Author: bugman
Date: Sun Nov 4 17:28:45 2007
New Revision: 3416
URL: http://svn.gna.org/viewcvs/relax?rev=3416&view=rev
Log:
Created the molecule.create() user function.
The user function and the function generic_fns.molecule.create() have been
written. Two unit tests
for the function have been created.
Modified:
1.3/generic_fns/molecule.py
1.3/prompt/molecule.py
1.3/test_suite/unit_tests/generic_fns/test_molecule.py
Modified: 1.3/generic_fns/molecule.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/molecule.py?rev=3416&r1=3415&r2=3416&view=diff
==============================================================================
--- 1.3/generic_fns/molecule.py (original)
+++ 1.3/generic_fns/molecule.py Sun Nov 4 17:28:45 2007
@@ -32,22 +32,21 @@
"""
-def copy(pipe_from=None, res_from=None, pipe_to=None, res_to=None):
- """Copy the contents of the residue structure from one residue to a new
residue.
-
- For copying to be successful, the res_from identification string must
match an existent residue.
- The new residue number must be unique.
-
- @param pipe_from: The data pipe to copy the residue from. This
defaults to the current data
- pipe.
+def copy(pipe_from=None, mol_from=None, pipe_to=None, mol_to=None):
+ """Copy the contents of a molecule container to a new molecule.
+
+ For copying to be successful, the mol_from identification string must
match an existent molecule.
+
+ @param pipe_from: The data pipe to copy the molecule data from. This
defaults to the current
+ data pipe.
@type pipe_from: str
- @param res_from: The residue identification string for the structure
to copy the data from.
- @type res_from: str
- @param pipe_to: The data pipe to copy the residue to. This defaults
to the current data
- pipe.
+ @param mol_from: The molecule identification string for the structure
to copy the data from.
+ @type mol_from: str
+ @param pipe_to: The data pipe to copy the molecule data to. This
defaults to the current
+ data pipe.
@type pipe_to: str
- @param res_to: The residue identification string for the structure
to copy the data to.
- @type res_to: str
+ @param mol_to: The molecule identification string for the structure
to copy the data to.
+ @type mol_to: str
"""
# The current data pipe.
@@ -99,8 +98,8 @@
mol_to_container.res[-1].name = res_name_to
-def create(res_num=None, res_name=None):
- """Function for adding a residue into the relax data store."""
+def create(mol_name=None):
+ """Function for adding a molecule into the relax data store."""
# Test if the current data pipe exists.
if not relax_data_store.current_pipe:
@@ -109,19 +108,18 @@
# Alias the current data pipe.
cdp = relax_data_store[relax_data_store.current_pipe]
- # Test if the residue number already exists.
- for i in xrange(len(cdp.mol[0].res)):
- if cdp.mol[0].res[i].num == res_num:
- raise RelaxError, "The residue number '" + `res_num` + "'
already exists in the sequence."
-
- # If no residue data exists, replace the empty first residue with this
residue.
- if cdp.mol[0].res[0].num == None and cdp.mol[0].res[0].name == None and
len(cdp.mol[0].res) == 1:
- cdp.mol[0].res[0].num = res_num
- cdp.mol[0].res[0].name = res_name
-
- # Append the residue.
+ # Test if the molecule name already exists.
+ for i in xrange(len(cdp.mol)):
+ if cdp.mol[i].name == mol_name:
+ raise RelaxError, "The molecule '" + `mol_name` + "' already
exists in the relax data store."
+
+ # If no molecule data exists, replace the empty first molecule with this
molecule (just a renaming).
+ if cdp.mol[0].name == None and len(cdp.mol[0].res) == 1 and
len(cdp.mol[0].res[0].spin) == 1:
+ cdp.mol[0].name = mol_name
+
+ # Append the molecule.
else:
- cdp.mol[0].res.add_item(res_num=res_num, res_name=res_name)
+ cdp.mol.add_item(mol_name=mol_name)
def delete(res_id=None):
Modified: 1.3/prompt/molecule.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/prompt/molecule.py?rev=3416&r1=3415&r2=3416&view=diff
==============================================================================
--- 1.3/prompt/molecule.py (original)
+++ 1.3/prompt/molecule.py Sun Nov 4 17:28:45 2007
@@ -42,55 +42,44 @@
self.__relax__ = relax
- def create(self, res_num=None, res_name=None):
- """Function for creating a new residue.
-
- Keyword Arguments
- ~~~~~~~~~~~~~~~~~
-
- res_num: The residue number.
-
- res_name: The name of the residue.
-
-
- Description
- ~~~~~~~~~~~
-
- Using this function a new sequence can be generated without using
the sequence user
- functions. However if the sequence already exists, the new residue
will be added to the end
- of the residue list (the residue numbers of this list need not be
sequential). The same
- residue number cannot be used more than once. A corresponding
single spin system will be
- created for this residue. The spin system number and name or
additional spin systems can be
- added later if desired.
+ def create(self, mol_name=None):
+ """Function for creating a new molecule.
+
+ Keyword Arguments
+ ~~~~~~~~~~~~~~~~~
+
+ mol_name: The name of the 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.
Examples
~~~~~~~~
- The following sequence of commands will generate the sequence 1 ALA,
2 GLY, 3 LYS:
-
- relax> residue.create(1, 'ALA')
- relax> residue.create(2, 'GLY')
- relax> residue.create(3, 'LYS')
- """
-
- # Function intro text.
- if self.__relax__.interpreter.intro:
- text = sys.ps3 + "residue.create("
- text = text + ", res_num=" + `res_num`
- text = text + ", res_name=" + `res_name` + ")"
- print text
-
- # Residue number.
- if type(res_num) != int:
- raise RelaxIntError, ('residue number', res_num)
-
- # Residue name.
- if type(res_name) != str:
- raise RelaxStrError, ('residue name', res_name)
-
- # Execute the functional code.
- residue.create(res_num=res_num, res_name=res_name)
+ To create the molecules 'Ap4Aase', 'ATP', and 'MgF4', type:
+
+ relax> molecule.create('Ap4Aase')
+ relax> molecule.create('ATP')
+ relax> molecule.create('MgF4')
+ """
+
+ # Function intro text.
+ if self.__relax__.interpreter.intro:
+ text = sys.ps3 + "molecule.create("
+ text = text + "mol_name=" + `mol_name` + ")"
+ print text
+
+ # Molecule name.
+ if type(mol_name) != str:
+ raise RelaxStrError, ('molecule name', mol_name)
+
+ # Execute the functional code.
+ molecule.create(mol_name=mol_name)
def copy(self, run1=None, run2=None):
Modified: 1.3/test_suite/unit_tests/generic_fns/test_molecule.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/unit_tests/generic_fns/test_molecule.py?rev=3416&r1=3415&r2=3416&view=diff
==============================================================================
--- 1.3/test_suite/unit_tests/generic_fns/test_molecule.py (original)
+++ 1.3/test_suite/unit_tests/generic_fns/test_molecule.py Sun Nov 4
17:28:45 2007
@@ -24,15 +24,17 @@
from unittest import TestCase
# relax module imports.
+from data import Data as relax_data_store
from generic_fns import molecule
+from relax_errors import RelaxError
-class Test_spin(TestCase):
+class Test_molecule(TestCase):
"""Unit tests for the functions of the 'generic_fns.molecule' module."""
def setUp(self):
- """Set up for all the residue unit tests."""
+ """Set up for all the molecule unit tests."""
# Reset the relax data storage object.
relax_data_store.__reset__()
@@ -74,4 +76,32 @@
relax_data_store['orig'].mol[0].res[0].spin[0].x = 2
+ def test_creation(self):
+ """Test the creation of a molecule data structure.
+ The function used is generic_fns.molecule.create().
+ """
+
+ # Create a few new molecules.
+ molecule.create('Ap4Aase')
+ molecule.create('ATP')
+ molecule.create(mol_name='MgF4')
+
+ # Test that the molecule names are correct.
+ self.assertEqual(relax_data_store['orig'].mol[0].name, 'Ap4Aase')
+ self.assertEqual(relax_data_store['orig'].mol[1].name, 'ATP')
+ self.assertEqual(relax_data_store['orig'].mol[2].name, 'MgF4')
+
+
+ def test_creation_fail(self):
+ """Test the failure of molecule creation by supplying two molecules
with the same name.
+
+ The function used is generic_fns.molecule.create().
+ """
+
+ # Create the first molecule.
+ molecule.create('CaM')
+
+ # Assert that a RelaxError occurs when the next added molecule has
the same name as the first.
+ self.assertRaises(RelaxError, molecule.create, 'CaM')
+
r3416 - in /1.3: generic_fns/molecule.py prompt/molecule.py test_suite/unit_tests/generic_fns/test_molecule.py