Author: bugman
Date: Sun Nov 4 14:37:59 2007
New Revision: 3405
URL: http://svn.gna.org/viewcvs/relax?rev=3405&view=rev
Log:
Created the residue.display() user function.
This has been added to the data model redesign document. Two unit tests have
also been created for
the function.
Modified:
1.3/docs/data_model_redesign
1.3/generic_fns/residue.py
1.3/prompt/residue.py
1.3/test_suite/unit_tests/generic_fns/test_residue.py
Modified: 1.3/docs/data_model_redesign
URL:
http://svn.gna.org/viewcvs/relax/1.3/docs/data_model_redesign?rev=3405&r1=3404&r2=3405&view=diff
==============================================================================
--- 1.3/docs/data_model_redesign (original)
+++ 1.3/docs/data_model_redesign Sun Nov 4 14:37:59 2007
@@ -72,6 +72,7 @@
residue.copy()
residue.create() # This is currently named 'sequence.add()'.
residue.delete()
+ residue.display()
residue.rename()
residue.renumber()
Modified: 1.3/generic_fns/residue.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/residue.py?rev=3405&r1=3404&r2=3405&view=diff
==============================================================================
--- 1.3/generic_fns/residue.py (original)
+++ 1.3/generic_fns/residue.py Sun Nov 4 14:37:59 2007
@@ -158,6 +158,43 @@
mol.res.add_item()
+def display(res_id=None):
+ """Function for displaying the information associated with the residue.
+
+ @param res_id: The molecule and residue identifier string.
+ @type res_id: str
+ """
+
+ # Split up the selection string.
+ mol_token, res_token, spin_token = tokenise(res_id)
+
+ # Disallow spin selections.
+ if spin_token != None:
+ raise RelaxSpinSelectDisallowError
+
+ # The molecule selection string.
+ if mol_token:
+ mol_sel = '#' + mol_token
+ else:
+ mol_sel = None
+
+ # Molecule loop.
+ for mol in molecule_loop(mol_sel):
+ # Print a header.
+ print "\n\nMolecule: " + `mol.name`
+ print "%-8s%-8s%-10s" % ("Number", "Name", "Number of spins")
+
+ # The residue identifier for this molecule.
+ res_sel = '#' + mol.name
+ if res_token:
+ res_sel = res_sel + ':' + res_token
+
+ # Loop over the residues of this molecule.
+ for res in residue_loop(res_sel):
+ # Print the residue data.
+ print "%-8i%-8s%-10i" % (res.num, res.name, len(res.spin))
+
+
def rename(res_id, new_name=None):
"""Function for renaming residues.
@@ -239,24 +276,6 @@
return [ 'res' ]
-
- def display(self, run=None):
- """Function for displaying the sequence."""
-
- # Test if the run exists.
- if not run in relax_data_store.run_names:
- raise RelaxNoPipeError, run
-
- # Test if the sequence data is loaded.
- if not relax_data_store.res.has_key(run):
- raise RelaxNoSequenceError, run
-
- # Print a header.
- print "%-8s%-8s%-10s" % ("Number", "Name", "Selected")
-
- # Print the sequence.
- for i in xrange(len(relax_data_store.res[run])):
- print "%-8i%-8s%-10i" % (relax_data_store.res[run][i].num,
relax_data_store.res[run][i].name, relax_data_store.res[run][i].select)
def load_PDB_sequence(self, run=None):
Modified: 1.3/prompt/residue.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/prompt/residue.py?rev=3405&r1=3404&r2=3405&view=diff
==============================================================================
--- 1.3/prompt/residue.py (original)
+++ 1.3/prompt/residue.py Sun Nov 4 14:37:59 2007
@@ -198,27 +198,27 @@
residue.delete(res_id=res_id)
- def display(self, run=None):
- """Function for displaying the sequence.
-
- Keyword Arguments
- ~~~~~~~~~~~~~~~~~
-
- run: The name of the run.
- """
-
- # Function intro text.
- if self.__relax__.interpreter.intro:
- text = sys.ps3 + "sequence.display("
- text = text + "run=" + `run` + ")"
- print text
-
- # The run argument.
- if type(run) != str:
- raise RelaxStrError, ('run', run)
-
- # Execute the functional code.
- self.__relax__.generic.sequence.display(run=run)
+ def display(self, res_id=None):
+ """Function for displaying information about the residue(s).
+
+ Keyword Arguments
+ ~~~~~~~~~~~~~~~~~
+
+ res_id: The residue identification string.
+ """
+
+ # Function intro text.
+ if self.__relax__.interpreter.intro:
+ text = sys.ps3 + "residue.display("
+ text = text + "res_id=" + `res_id` + ")"
+ print text
+
+ # The res_id argument.
+ if type(res_id) != str:
+ raise RelaxStrError, ('residue identification string', res_id)
+
+ # Execute the functional code.
+ residue.display(res_id=res_id)
def rename(self, res_id=None, new_name=None):
@@ -328,5 +328,6 @@
# Add the residue identification string description.
copy.__doc__ = copy.__doc__ + "\n\n" + id_string_doc + "\n"
delete.__doc__ = delete.__doc__ + "\n\n" + id_string_doc + "\n"
+ display.__doc__ = display.__doc__ + "\n\n" + id_string_doc + "\n"
rename.__doc__ = rename.__doc__ + "\n\n" + id_string_doc + "\n"
renumber.__doc__ = renumber.__doc__ + "\n\n" + id_string_doc + "\n"
Modified: 1.3/test_suite/unit_tests/generic_fns/test_residue.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/unit_tests/generic_fns/test_residue.py?rev=3405&r1=3404&r2=3405&view=diff
==============================================================================
--- 1.3/test_suite/unit_tests/generic_fns/test_residue.py (original)
+++ 1.3/test_suite/unit_tests/generic_fns/test_residue.py Sun Nov 4 14:37:59
2007
@@ -55,12 +55,7 @@
relax_data_store.__reset__()
- def test_copy_between_molecules(self):
- """Test the copying of the residue data between different molecules.
-
- The function used is generic_fns.residue.copy().
- """
-
+ def setup_data(self):
# Create the first residue and add some data to its spin container.
residue.create(1, 'Ala')
relax_data_store['orig'].mol[0].res[0].spin[0].num = 111
@@ -77,6 +72,16 @@
# Change the first residue's data.
relax_data_store['orig'].mol[0].res[0].spin[0].num = 222
relax_data_store['orig'].mol[0].res[0].spin[0].x = 2
+
+
+ def test_copy_between_molecules(self):
+ """Test the copying of the residue data between different molecules.
+
+ The function used is generic_fns.residue.copy().
+ """
+
+ # Set up some data.
+ self.setup_data()
# Test the original residue.
self.assertEqual(relax_data_store['orig'].mol[0].res[0].num, 1)
@@ -359,6 +364,35 @@
self.assertRaises(RelaxSpinSelectDisallowError, residue.delete,
res_id='@2')
+ def test_display(self):
+ """Test the display of residue information.
+
+ The function used is generic_fns.residue.display().
+ """
+
+ # Set up some data.
+ self.setup_data()
+
+ # The following should all work without error.
+ residue.display()
+ residue.display(':1')
+ residue.display('#New mol:5')
+ residue.display('#Old mol:1')
+
+
+ def test_display_fail(self):
+ """Test the failure of the display of residue information.
+
+ The function used is generic_fns.residue.display().
+ """
+
+ # Set up some data.
+ self.setup_data()
+
+ # The following should fail.
+ self.assertRaises(RelaxSpinSelectDisallowError, residue.display,
'@N')
+
+
def test_rename(self):
"""Test the renaming of a residue.
r3405 - in /1.3: docs/ generic_fns/ prompt/ test_suite/unit_tests/generic_fns/