Author: bugman
Date: Mon Jun 11 22:27:24 2012
New Revision: 16871
URL: http://svn.gna.org/viewcvs/relax?rev=16871&view=rev
Log:
Shifted the id_match() method to the correct class!
Modified:
branches/interatomic/data/interatomic.py
Modified: branches/interatomic/data/interatomic.py
URL:
http://svn.gna.org/viewcvs/relax/branches/interatomic/data/interatomic.py?rev=16871&r1=16870&r2=16871&view=diff
==============================================================================
--- branches/interatomic/data/interatomic.py (original)
+++ branches/interatomic/data/interatomic.py Mon Jun 11 22:27:24 2012
@@ -77,118 +77,6 @@
text += " %s: %s\n" % (name, repr(getattr(self, name)))
return text
-
-
- def is_empty(self):
- """Method for testing if this InteratomContainer object is empty.
-
- @return: True if this container is empty, False otherwise.
- @rtype: bool
- """
-
- # An object has been added to the container.
- for name in dir(self):
- # Skip the objects initialised in __init__().
- if name in ['spin_id1', 'spin_id2']:
- continue
-
- # Skip the SpinContainer methods.
- if name == 'is_empty':
- continue
-
- # Skip special objects.
- if match("^_", name):
- continue
-
- # An object has been added.
- return False
-
- # The SpinContainer is unmodified.
- return True
-
-
-
-class InteratomList(list):
- """List type data container for interatomic specific data."""
-
- 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 = "Interatomic data.\n\n"
-
- # The data.
- text += "%-25s%-25s%-25s" % ("Index", "Spin ID 1", "Spin ID 2") +
"\n"
- for i in xrange(len(self)):
- text += "%-25i%-25s%-25s\n\n" % (i, self[i].spin_id1,
self[i].spin_id2)
-
- return text
-
-
- def add_item(self, spin_id1=None, spin_id2=None):
- """Append an empty container to the list.
-
- @keyword spin_id1: The spin ID string of the first atom.
- @type spin_id1: str
- @keyword spin_id2: The spin ID string of the first atom.
- @type spin_id2: str
- @return: The new interatomic data container.
- @rtype: InteratomContainer instance
- """
-
- # Check if the two spin ID have already been added.
- for i in range(len(self)):
- if self[i].id_match(spin_id1, spin_id2):
- raise RelaxError("The spin pair %s and %s have already been
added." % (spin_id1, spin_id2))
-
- # Append a new InteratomContainer.
- cont = InteratomContainer(spin_id1, spin_id2)
- self.append(cont)
-
- # Return the container.
- return cont
-
-
- def is_empty(self):
- """Method for testing if this InteratomList object is empty.
-
- @return: True if this list contains no InteratomContainers, False
otherwise.
- @rtype: bool
- """
-
- # There are no InteratomContainers.
- if len(self) == 0:
- return True
-
- # Otherwise.
- return False
-
-
- def from_xml(self, interatom_nodes, file_version=None):
- """Recreate an interatomic list data structure from the XML spin
nodes.
-
- @param interatom_nodes: The spin XML nodes.
- @type interatom_nodes: xml.dom.minicompat.NodeList instance
- @keyword file_version: The relax XML version of the XML file.
- @type file_version: int
- """
-
- # Test if empty.
- if not self.is_empty():
- raise RelaxFromXMLNotEmptyError(self.__class__.__name__)
-
- # Loop over the containers.
- for interatom_node in interatom_nodes:
- # Get the interatomic spin details and add a container to the
InteratomList structure.
- spin_id1 = str(interatom_node.getAttribute('spin_id1'))
- spin_id2 = str(interatom_node.getAttribute('spin_id2'))
- self.add_item(spin_id1=spin_id1, spin_id2=spin_id2)
-
- # Recreate the current container.
- xml_to_object(interatom_node, self[-1],
file_version=file_version)
def id_match(self, spin_id1, spin_id2):
@@ -207,6 +95,118 @@
return True
else:
return False
+
+
+ def is_empty(self):
+ """Method for testing if this InteratomContainer object is empty.
+
+ @return: True if this container is empty, False otherwise.
+ @rtype: bool
+ """
+
+ # An object has been added to the container.
+ for name in dir(self):
+ # Skip the objects initialised in __init__().
+ if name in ['spin_id1', 'spin_id2']:
+ continue
+
+ # Skip the SpinContainer methods.
+ if name == 'is_empty':
+ continue
+
+ # Skip special objects.
+ if match("^_", name):
+ continue
+
+ # An object has been added.
+ return False
+
+ # The SpinContainer is unmodified.
+ return True
+
+
+
+class InteratomList(list):
+ """List type data container for interatomic specific data."""
+
+ 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 = "Interatomic data.\n\n"
+
+ # The data.
+ text += "%-25s%-25s%-25s" % ("Index", "Spin ID 1", "Spin ID 2") +
"\n"
+ for i in xrange(len(self)):
+ text += "%-25i%-25s%-25s\n\n" % (i, self[i].spin_id1,
self[i].spin_id2)
+
+ return text
+
+
+ def add_item(self, spin_id1=None, spin_id2=None):
+ """Append an empty container to the list.
+
+ @keyword spin_id1: The spin ID string of the first atom.
+ @type spin_id1: str
+ @keyword spin_id2: The spin ID string of the first atom.
+ @type spin_id2: str
+ @return: The new interatomic data container.
+ @rtype: InteratomContainer instance
+ """
+
+ # Check if the two spin ID have already been added.
+ for i in range(len(self)):
+ if self[i].id_match(spin_id1, spin_id2):
+ raise RelaxError("The spin pair %s and %s have already been
added." % (spin_id1, spin_id2))
+
+ # Append a new InteratomContainer.
+ cont = InteratomContainer(spin_id1, spin_id2)
+ self.append(cont)
+
+ # Return the container.
+ return cont
+
+
+ def is_empty(self):
+ """Method for testing if this InteratomList object is empty.
+
+ @return: True if this list contains no InteratomContainers, False
otherwise.
+ @rtype: bool
+ """
+
+ # There are no InteratomContainers.
+ if len(self) == 0:
+ return True
+
+ # Otherwise.
+ return False
+
+
+ def from_xml(self, interatom_nodes, file_version=None):
+ """Recreate an interatomic list data structure from the XML spin
nodes.
+
+ @param interatom_nodes: The spin XML nodes.
+ @type interatom_nodes: xml.dom.minicompat.NodeList instance
+ @keyword file_version: The relax XML version of the XML file.
+ @type file_version: int
+ """
+
+ # Test if empty.
+ if not self.is_empty():
+ raise RelaxFromXMLNotEmptyError(self.__class__.__name__)
+
+ # Loop over the containers.
+ for interatom_node in interatom_nodes:
+ # Get the interatomic spin details and add a container to the
InteratomList structure.
+ spin_id1 = str(interatom_node.getAttribute('spin_id1'))
+ spin_id2 = str(interatom_node.getAttribute('spin_id2'))
+ self.add_item(spin_id1=spin_id1, spin_id2=spin_id2)
+
+ # Recreate the current container.
+ xml_to_object(interatom_node, self[-1],
file_version=file_version)
def to_xml(self, doc, element):
r16871 - /branches/interatomic/data/interatomic.py