Author: bugman
Date: Tue Jul 3 10:18:17 2012
New Revision: 17149
URL: http://svn.gna.org/viewcvs/relax?rev=17149&view=rev
Log:
Better backwards compatibility of old relax results and state XML files for
the interatomic design.
The MoleculeContainer._back_compat_hook() method has been shifted into the
Relax_data_store._back_compat_hook() method. This allows the spin containers
with attached protons
to be converted (with new spin containers for the attached protons added)
after loading of the XML
state.
Modified:
branches/interatomic/data/__init__.py
branches/interatomic/data/mol_res_spin.py
Modified: branches/interatomic/data/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/interatomic/data/__init__.py?rev=17149&r1=17148&r2=17149&view=diff
==============================================================================
--- branches/interatomic/data/__init__.py (original)
+++ branches/interatomic/data/__init__.py Tue Jul 3 10:18:17 2012
@@ -188,6 +188,77 @@
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 interatomic data container design.
+ if 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):
+ spin.name = 'N'
+ elif search('C', spin.isotope):
+ spin.name = 'C'
+
+ # An attached proton - convert into a spin
container.
+ if hasattr(spin, 'attached_proton'):
+ # Create a new spin container for the
proton, then set up a dipole interaction between the two spins.
+ h_spin =
generic_fns.mol_res_spin.create_spin(mol_name=mol.name, res_num=res.num,
res_name=res.name, spin_name=spin.attached_proton)
+ h_spin.select = False
+ h_spin.element = 'H'
+ h_spin.isotope = '1H'
+ spin_id1 =
generic_fns.mol_res_spin.generate_spin_id(mol_name=mol.name, res_num=res.num,
res_name=res.name, spin_name=spin.name, spin_num=spin.num)
+ spin_id2 =
generic_fns.mol_res_spin.generate_spin_id(mol_name=mol.name, res_num=res.num,
res_name=res.name, spin_name='H')
+ generic_fns.dipole_pair.define(spin_id1,
spin_id2, verbose=False)
+
+ # Get the interatomic data container.
+ interatom =
generic_fns.interatomic.return_interatom(spin_id1=spin_id1, spin_id2=spin_id2)
+
+ # 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
+
+ # Delete the old structures.
+ if hasattr(spin, 'heteronuc_type'):
+ del spin.heteronuc_type
+ if hasattr(spin, 'proton_type'):
+ del spin.proton_type
+ if hasattr(spin, 'attached_proton'):
+ del spin.attached_proton
+ if hasattr(spin, 'r'):
+ del spin.r
+ if hasattr(spin, 'r_err'):
+ del spin.r_err
+ if hasattr(spin, 'r_sim'):
+ del spin.r_sim
+ if hasattr(spin, 'xh_vect'):
+ del spin.xh_vect
+
+
def add(self, pipe_name, pipe_type, bundle=None, switch=True):
"""Method for adding a new data pipe container to the dictionary.
@@ -329,6 +400,9 @@
# 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.
@@ -352,6 +426,9 @@
# 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:
@@ -384,12 +461,18 @@
# 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.keys():
__builtin__.cdp = self[self.current_pipe]
# Finally update the molecule, residue, and spin metadata.
generic_fns.mol_res_spin.metadata_update()
+
+ # Backwards compatibility transformations.
+ self._back_compat_hook(file_version, pipes=pipes)
def to_xml(self, file, pipes=None):
Modified: branches/interatomic/data/mol_res_spin.py
URL:
http://svn.gna.org/viewcvs/relax/branches/interatomic/data/mol_res_spin.py?rev=17149&r1=17148&r2=17149&view=diff
==============================================================================
--- branches/interatomic/data/mol_res_spin.py (original)
+++ branches/interatomic/data/mol_res_spin.py Tue Jul 3 10:18:17 2012
@@ -222,13 +222,26 @@
def add_item(self, spin_name=None, spin_num=None, select=True):
- """Function for appending an empty container to the list."""
+ """Appending an empty container to the list.
+
+ @keyword spin_name: The name of the new spin.
+ @type spin_name: str or None
+ @keyword spin_num: The number of the new spin.
+ @type spin_num: str or None
+ @keyword select: The selection flag.
+ @type select: bool
+ @return: The new container.
+ @rtype: SpinContainer instance
+ """
# If no spin data exists, replace the empty first spin with this
spin.
if self.is_empty():
self[0].num = spin_num
self[0].name = spin_name
self[0].select = select
+
+ # Return the container.
+ return self[0]
# Otherwise append a new SpinContainer.
else:
@@ -237,15 +250,18 @@
# Spin number has been supplied.
if spin_num != None:
if self[i].num == spin_num:
- raise RelaxError("The spin number '" +
repr(spin_num) + "' already exists.")
+ raise RelaxError("The spin number '%s' already
exists." % spin_name)
# No spin numbers.
else:
if self[i].name == spin_name:
- raise RelaxError("The unnumbered spin name '" +
repr(spin_name) + "' already exists.")
+ raise RelaxError("The unnumbered spin name '%s'
already exists." % spin_name)
# Append a new SpinContainer.
self.append(SpinContainer(spin_name, spin_num, select))
+
+ # Return the container.
+ return self[-1]
def is_empty(self):
@@ -634,66 +650,6 @@
text = text + " " + name + ": " + repr(getattr(self, name)) +
"\n"
return text
-
-
- def _back_compat_hook(self, file_version=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
- """
-
- # Loop over the residues.
- for res in self.res:
- # Loop over the spins.
- for spin in res.spin:
- # The interatomic data container design.
- if 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):
- spin.name = 'N'
- elif search('C', spin.isotope):
- spin.name = 'C'
-
- # Create a new spin container for the proton, then set
up a dipole interaction between the two spins.
- h_spin =
generic_fns.mol_res_spin.create_spin(mol_name=self.name, res_num=res.num,
res_name=res.name, spin_name='H')
- h_spin.select = False
- h_spin.element = 'H'
- h_spin.isotope = '1H'
- spin_id1 =
generic_fns.mol_res_spin.generate_spin_id(mol_name=self.name,
res_num=res.num, res_name=res.name, spin_name=spin.name, spin_num=spin.num)
- spin_id2 =
generic_fns.mol_res_spin.generate_spin_id(mol_name=self.name,
res_num=res.num, res_name=res.name, spin_name='H')
- generic_fns.dipole_pair.define(spin_id1, spin_id2,
verbose=False)
-
- # Get the interatomic data container.
- interatom =
generic_fns.interatomic.return_interatom(spin_id1=spin_id1, spin_id2=spin_id2)
-
- # 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
-
- # Delete the old structures.
- if hasattr(spin, 'heteronuc_type'):
- del spin.heteronuc_type
- if hasattr(spin, 'proton_type'):
- del spin.proton_type
- if hasattr(spin, 'attached_proton'):
- del spin.attached_proton
- if hasattr(spin, 'r'):
- del spin.r
- if hasattr(spin, 'r_err'):
- del spin.r_err
- if hasattr(spin, 'r_sim'):
- del spin.r_sim
- if hasattr(spin, 'xh_vect'):
- del spin.xh_vect
def is_empty(self):
@@ -826,9 +782,6 @@
# Recreate the residue data structures for the current molecule.
self[-1].res.from_xml(res_nodes, file_version=file_version)
- # Backwards compatibility transformations.
- self[-1]._back_compat_hook(file_version)
-
def to_xml(self, doc, element):
"""Create XML elements for each molecule.
r17149 - in /branches/interatomic/data: __init__.py mol_res_spin.py