Author: bugman
Date: Fri Dec 10 16:27:22 2010
New Revision: 11758
URL: http://svn.gna.org/viewcvs/relax?rev=11758&view=rev
Log:
The molecule type can now be specified.
Modified:
1.3/data/mol_res_spin.py
1.3/generic_fns/mol_res_spin.py
1.3/prompt/molecule.py
1.3/test_suite/shared_data/model_free/OMP/final_results_trunc_1.3.bz2
Modified: 1.3/data/mol_res_spin.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/data/mol_res_spin.py?rev=11758&r1=11757&r2=11758&view=diff
==============================================================================
--- 1.3/data/mol_res_spin.py (original)
+++ 1.3/data/mol_res_spin.py Fri Dec 10 16:27:22 2010
@@ -500,11 +500,14 @@
class MoleculeContainer(Prototype):
"""Class containing all the molecule specific data."""
- def __init__(self, mol_name=None):
+ def __init__(self, mol_name=None, mol_type=None):
"""Set up the default objects of the molecule data container."""
# The name of the molecule, corresponding to that of the structure
file if specified.
self.name = mol_name
+
+ # The type of molecule.
+ self.type = mol_type
# The empty residue list.
self.res = ResidueList()
@@ -558,7 +561,7 @@
# An object has been added to the container.
for name in dir(self):
# Skip the objects initialised in __init__().
- if name == 'name' or name == 'res':
+ if name in ['name', 'res', 'type']:
continue
# Skip the MoleculeContainer methods.
@@ -605,12 +608,13 @@
return text
- def add_item(self, mol_name=None):
+ def add_item(self, mol_name=None, mol_type=None):
"""Append an empty MoleculeContainer to the MoleculeList."""
# If no molecule data exists, replace the empty first molecule with
this molecule (just a renaming).
if self.is_empty():
self[0].name = mol_name
+ self[0].type = mol_type
# Otherwise append an empty MoleculeContainer.
else:
@@ -620,7 +624,7 @@
raise RelaxError("The molecule '%s' already exists in
the sequence." % mol_name)
# Append an empty MoleculeContainer.
- self.append(MoleculeContainer(mol_name))
+ self.append(MoleculeContainer(mol_name, mol_type))
def is_empty(self):
@@ -656,7 +660,10 @@
name = mol_node.getAttribute('name')
if name == 'None':
name = None
- self.add_item(mol_name=name)
+ type = mol_node.getAttribute('type')
+ if type == 'None':
+ type = None
+ self.add_item(mol_name=name, mol_type=type)
# Get the residue nodes.
res_nodes = mol_node.getElementsByTagName('res')
@@ -683,9 +690,10 @@
# Set the molecule attributes.
mol_element.setAttribute('desc', 'Molecule container')
mol_element.setAttribute('name', str(self[i].name))
+ mol_element.setAttribute('type', str(self[i].type))
# Add all simple python objects within the MoleculeContainer to
the XML element.
- fill_object_contents(doc, mol_element, object=self[i],
blacklist=['name', 'res'] + list(self[i].__class__.__dict__.keys()))
+ fill_object_contents(doc, mol_element, object=self[i],
blacklist=['name', 'res', 'type'] + list(self[i].__class__.__dict__.keys()))
# Add the residue data.
self[i].res.to_xml(doc, mol_element)
Modified: 1.3/generic_fns/mol_res_spin.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/mol_res_spin.py?rev=11758&r1=11757&r2=11758&view=diff
==============================================================================
--- 1.3/generic_fns/mol_res_spin.py (original)
+++ 1.3/generic_fns/mol_res_spin.py Fri Dec 10 16:27:22 2010
@@ -50,6 +50,14 @@
from relax_warnings import RelaxWarning
+ALLOWED_MOL_TYPES = ['protein',
+ 'DNA',
+ 'RNA',
+ 'organic molecule',
+ 'inorganic molecule'
+]
+"""The list of allowable molecule types."""
+
id_string_doc = """
Identification string documentation
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -803,15 +811,21 @@
return spin_num
-def create_molecule(mol_name=None):
+def create_molecule(mol_name=None, mol_type=None):
"""Add a molecule into the relax data store.
@keyword mol_name: The name of the molecule.
@type mol_name: str
+ @keyword mol_type: The type of molecule.
+ @type mol_type: str
"""
# Test if the current data pipe exists.
pipes.test()
+
+ # Test the molecule type.
+ if mol_type and mol_type not in ALLOWED_MOL_TYPES:
+ raise RelaxError("The molecule type '%s' must be one of %s" %
(mol_type, ALLOWED_MOL_TYPES))
# Test if the molecule name already exists.
for i in xrange(len(cdp.mol)):
@@ -819,7 +833,7 @@
raise RelaxError("The molecule '" + repr(mol_name) + "' already
exists in the relax data store.")
# Append the molecule.
- cdp.mol.add_item(mol_name=mol_name)
+ cdp.mol.add_item(mol_name=mol_name, mol_type=mol_type)
def create_residue(res_num=None, res_name=None, mol_name=None):
Modified: 1.3/prompt/molecule.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/prompt/molecule.py?rev=11758&r1=11757&r2=11758&view=diff
==============================================================================
--- 1.3/prompt/molecule.py (original)
+++ 1.3/prompt/molecule.py Fri Dec 10 16:27:22 2010
@@ -91,7 +91,7 @@
copy_molecule(pipe_from=pipe_from, mol_from=mol_from,
pipe_to=pipe_to, mol_to=mol_to)
- def create(self, mol_name=None):
+ def create(self, mol_name=None, type=None):
"""Function for creating a new molecule.
Keyword Arguments
@@ -99,12 +99,16 @@
mol_name: The name of the molecule.
+ type: The type of molecule.
+
Description
~~~~~~~~~~~
This function will add a new molecule data container to the relax
data storage object. The
- same molecule name cannot be used more than once.
+ same molecule name cannot be used more than once. The molecule type
need not be specified.
+ However if it given, it should be one of 'protein', 'RNA', 'DNA',
'organic molecule',
+ 'inorganic molecule'.
Examples
@@ -120,14 +124,16 @@
# Function intro text.
if self._exec_info.intro:
text = self._exec_info.ps3 + "molecule.create("
- text = text + "mol_name=" + repr(mol_name) + ")"
+ text = text + "mol_name=" + repr(mol_name)
+ text = text + ", type=" + repr(type) + ")"
print(text)
# The argument checks.
arg_check.is_str(mol_name, 'molecule name')
-
- # Execute the functional code.
- create_molecule(mol_name=mol_name)
+ arg_check.is_str(type, 'molecule type', can_be_none=True)
+
+ # Execute the functional code.
+ create_molecule(mol_name=mol_name, mol_type=type)
def delete(self, mol_id=None):
Modified:
1.3/test_suite/shared_data/model_free/OMP/final_results_trunc_1.3.bz2
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/shared_data/model_free/OMP/final_results_trunc_1.3.bz2?rev=11758&r1=11757&r2=11758&view=diff
==============================================================================
Binary files - no diff available.
r11758 - in /1.3: data/ generic_fns/ prompt/ test_suite/shared_data/model_free/OMP/