.
self._back_compat_hook(file_version, pipes=pipes)
def setUp(self):
"""Set 'self.seq_align' to an empty instance of the Sequence_alignments class."""
self.seq_align = Sequence_alignments()
class Test_seq_align(TestCase):
"""Unit tests for the data.seq_align relax module."""
def setUp(self):
"""Set 'self.seq_align' to an empty instance of the Sequence_alignments class."""
self.seq_align = Sequence_alignments()
def generate_ids(self, object_ids, models, molecules):
"""Generate the expected IDs."""
# Generate the IDs.
ids = []
for i in range(len(object_ids)):
ids.append("Object '%s'" % object_ids[i])
if models[i] != None:
ids[-1] += "; Model %i" % models[i]
ids[-1] += "; Molecule '%s'" % molecules[i]
# Return the IDs.
return ids
def return_align_data(self):
"""Return a data set for alignment testing."""
# The data.
object_ids = ['frame_order', 'ensemble', 'ensemble', 'ensemble', 'ensemble', 'ensemble', 'ensemble', 'ensemble']
models = [None, 1, 1, 1, 1, 1, 1, 1]
molecules = [
'N-dom',
'ensemble 4M A',
'ensemble 4M B',
'ensemble 4M C',
'ensemble 4M D',
'CaM-IQ A',
'CaM-IQ B',
'CaM-IQ C'
]
sequences = [
'LTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARK*****',
'*DQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTA*****',
'*DQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTA*****',
'*DQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTA*****',
'*DQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTA*****',
' QLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMT*****',
' LTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMT*****',
' LTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMT*****',
'TEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADG',
'ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKM',
'LTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMAR'
]
strings = [
'---LTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARK------------------------------------------------------------------------*****----------------------------------------------------------------------------',
'*DQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARK----------------------------------------------------------------------------MKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTA*****',
'*DQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTA*****----------------------------------------------------------------------------',
'*DQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTA*****----------------------------------------------------------------------------',
'*DQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTA*****----------------------------------------------------------------------------',
'--QLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARK----MKSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMT*****----------------------------------------------------------------------------',
'---LTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARK----MKDEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMT*****----------------------------------------------------------------------------',
'---LTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARK-------EEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMT*****----------------------------------------------------------------------------',
]
gaps = []
for i in range(len(strings)):
gaps.append([])
for j in range(len(strings[0])):
if strings[i][j] == '-':
gaps[i].append(1)
else:
gaps[i].append(0)
msa_algorithm = 'Central Star'
pairwise_algorithm = 'NW70'
matrix = 'BLOSUM62'
gap_open_penalty = 10.0
gap_extend_penalty = 1.0
end_gap_open_penalty = 0.0
end_gap_extend_penalty = 0.0
# Return the data.
return object_ids, models, molecules, sequences, strings, gaps, msa_algorithm, pairwise_algorithm, matrix, gap_open_penalty, gap_extend_penalty, end_gap_open_penalty, end_gap_extend_penalty
def test_alignment_addition(self):
"""Test the creation of a new sequence alignment object."""
# The data.
object_ids, models, molecules, sequences, strings, gaps, msa_algorithm, pairwise_algorithm, matrix, gap_open_penalty, gap_extend_penalty, end_gap_open_penalty, end_gap_extend_penalty = self.return_align_data()
# Add the alignment.
self.seq_align.add(object_ids=object_ids, models=models, molecules=molecules, sequences=sequences, strings=strings, gaps=gaps, msa_algorithm=msa_algorithm, pairwise_algorithm=pairwise_algorithm, matrix=matrix, gap_open_penalty=gap_open_penalty, gap_extend_penalty=gap_extend_penalty, end_gap_open_penalty=end_gap_open_penalty, end_gap_extend_penalty=end_gap_extend_penalty)
# Generate the expected IDs.
ids = self.generate_ids(object_ids, models, molecules)
# Check the data.
for i in range(8):
print("Checking \"%s\"" % ids[i])
self.assertEqual(self.seq_align[0].ids[i], ids[i])
self.assertEqual(self.seq_align[0].object_ids[i], object_ids[i])
self.assertEqual(self.seq_align[0].models[i], models[i])
self.assertEqual(self.seq_align[0].molecules[i], molecules[i])
self.assertEqual(self.seq_align[0].sequences[i], sequences[i])
self.assertEqual(self.seq_align[0].strings[i], strings[i])
self.assertEqual(self.seq_align[0].gaps[i], gaps[i])
self.assertEqual(self.seq_align[0].msa_algorithm, msa_algorithm)
self.assertEqual(self.seq_align[0].pairwise_algorithm, pairwise_algorithm)
self.assertEqual(self.seq_align[0].matrix, matrix)
self.assertEqual(self.seq_align[0].gap_open_penalty, gap_open_penalty)
self.assertEqual(self.seq_align[0].gap_extend_penalty, gap_extend_penalty)
self.assertEqual(self.seq_align[0].end_gap_open_penalty, end_gap_open_penalty)
self.assertEqual(self.seq_align[0].end_gap_extend_penalty, end_gap_extend_penalty)
def test_find_alignment(self):
"""Test the retrieval of pre-existing alignment."""
# Execute the body of the test_alignment_addition() unit test to set up the object.
self.test_alignment_addition()
# The identifying data.
object_ids, models, molecules, sequences, strings, gaps, msa_algorithm, pairwise_algorithm, matrix, gap_open_penalty, gap_extend_penalty, end_gap_open_penalty, end_gap_extend_penalty = self.return_align_data()
# Retrieve the alignment.
align = self.seq_align.find_alignment(object_ids=object_ids, models=models, molecules=molecules, sequences=sequences, msa_algorithm=msa_algorithm, pairwise_algorithm=pairwise_algorithm, matrix=matrix, gap_open_penalty=gap_open_penalty, gap_extend_penalty=gap_extend_penalty, end_gap_open_penalty=end_gap_open_penalty, end_gap_extend_penalty=end_gap_extend_penalty)
# Check that something was returned.
self.assertNotEqual(align, None)
# Generate the expected IDs.
ids = self.generate_ids(object_ids, models, molecules)
# Check some of the data.
for i in range(8):
print("Checking \"%s\"" % ids[i])
self.assertEqual(self.seq_align[0].object_ids[i], object_ids[i])
self.assertEqual(self.seq_align[0].models[i], models[i])
self.assertEqual(self.seq_align[0].molecules[i], molecules[i])
def test_find_missing_alignment(self):
"""Test the retrieval of non-existent alignment."""
# Execute the body of the test_alignment_addition() unit test to set up the object.
self.test_alignment_addition()
# The identifying data.
object_ids, models, molecules, sequences, strings, gaps, msa_algorithm, pairwise_algorithm, matrix, gap_open_penalty, gap_extend_penalty, end_gap_open_penalty, end_gap_extend_penalty = self.return_align_data()
# Change a gap penalty.
gap_open_penalty = 0.5
# Retrieve the alignment.
align = self.seq_align.find_alignment(object_ids=object_ids, models=models, molecules=molecules, sequences=sequences, msa_algorithm=msa_algorithm, pairwise_algorithm=pairwise_algorithm, matrix=matrix, gap_open_penalty=gap_open_penalty, gap_extend_penalty=gap_extend_penalty, end_gap_open_penalty=end_gap_open_penalty, end_gap_extend_penalty=end_gap_extend_penalty)
# Check that nothing was returned.
self.assertEqual(align, None)
def from_xml(self, file, dir=None, pipe_to=None, verbosity=1):
"""Parse a XML document representation of a data pipe, and load it into the relax data store.
@param file: The open file object.
@type file: file
@keyword dir: The name of the directory containing the results file (needed for loading external files).
@type dir: str
@keyword pipe_to: The data pipe to load the XML data pipe into (the file must only contain one data pipe).
@type pipe_to: str
@keyword verbosity: A flag specifying the amount of information to print. The higher the value, the greater the verbosity.
@type verbosity: int
@raises RelaxError: If pipe_to is given and the file contains multiple pipe elements; or if the data pipes in the XML file already exist in the relax data store; or if the data pipe type is invalid; or if the target data pipe is not empty.
@raises RelaxNoPipeError: If pipe_to is given but the data pipe does not exist.
@raises RelaxError: If the data pipes in the XML file already exist in the relax data store, or if the data pipe type is invalid.
@raises RelaxPipeError: If the data pipes of the XML file are already present in the relax data store.
"""
# Create the XML document from the file.
doc = xml.dom.minidom.parse(file)
# Get the relax node.
relax_node = doc.childNodes[0]
# Get the relax version of the XML file.
file_version = relax_node.getAttribute('file_version')
if file_version == '':
file_version = 1
else:
file_version = int(file_version)
# Get the pipe nodes.
pipe_nodes = relax_node.getElementsByTagName('pipe')
# Structure for the names of the new pipes.
pipes = []
# Target loading to a specific pipe (for pipe results reading).
if pipe_to:
# Check if there are multiple pipes in the XML file.
if len(pipe_nodes) > 1:
raise RelaxError(
"The pipe_to target pipe argument '%s' cannot be given as the file contains multiple pipe elements."
% pipe_to)
# The pipe type.
pipe_type = pipe_nodes[0].getAttribute('type')
# Check that the pipe already exists.
if not pipe_to in self:
raise RelaxNoPipeError(pipe_to)
# Check if the pipe type matches.
if pipe_type != self[pipe_to].pipe_type:
raise RelaxError(
"The XML file pipe type '%s' does not match the pipe type '%s'"
% (pipe_type, self[pipe_to].pipe_type))
# Check if the pipe is empty.
if not self[pipe_to].is_empty():
raise RelaxError("The data pipe '%s' is not empty." % pipe_to)
# Load the data.
self[pipe_to].from_xml(pipe_nodes[0],
dir=dir,
file_version=file_version)
# Store the pipe name.
pipes.append(pipe_to)
# Load the state.
else:
# Get the GUI nodes.
gui_nodes = relax_node.getElementsByTagName('relax_gui')
if gui_nodes:
self.relax_gui.from_xml(gui_nodes[0],
file_version=file_version)
# Get the sequence alignment nodes.
seq_align_nodes = relax_node.getElementsByTagName(
'sequence_alignments')
if seq_align_nodes:
# Initialise the object.
self.sequence_alignments = Sequence_alignments()
# Populate it.
self.sequence_alignments.from_xml(seq_align_nodes[0],
file_version=file_version)
# Recreate all the data store data structures.
xml_to_object(
relax_node,
self,
file_version=file_version,
blacklist=['pipe', 'relax_gui', 'sequence_alignments'])
# Checks.
for pipe_node in pipe_nodes:
# The pipe name and type.
pipe_name = str(pipe_node.getAttribute('name'))
pipe_type = pipe_node.getAttribute('type')
# Existence check.
if pipe_name in self:
raise RelaxPipeError(pipe_name)
# Valid type check.
if not pipe_type in pipe_control.pipes.VALID_TYPES:
raise RelaxError(
"The data pipe type '%s' is invalid and must be one of the strings in the list %s."
% (pipe_type, pipe_control.pipes.VALID_TYPES))
# Load the data pipes.
for pipe_node in pipe_nodes:
# The pipe name and type.
pipe_name = str(pipe_node.getAttribute('name'))
pipe_type = pipe_node.getAttribute('type')
# Add the data pipe.
switch = False
if self.current_pipe == None:
switch = True
self.add(pipe_name, pipe_type, switch=switch)
# Fill the pipe.
self[pipe_name].from_xml(pipe_node,
file_version=file_version,
dir=dir)
# Store the pipe name.
pipes.append(pipe_name)
# Set the current pipe.
if self.current_pipe in self:
builtins.cdp = self[self.current_pipe]
# Finally update the molecule, residue, and spin metadata for each data pipe.
for pipe in pipes:
pipe_control.mol_res_spin.metadata_update(pipe=pipe)
# Backwards compatibility transformations.
self._back_compat_hook(file_version, pipes=pipes)
class Relax_data_store(dict):
"""The relax data storage object."""
# The current data pipe.
current_pipe = None
builtins.cdp = None
# Class variable for storing the class instance.
instance = None
def __new__(self, *args, **kargs):
"""Replacement function for implementing the singleton design pattern."""
# First initialisation.
if self.instance is None:
# Create a new instance.
self.instance = dict.__new__(self, *args, **kargs)
# Add some initial structures.
self.instance.pipe_bundles = {}
self.instance.relax_gui = Gui()
# Already initialised, so return the instance.
return self.instance
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 relax data storage object.\n"
# The data pipes.
text = text + "\n"
text = text + "Data pipes:\n"
pipes = sorted(self.instance.keys())
if pipes:
for pipe in pipes:
text = text + " %s\n" % repr(pipe)
else:
text = text + " None\n"
# Data store objects.
text = text + "\n"
text = text + "Data store objects:\n"
names = sorted(self.__class__.__dict__.keys())
for name in names:
# The object.
obj = getattr(self, name)
# The text.
if obj == None or isinstance(obj, str):
text = text + " %s %s: %s\n" % (name, type(obj), obj)
else:
text = text + " %s %s: %s\n" % (name, type(obj),
obj.__doc__.split('\n')[0])
# dict methods.
text = text + "\n"
text = text + "Inherited dictionary methods:\n"
for name in dir(dict):
# Skip special methods.
if search("^_", name):
continue
# Skip overwritten methods.
if name in self.__class__.__dict__:
continue
# The object.
obj = getattr(self, name)
# The text.
text = text + " %s %s: %s\n" % (name, type(obj),
obj.__doc__.split('\n')[0])
# All other objects.
text = text + "\n"
text = text + "All other objects:\n"
for name in dir(self):
# Skip special methods.
if search("^_", name):
continue
# Skip overwritten methods.
if name in self.__class__.__dict__:
continue
# Skip dictionary methods.
if name in dir(dict):
continue
# The object.
obj = getattr(self, name)
# The text.
text = text + " %s %s: %s\n" % (name, type(obj), obj)
# Return the text.
return text
def __reset__(self):
"""Delete all the data from the relax data storage object.
This method is to make the current single instance of the Data object identical to a newly
created instance of Data, hence resetting the relax program state.
"""
# Loop over the keys of self.__dict__ and delete the corresponding object.
keys = list(self.__dict__.keys())
for key in keys:
# Delete the object.
del self.__dict__[key]
# Remove all items from the dictionary.
self.instance.clear()
# Reset the current data pipe.
builtins.cdp = None
# Recreate the pipe bundle object.
self.instance.pipe_bundles = {}
# Re-add the GUI object.
self.instance.relax_gui = Gui()
# Signal the change.
status.observers.reset.notify()
status.observers.pipe_alteration.notify()
def _back_compat_hook(self, file_version=None, pipes=None):
"""Method for converting the old data structures to the new ones.
@keyword file_version: The relax XML version of the XML file.
@type file_version: int
@keyword pipes: The list of new pipe names to update.
@type pipes: list of str
"""
# Loop over the new data pipes.
for pipe_name in pipes:
# The data pipe object.
dp = self[pipe_name]
# Convert the molecule-residue-spin data.
for mol in dp.mol:
# Loop over the residues.
for res in mol.res:
# Loop over the spins.
for spin in res.spin:
# The list of objects to remove at the end.
eliminate = []
# The current spin ID.
spin_id = pipe_control.mol_res_spin.generate_spin_id_unique(
pipe_cont=dp, mol=mol, res=res, spin=spin)
# Rename the old peak intensity data structures.
if hasattr(spin, 'intensities'):
spin.peak_intensity = spin.intensities
eliminate.append('intensities')
if hasattr(spin, 'intensity_err'):
spin.peak_intensity_err = spin.intensity_err
eliminate.append('intensity_err')
if hasattr(spin, 'intensity_sim'):
spin.peak_intensity_sim = spin.intensity_sim
eliminate.append('intensity_sim')
if hasattr(spin, 'sim_intensity'):
spin.peak_intensity_sim = spin.sim_intensity
eliminate.append('sim_intensity')
if hasattr(spin, 'intensity_bc'):
spin.peak_intensity_bc = spin.intensity_bc
eliminate.append('intensity_bc')
# Convert proton spins (the 'heteronuc_type' variable indicates a pre-interatomic container design state).
if hasattr(spin, 'heteronuc_type') and hasattr(
spin, 'element') and spin.element == 'H':
# Rename the nuclear isotope.
spin.isotope = spin.proton_type
# Append the old structures to be eliminated.
eliminate.append('proton_type')
# Convert heteronuclear spins (the 'heteronuc_type' variable indicates a pre-interatomic container design state).
elif hasattr(spin, 'heteronuc_type'):
# Rename the nuclear isotope.
spin.isotope = spin.heteronuc_type
# Name the spin if needed.
if spin.name == None:
if search('N', spin.isotope):
pipe_control.mol_res_spin.name_spin(
spin_id=spin_id,
name='N',
pipe=pipe_name)
elif search('C', spin.isotope):
pipe_control.mol_res_spin.name_spin(
spin_id=spin_id,
name='C',
pipe=pipe_name)
# An attached proton - convert into a spin container.
if (hasattr(spin, 'attached_proton')
and spin.attached_proton != None) or (
hasattr(spin, 'proton_type')
and spin.proton_type != None):
# The proton name.
if hasattr(spin, 'attached_proton'
) and spin.attached_proton != None:
proton_name = spin.attached_proton
else:
proton_name = 'H'
# The two spin IDs (newly regenerated due to the above renaming).
spin_id1 = pipe_control.mol_res_spin.generate_spin_id_unique(
pipe_cont=dp, mol=mol, res=res, spin=spin)
spin_id2 = pipe_control.mol_res_spin.generate_spin_id_unique(
pipe_cont=dp,
mol=mol,
res=res,
spin_name=proton_name)
# Fetch the proton spin if it exists.
h_spin = pipe_control.mol_res_spin.return_spin(
spin_id=spin_id2, pipe=pipe_name)
if h_spin:
spin_id2 = pipe_control.mol_res_spin.generate_spin_id_unique(
pipe_cont=dp,
mol=mol,
res=res,
spin_name=proton_name,
spin_num=h_spin.num)
# Create a new spin container for the proton if needed.
if not h_spin:
h_spin = pipe_control.mol_res_spin.create_spin(
mol_name=mol.name,
res_num=res.num,
res_name=res.name,
spin_name=proton_name,
pipe=pipe_name)[0]
h_spin.select = False
# Set up a dipole interaction between the two spins if needed.
if not hasattr(h_spin, 'element'):
pipe_control.mol_res_spin.set_spin_element(
spin_id=spin_id2,
element='H',
pipe=pipe_name)
if not hasattr(h_spin, 'isotope'):
pipe_control.mol_res_spin.set_spin_isotope(
spin_id=spin_id2,
isotope='1H',
pipe=pipe_name)
pipe_control.interatomic.define_dipole_pair(
spin_id1=spin_id1,
spin_id2=spin_id2,
spin1=spin,
spin2=h_spin,
verbose=False,
pipe=pipe_name)
# Get the interatomic data container.
interatom = pipe_control.interatomic.return_interatom(
spin_hash1=spin._hash,
spin_hash2=h_spin._hash,
pipe=pipe_name)
# Set the interatomic distance.
if hasattr(spin, 'r'):
interatom.r = spin.r
# Set the interatomic unit vectors.
if hasattr(spin, 'xh_vect'):
interatom.vector = spin.xh_vect
# Set the RDC values.
if hasattr(spin, 'rdc'):
interatom.rdc = spin.rdc
if hasattr(spin, 'rdc_err'):
interatom.rdc_err = spin.rdc_err
if hasattr(spin, 'rdc_sim'):
interatom.rdc_sim = spin.rdc_sim
if hasattr(spin, 'rdc_bc'):
interatom.rdc_bc = spin.rdc_bc
# Append the old structures to be eliminated.
eliminate += [
'heteronuc_type', 'proton_type',
'attached_proton', 'r', 'r_err', 'r_sim',
'rdc', 'rdc_err', 'rdc_sim', 'rdc_bc',
'xh_vect'
]
# Delete the old structures.
for name in eliminate:
if hasattr(spin, name):
delattr(spin, name)
# Conversions for the interatomic data containers.
if hasattr(dp, 'interatomic'):
for interatom in dp.interatomic:
# RDC data.
if hasattr(interatom, 'rdc') and not hasattr(
interatom, 'rdc_data_types'):
# Initialise.
interatom.rdc_data_types = {}
# Add the data type, assumed to be 'D', for each alignment ID.
for id in dp.rdc_ids:
interatom.rdc_data_types[id] = 'D'
# Convert the alignment tensors.
if hasattr(dp, 'align_tensors'):
for i in range(len(dp.align_tensors)):
# Fix for the addition of the alignment ID structure as opposed to the tensor name or tag.
if not hasattr(dp.align_tensors[i], 'align_id'):
dp.align_tensors[i].set('align_id',
dp.align_tensors[i].name)
# Convert spectrometer frequency information.
if hasattr(dp, 'frq'):
# Convert to the new structure.
dp.spectrometer_frq = dp.frq
del dp.frq
# Build the new frequency list structure.
dp.spectrometer_frq_list = []
for frq in list(dp.spectrometer_frq.values()):
if frq not in dp.spectrometer_frq_list:
dp.spectrometer_frq_list.append(frq)
# And finally count the elements and sort the list.
dp.spectrometer_frq_count = len(dp.spectrometer_frq_list)
dp.spectrometer_frq_list.sort()
# Convert the Sobol' integration information.
if hasattr(dp, 'num_int_pts'):
# Convert to the new structure.
dp.sobol_max_points = dp.num_int_pts
del dp.num_int_pts
# Add the oversampling variable.
cdp.sobol_oversample = 1
# PCS Q factor conversions.
if hasattr(dp, 'q_factors_pcs'):
dp.q_factors_pcs_norm_squared_sum = dp.q_factors_pcs
del dp.q_factors_pcs
if hasattr(dp, 'q_pcs'):
dp.q_pcs_norm_squared_sum = dp.q_pcs
del dp.q_pcs
# RDC Q factor conversions.
if hasattr(dp, 'q_factors_rdc'):
dp.q_factors_rdc_norm_tensor_size = dp.q_factors_rdc
del dp.q_factors_rdc
if hasattr(dp, 'q_rdc'):
dp.q_rdc_norm_tensor_size = dp.q_rdc
del dp.q_rdc
if hasattr(dp, 'q_factors_rdc_norm2'):
dp.q_factors_rdc_norm_squared_sum = dp.q_factors_rdc_norm2
del dp.q_factors_rdc_norm2
if hasattr(dp, 'q_rdc_norm2'):
dp.q_rdc_norm_squared_sum = dp.q_rdc_norm2
del dp.q_rdc_norm2
def add(self, pipe_name, pipe_type, bundle=None, switch=True):
"""Method for adding a new data pipe container to the dictionary.
This method should be used rather than importing the PipeContainer class and using the statement 'D[pipe] = PipeContainer()', where D is the relax data storage object and pipe is the name of the data pipe.
@param pipe_name: The name of the new data pipe.
@type pipe_name: str
@param pipe_type: The data pipe type.
@type pipe_type: str
@keyword bundle: The optional data pipe bundle to associate the data pipe with.
@type bundle: str or None
@keyword switch: A flag which if True will cause the new data pipe to be set to the current data pipe.
@type switch: bool
"""
# Test if the pipe already exists.
if pipe_name in self.instance:
raise RelaxPipeError(pipe_name)
# Create a new container.
self[pipe_name] = PipeContainer()
# Add the data pipe type string to the container.
self[pipe_name].pipe_type = pipe_type
# The pipe bundle.
if bundle:
# A new bundle.
if bundle not in self.pipe_bundles:
self.pipe_bundles[bundle] = []
# Add the pipe to the bundle.
self.pipe_bundles[bundle].append(pipe_name)
# Change the current data pipe.
if switch:
# Set the current data pipe.
self.instance.current_pipe = pipe_name
builtins.cdp = self[pipe_name]
# Signal the switch.
status.observers.pipe_alteration.notify()
def is_empty(self, verbosity=False):
"""Method for testing if the relax data store is empty.
@keyword verbosity: A flag which if True will cause messages to be printed to STDERR.
@type verbosity: bool
@return: True if the data store is empty, False otherwise.
@rtype: bool
"""
# No pipes should exist.
if len(self):
if verbosity:
stderr.write(
"The relax data store contains the data pipes %s.\n" %
sorted(self.keys()))
return False
# Objects which should be in here.
blacklist = ['pipe_bundles', 'relax_gui']
# An object has been added to the data store.
for name in dir(self):
# Skip the data store methods.
if name in self.__class__.__dict__:
continue
# Skip the dict methods.
if name in dict.__dict__:
continue
# Skip special objects.
if search("^__", name):
continue
# Blacklisted objects to skip.
if name in blacklist:
continue
# An object has been added.
if verbosity:
stderr.write("The relax data store contains the object %s.\n" %
name)
return False
# The data store is empty.
return True
def from_xml(self, file, dir=None, pipe_to=None, verbosity=1):
"""Parse a XML document representation of a data pipe, and load it into the relax data store.
@param file: The open file object.
@type file: file
@keyword dir: The name of the directory containing the results file (needed for loading external files).
@type dir: str
@keyword pipe_to: The data pipe to load the XML data pipe into (the file must only contain one data pipe).
@type pipe_to: str
@keyword verbosity: A flag specifying the amount of information to print. The higher the value, the greater the verbosity.
@type verbosity: int
@raises RelaxError: If pipe_to is given and the file contains multiple pipe elements; or if the data pipes in the XML file already exist in the relax data store; or if the data pipe type is invalid; or if the target data pipe is not empty.
@raises RelaxNoPipeError: If pipe_to is given but the data pipe does not exist.
@raises RelaxError: If the data pipes in the XML file already exist in the relax data store, or if the data pipe type is invalid.
@raises RelaxPipeError: If the data pipes of the XML file are already present in the relax data store.
"""
# Create the XML document from the file.
doc = xml.dom.minidom.parse(file)
# Get the relax node.
relax_node = doc.childNodes[0]
# Get the relax version of the XML file.
file_version = relax_node.getAttribute('file_version')
if file_version == '':
file_version = 1
else:
file_version = int(file_version)
# Get the pipe nodes.
pipe_nodes = relax_node.getElementsByTagName('pipe')
# Structure for the names of the new pipes.
pipes = []
# Target loading to a specific pipe (for pipe results reading).
if pipe_to:
# Check if there are multiple pipes in the XML file.
if len(pipe_nodes) > 1:
raise RelaxError(
"The pipe_to target pipe argument '%s' cannot be given as the file contains multiple pipe elements."
% pipe_to)
# The pipe type.
pipe_type = pipe_nodes[0].getAttribute('type')
# Check that the pipe already exists.
if not pipe_to in self:
raise RelaxNoPipeError(pipe_to)
# Check if the pipe type matches.
if pipe_type != self[pipe_to].pipe_type:
raise RelaxError(
"The XML file pipe type '%s' does not match the pipe type '%s'"
% (pipe_type, self[pipe_to].pipe_type))
# Check if the pipe is empty.
if not self[pipe_to].is_empty():
raise RelaxError("The data pipe '%s' is not empty." % pipe_to)
# Load the data.
self[pipe_to].from_xml(pipe_nodes[0],
dir=dir,
file_version=file_version)
# Store the pipe name.
pipes.append(pipe_to)
# Load the state.
else:
# Get the GUI nodes.
gui_nodes = relax_node.getElementsByTagName('relax_gui')
if gui_nodes:
self.relax_gui.from_xml(gui_nodes[0],
file_version=file_version)
# Get the sequence alignment nodes.
seq_align_nodes = relax_node.getElementsByTagName(
'sequence_alignments')
if seq_align_nodes:
# Initialise the object.
self.sequence_alignments = Sequence_alignments()
# Populate it.
self.sequence_alignments.from_xml(seq_align_nodes[0],
file_version=file_version)
# Recreate all the data store data structures.
xml_to_object(
relax_node,
self,
file_version=file_version,
blacklist=['pipe', 'relax_gui', 'sequence_alignments'])
# Checks.
for pipe_node in pipe_nodes:
# The pipe name and type.
pipe_name = str(pipe_node.getAttribute('name'))
pipe_type = pipe_node.getAttribute('type')
# Existence check.
if pipe_name in self:
raise RelaxPipeError(pipe_name)
# Valid type check.
if not pipe_type in pipe_control.pipes.VALID_TYPES:
raise RelaxError(
"The data pipe type '%s' is invalid and must be one of the strings in the list %s."
% (pipe_type, pipe_control.pipes.VALID_TYPES))
# Load the data pipes.
for pipe_node in pipe_nodes:
# The pipe name and type.
pipe_name = str(pipe_node.getAttribute('name'))
pipe_type = pipe_node.getAttribute('type')
# Add the data pipe.
switch = False
if self.current_pipe == None:
switch = True
self.add(pipe_name, pipe_type, switch=switch)
# Fill the pipe.
self[pipe_name].from_xml(pipe_node,
file_version=file_version,
dir=dir)
# Store the pipe name.
pipes.append(pipe_name)
# Set the current pipe.
if self.current_pipe in self:
builtins.cdp = self[self.current_pipe]
# Finally update the molecule, residue, and spin metadata for each data pipe.
for pipe in pipes:
pipe_control.mol_res_spin.metadata_update(pipe=pipe)
# Backwards compatibility transformations.
self._back_compat_hook(file_version, pipes=pipes)
def to_xml(self, file, pipes=None):
"""Create a XML document representation of the current data pipe.
This method creates the top level XML document including all the information needed
about relax, calls the PipeContainer.xml_write() method to fill in the document contents,
and writes the XML into the file object.
@param file: The open file object.
@type file: file
@param pipes: The name of the pipe, or list of pipes to place in the XML file.
@type pipes: str or list of str
"""
# The pipes to include in the XML file.
all = False
if not pipes:
all = True
pipes = list(self.keys())
elif isinstance(pipes, str):
pipes = [pipes]
# Sort the pipes.
pipes.sort()
# Create the XML document object.
xmldoc = xml.dom.minidom.Document()
# Create the top level element, including the relax URL.
top_element = xmldoc.createElementNS('http://www.nmr-relax.com',
'relax')
top_element.setAttribute("xmlns", "http://www.nmr-relax.com")
# Append the element.
xmldoc.appendChild(top_element)
# Set the relax version number, and add a creation time.
top_element.setAttribute('version', version.version)
top_element.setAttribute('time', asctime())
top_element.setAttribute('file_version', "2")
if version.repo_head:
top_element.setAttribute('head', version.repo_head)
if version.repo_url:
top_element.setAttribute('url',
version.repo_url.replace('\n', '; '))
# Add all objects in the data store base object to the XML element.
if all:
blacklist = list(self.__class__.__dict__.keys()) + list(
dict.__dict__.keys())
for name in dir(self):
# Skip blacklisted objects.
if name in blacklist:
continue
# Skip special objects.
if search('^_', name):
continue
# Execute any to_xml() methods, and add that object to the blacklist.
obj = getattr(self, name)
if hasattr(obj, 'to_xml'):
obj.to_xml(xmldoc, top_element)
blacklist = blacklist + [name]
# Remove the current data pipe from the blacklist!
blacklist.remove('current_pipe')
# Add all simple python objects within the store.
fill_object_contents(xmldoc,
top_element,
object=self,
blacklist=blacklist)
# Loop over the pipes.
for pipe in pipes:
# Create the pipe XML element and add it to the top level XML element.
pipe_element = xmldoc.createElement('pipe')
top_element.appendChild(pipe_element)
# Set the data pipe attributes.
pipe_element.setAttribute('desc',
'The contents of a relax data pipe')
pipe_element.setAttribute('name', pipe)
pipe_element.setAttribute('type', self[pipe].pipe_type)
# Fill the data pipe XML element.
self[pipe].to_xml(xmldoc,
pipe_element,
pipe_type=self[pipe].pipe_type)
# Write out the XML file.
file.write(xmldoc.toprettyxml(indent=' '))
