Author: bugman
Date: Mon Jan 12 10:26:56 2009
New Revision: 8402
URL: http://svn.gna.org/viewcvs/relax?rev=8402&view=rev
Log:
Large renaming of 'structure' to 'molecule' for the structral objects.
Modified:
branches/multi_structure/generic_fns/structure/api_base.py
Modified: branches/multi_structure/generic_fns/structure/api_base.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_structure/generic_fns/structure/api_base.py?rev=8402&r1=8401&r2=8402&view=diff
==============================================================================
--- branches/multi_structure/generic_fns/structure/api_base.py (original)
+++ branches/multi_structure/generic_fns/structure/api_base.py Mon Jan 12
10:26:56 2009
@@ -689,11 +689,11 @@
num = None
self.add_item(model_num=num)
- # Get the structure nodes.
- struct_nodes = model_node.getElementsByTagName('struct')
-
- # Recreate the structure data structures for the current model.
- self[-1].struct.from_xml(struct_nodes)
+ # Get the molecule nodes.
+ mol_nodes = model_node.getElementsByTagName('mol')
+
+ # Recreate the molecule data structures for the current model.
+ self[-1].mol.from_xml(mol_nodes)
def to_xml(self, doc, element):
@@ -716,10 +716,10 @@
model_element.setAttribute('num', str(self[i].num))
# Add all simple python objects within the ModelContainer to the
XML element.
- fill_object_contents(doc, model_element, object=self[i],
blacklist=['num', 'struct'] + self[i].__class__.__dict__.keys())
-
- # Add the structure data.
- self[i].struct.to_xml(doc, model_element)
+ fill_object_contents(doc, model_element, object=self[i],
blacklist=['num', 'mol'] + self[i].__class__.__dict__.keys())
+
+ # Add the molecule data.
+ self[i].mol.to_xml(doc, model_element)
@@ -732,8 +732,8 @@
# The model number.
self.num = model_num
- # The empty structure list.
- self.struct = StructList()
+ # The empty molecule list.
+ self.mol = MolList()
def __repr__(self):
@@ -750,9 +750,9 @@
text = text + "\n"
text = text + "Objects:\n"
for name in dir(self):
- # Structure list.
- if name == 'struct':
- text = text + " struct: The list of %s structures within the
model.\n" % len(self.struct)
+ # Molecule list.
+ if name == 'mol':
+ text = text + " mol: The list of %s molecules within the
model.\n" % len(self.mol)
continue
# Skip the ModelContainer methods.
@@ -784,7 +784,7 @@
# An object has been added to the container.
for name in dir(self):
# Skip the objects initialised in __init__().
- if name == 'num' or name == 'struct':
+ if name == 'num' or name == 'mol':
continue
# Skip the ModelContainer methods.
@@ -798,8 +798,8 @@
# An object has been added.
return False
- # The structure list is not empty.
- if not self.struct.is_empty():
+ # The molecule list is not empty.
+ if not self.mol.is_empty():
return False
# The ModelContainer is unmodified.
@@ -807,8 +807,8 @@
-class StructList(list):
- """List type data container for holding the different structures within
one model."""
+class MolList(list):
+ """List type data container for holding the different molecules of one
model."""
def __repr__(self):
"""The string representation of the object.
@@ -817,46 +817,46 @@
value or the "<...desc...>" notation), a rich-formatted description of
the object is given.
"""
- text = "Structures.\n\n"
+ text = "Molecules.\n\n"
text = text + "%-8s%-8s" % ("Index", "Name") + "\n"
for i in xrange(len(self)):
text = text + "%-8i%-8s" % (i, self[i].name) + "\n"
return text
- def add_item(self, struct_name=None, struct_cont=None):
- """Append the given StructContainer instance to the StructList.
-
- @keyword struct_name: The structure number.
- @type struct_name: int
- @keyword struct_cont: The data structure for the structure.
- @type struct_cont: StructContainer instance
- """
-
- # If no structure data exists, replace the empty first structure with
this structure (just a renaming).
+ def add_item(self, mol_name=None, mol_cont=None):
+ """Append the given MolContainer instance to the MolList.
+
+ @keyword mol_name: The molecule number.
+ @type mol_name: int
+ @keyword mol_cont: The data structure for the molecule.
+ @type mol_cont: MolContainer instance
+ """
+
+ # If no molecule data exists, replace the empty first molecule with
this molecule (just a renaming).
if self.is_empty():
- self[0].name = struct_name
-
- # Otherwise append an empty StructContainer.
+ self[0].name = mol_name
+
+ # Otherwise append an empty MolContainer.
else:
- # Test if the structure already exists.
+ # Test if the molecule already exists.
for i in xrange(len(self)):
- if self[i].name == struct_name:
- raise RelaxError, "The structure '" + `struct_name` + "'
already exists."
-
- # Append an empty StructContainer.
- self.append(struct_cont)
+ if self[i].name == mol_name:
+ raise RelaxError, "The molecule '" + `mol_name` + "'
already exists."
+
+ # Append an empty MolContainer.
+ self.append(mol_cont)
def is_empty(self):
- """Method for testing if this StructList object is empty.
-
- @return: True if this list only has one StructContainer and the
structure name has not
+ """Method for testing if this MolList object is empty.
+
+ @return: True if this list only has one MolContainer and the
molecule name has not
been set, False otherwise.
@rtype: bool
"""
- # There is only one StructContainer and it is empty.
+ # There is only one MolContainer and it is empty.
if len(self) == 1 and self[0].is_empty():
return True
@@ -864,53 +864,53 @@
return False
- def from_xml(self, struct_nodes):
- """Recreate a structure list data structure from the XML structure
nodes.
-
- @param struct_nodes: The structure XML nodes.
- @type struct_nodes: xml.dom.minicompat.NodeList instance
+ def from_xml(self, mol_nodes):
+ """Recreate a molecule list data structure from the XML molecule nodes.
+
+ @param mol_nodes: The molecule XML nodes.
+ @type mol_nodes: xml.dom.minicompat.NodeList instance
"""
# Test if empty.
if not self.is_empty():
raise RelaxFromXMLNotEmptyError, self.__class__.__name__
- # Loop over the structures.
- for struct_node in struct_nodes:
- # Get the structure details and add the structure to the
StructList structure.
- name = eval(struct_node.getAttribute('name'))
+ # Loop over the molecules.
+ for mol_node in mol_nodes:
+ # Get the molecule details and add the molecule to the MolList
structure.
+ name = eval(mol_node.getAttribute('name'))
if name == 'None':
name = None
- self.add_item(struct_name=name)
-
- # Get the structure nodes.
- struct_nodes = struct_node.getElementsByTagName('struct')
-
- # Recreate the structure data structures for the current structure.
- self[-1].struct.from_xml(struct_nodes)
+ self.add_item(mol_name=name)
+
+ # Get the molecule nodes.
+ mol_nodes = mol_node.getElementsByTagName('mol')
+
+ # Recreate the molecule data structures for the current molecule.
+ self[-1].mol.from_xml(mol_nodes)
def to_xml(self, doc, element):
- """Create XML elements for each structure.
+ """Create XML elements for each molecule.
@param doc: The XML document object.
@type doc: xml.dom.minidom.Document instance
- @param element: The element to add the structure XML elements to.
+ @param element: The element to add the molecule XML elements to.
@type element: XML element object
"""
- # Loop over the structures.
+ # Loop over the molecules.
for i in xrange(len(self)):
- # Create an XML element for this structure and add it to the
higher level element.
- struct_element = doc.createElement('struct')
- element.appendChild(struct_element)
-
- # Set the structure attributes.
- struct_element.setAttribute('desc', 'Structure container')
- struct_element.setAttribute('name', str(self[i].name))
-
- # Add all simple python objects within the StructContainer to the
XML element.
- fill_object_contents(doc, struct_element, object=self[i],
blacklist=['name'] + self[i].__class__.__dict__.keys())
-
- # Add the structure data.
- self[i].struct.to_xml(doc, struct_element)
+ # Create an XML element for this molecule and add it to the higher
level element.
+ mol_element = doc.createElement('mol')
+ element.appendChild(mol_element)
+
+ # Set the molecule attributes.
+ mol_element.setAttribute('desc', 'Molecule container')
+ mol_element.setAttribute('name', str(self[i].name))
+
+ # Add all simple python objects within the MolContainer to the XML
element.
+ fill_object_contents(doc, mol_element, object=self[i],
blacklist=['name'] + self[i].__class__.__dict__.keys())
+
+ # Add the molecule data.
+ self[i].mol.to_xml(doc, mol_element)
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