Author: bugman
Date: Sat Mar 10 00:42:21 2007
New Revision: 3141
URL: http://svn.gna.org/viewcvs/relax?rev=3141&view=rev
Log:
Completion of the core of the molecule-residue-spin data structures.
All of the initialisation of the class variables and objects in all six
classes have been shifted
into __init__() methods so that new copies of the objects are created when
molecules, residues, or
spins are added to the structure.
The __repr__() methods of all classes have been updated and return a proper
text representation of
the objects.
The XList class docstrings have been updated.
Modified:
1.3/data/mol_res_spin.py
Modified: 1.3/data/mol_res_spin.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/data/mol_res_spin.py?rev=3141&r1=3140&r2=3141&view=diff
==============================================================================
--- 1.3/data/mol_res_spin.py (original)
+++ 1.3/data/mol_res_spin.py Sat Mar 10 00:42:21 2007
@@ -36,36 +36,69 @@
class SpinContainer:
"""Class containing all the spin system specific data."""
-
- def __repr__(self):
+ def __init__(self):
+ """Set up the default objects of the spin system data container."""
+
+ # The spin system name and number.
+ self.name = None
+ self.num = None
+ self.select = 1
+
+
+ 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 = "Class containing all the spin system specific data.\n\n"
- # Empty.
- if not len(self):
- text = text + "The class contains no data.\n"
-
- # Not empty.
- else:
- text = text + "The spin system container has the following
keys:\n"
- for key in self:
- text = text + " " + `key` + "\n"
- text = text + "\nThese can be accessed by typing
'relax_data_store.res[key]'.\n"
+ # Objects.
+ text = text + "\n"
+ text = text + "Objects:\n"
+ for name in dir(self):
+ # Spin systems.
+ if name == 'spin':
+ text = text + " spin: The list of spin systems of the
residues\n"
+
+ # Skip certain objects.
+ if match("^_", name) or name == 'spin':
+ continue
+
+ # Add the object's attribute to the text string.
+ text = text + " " + name + ": " + `getattr(self, name)` + "\n"
return text
class SpinList(ListType):
- """Empty data container for spin system specific data."""
-
-
- def __repr__(self):
+ """List type data container for spin system specific data."""
+
+ def __init__(self):
+ """Set up the first spin system data container."""
+
+ # Add the initial spin system container at index 0.
+ self.append(SpinContainer())
+
+
+ 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 = "Spin systems.\n\n"
+
+ # Residue data.
text = text + "%-8s%-8s%-8s%-10s" % ("Index", "Number", "Name",
"Selected") + "\n"
for i in xrange(len(self)):
- text = text + "%-8i%-8i%-8s%-10i" % (i, self[i].num,
self[i].name, self[i].select) + "\n"
- text = text + "\nThese can be accessed by typing
'relax_data_store.res[key][index]'.\n"
+ text = text + "%-8i%-8s%-8s%-10i" % (i, `self[i].num`,
self[i].name, self[i].select) + "\n"
+ text = text + "\nThese can be accessed by typing
'D.mol[i].res[j].spin[k]', where D is the relax data storage object.\n"
+
return text
@@ -82,40 +115,71 @@
class ResidueContainer:
"""Class containing all the residue specific data."""
-
- def __repr__(self):
- text = "Class containing all the residue specific data.\n\n"
-
- # Empty.
- if not len(self):
- text = text + "The class contains no data.\n"
-
- # Not empty.
- else:
- text = text + "The residue container has the following keys:\n"
- for key in self:
- text = text + " " + `key` + "\n"
- text = text + "\nThese can be accessed by typing
'relax_data_store.res[key]'.\n"
-
- return text
-
-
- def add_list(self, key):
- """Function for adding an empty container to the dictionary."""
-
- self[key] = ResidueList()
+ def __init__(self):
+ """Set up the default objects of the residue data container."""
+
+ # The residue name and number.
+ self.name = None
+ self.num = None
+
+ # The empty spin system list.
+ self.spin = SpinList()
+
+
+ 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 = "Class containing all the residue specific data.\n"
+
+ # Objects.
+ text = text + "\n"
+ text = text + "Objects:\n"
+ for name in dir(self):
+ # Spin systems.
+ if name == 'spin':
+ text = text + " spin: The list of spin systems of the
residues\n"
+
+ # Skip certain objects.
+ if match("^_", name) or name == 'spin':
+ continue
+
+ # Add the object's attribute to the text string.
+ text = text + " " + name + ": " + `getattr(self, name)` + "\n"
+
+ return text
class ResidueList(ListType):
- """Empty data container for residue specific data."""
-
-
- def __repr__(self):
- text = "Sequence data.\n\n"
- text = text + "%-8s%-8s%-8s%-10s" % ("Index", "Number", "Name",
"Selected") + "\n"
+ """List type data container for residue specific data."""
+
+ def __init__(self):
+ """Set up the first residue data container."""
+
+ # Add the initial residue container at index 0.
+ self.append(ResidueContainer())
+
+
+ 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 = "Residues.\n\n"
+
+ # Residue data.
+ text = text + "%-8s%-8s%-8s" % ("Index", "Number", "Name") + "\n"
for i in xrange(len(self)):
- text = text + "%-8i%-8i%-8s%-10i" % (i, self[i].num,
self[i].name, self[i].select) + "\n"
- text = text + "\nThese can be accessed by typing
'relax_data_store.res[key][index]'.\n"
+ text = text + "%-8i%-8s%-8s" % (i, `self[i].num`, self[i].name)
+ "\n"
+ text = text + "\nThese can be accessed by typing 'D.mol[i].res[j]',
where D is the relax data storage object.\n"
+
return text
@@ -132,11 +196,14 @@
class MoleculeContainer:
"""Class containing all the molecule specific data."""
- # The name of the molecule, corresponding to that of the structure file
if specified.
- name = None
-
- # The empty residue list.
- res = ResidueList()
+ def __init__(self):
+ """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 = None
+
+ # The empty residue list.
+ self.res = ResidueList()
def __repr__(self):
@@ -155,7 +222,7 @@
for name in dir(self):
# Residue list.
if name == 'res':
- text = text + " res: The list of the residues of the
molecule is the object\n"
+ text = text + " res: The list of the residues of the
molecule\n"
# Skip certain objects.
if match("^_", name) or name == 'res':
@@ -168,7 +235,13 @@
class MoleculeList(ListType):
- """Empty data container for the molecule specific data."""
+ """List type data container for the molecule specific data."""
+
+ def __init__(self):
+ """Set up the first molecule data container."""
+
+ # Add the initial molecule container at index 0.
+ self.append(MoleculeContainer())
def __repr__(self):
@@ -176,7 +249,7 @@
text = text + "%-8s%-8s" % ("Index", "Name") + "\n"
for i in xrange(len(self)):
text = text + "%-8i%-8s" % (i, self[i].name) + "\n"
- text = text + "\nThese can be accessed by typing 'D.mol[index]',
where D is the relax data storage object.\n"
+ text = text + "\nThese can be accessed by typing 'D.mol[i]', where D
is the relax data storage object.\n"
return text
r3141 - /1.3/data/mol_res_spin.py