Author: bugman
Date: Mon Mar 19 06:24:23 2007
New Revision: 3229
URL: http://svn.gna.org/viewcvs/relax?rev=3229&view=rev
Log:
Wrote the generic_fns.selection.tokenise() function and 28 unit tests
covering the function!
The unit tests attempt to cover all proper and improper combinations of the
selection string.
Modified:
1.3/generic_fns/selection.py
1.3/test_suite/unit_tests/generic_fns/test_selection.py
Modified: 1.3/generic_fns/selection.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/selection.py?rev=3229&r1=3228&r2=3229&view=diff
==============================================================================
--- 1.3/generic_fns/selection.py (original)
+++ 1.3/generic_fns/selection.py Mon Mar 19 06:24:23 2007
@@ -22,7 +22,7 @@
# Python module imports.
from os import F_OK, access
-from re import compile, match
+from re import compile, match, split
# relax module imports.
from data import Data as relax_data_store
@@ -510,4 +510,94 @@
def tokenise(selection):
- return None, None, None
+ """Split the input selection string returning the mol_token, res_token,
and spin_token strings.
+
+ The mol_token is identified as the text from the '#' to either the ':'
or '@' characters or the
+ end of the string.
+
+ The res_token is identified as the text from the ':' to either the '@'
character or the end of
+ the string.
+
+ The spin_token is identified as the text from the '@' to the end of the
string.
+
+ @param selection: The selection identifier.
+ @type selection: str
+ @return: The mol_token, res_token, and spin_token.
+ @rtype: 3-tuple of str or None
+ """
+
+ # No selection.
+ if selection == None:
+ return None, None, None
+
+
+ # Atoms.
+ ########
+
+ # Split by '@'.
+ atom_split = split('@', selection)
+
+ # Test that only one '@' character was supplied.
+ if len(atom_split) > 2:
+ raise RelaxError, "Only one '@' character is allowed within the
selection identifier string."
+
+ # No atom identifier.
+ if len(atom_split) == 1:
+ spin_token = None
+ else:
+ # Test for out of order identifiers.
+ if ':' in atom_split[1]:
+ raise RelaxError, "The atom identifier '@' must come after the
residue identifier ':'."
+ elif '#' in atom_split[1]:
+ raise RelaxError, "The atom identifier '@' must come after the
molecule identifier '#'."
+
+ # The token.
+ spin_token = atom_split[1]
+
+
+ # Residues.
+ ###########
+
+ # Split by ':'.
+ res_split = split(':', atom_split[0])
+
+ # Test that only one ':' character was supplied.
+ if len(res_split) > 2:
+ raise RelaxError, "Only one ':' character is allowed within the
selection identifier string."
+
+ # No residue identifier.
+ if len(res_split) == 1:
+ res_token = None
+ else:
+ # Test for out of order identifiers.
+ if '#' in res_split[1]:
+ raise RelaxError, "The residue identifier ':' must come after
the molecule identifier '#'."
+
+ # The token.
+ res_token = res_split[1]
+
+
+
+ # Molecules.
+ ############
+
+ # Split by '#'.
+ mol_split = split('#', res_split[0])
+
+ # Test that only one '#' character was supplied.
+ if len(mol_split) > 2:
+ raise RelaxError, "Only one '#' character is allowed within the
selection identifier string."
+
+ # No molecule identifier.
+ if len(mol_split) == 1:
+ mol_token = None
+ else:
+ mol_token = mol_split[1]
+
+
+ # Improper selection string.
+ if mol_token == None and res_token == None and spin_token == None:
+ raise RelaxError, "The selection string " + `selection` + " is
invalid."
+
+ # Return the three tokens.
+ return mol_token, res_token, spin_token
Modified: 1.3/test_suite/unit_tests/generic_fns/test_selection.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/unit_tests/generic_fns/test_selection.py?rev=3229&r1=3228&r2=3229&view=diff
==============================================================================
--- 1.3/test_suite/unit_tests/generic_fns/test_selection.py (original)
+++ 1.3/test_suite/unit_tests/generic_fns/test_selection.py Mon Mar 19
06:24:23 2007
@@ -26,6 +26,7 @@
# relax module imports.
from data import Data as relax_data_store
from generic_fns import selection
+from relax_errors import RelaxError
class Test_selection(TestCase):
@@ -204,3 +205,297 @@
# Increment i.
i = i + 1
+
+
+ def test_tokenise1(self):
+ """Test the generic_fns.selection.tokenise() function on the string
'@1'."""
+
+ # Tokenise.
+ mol_token, res_token, spin_token = selection.tokenise('@1')
+
+ # Check the tokens.
+ self.assertEqual(mol_token, None)
+ self.assertEqual(res_token, None)
+ self.assertEqual(spin_token, '1')
+
+
+ def test_tokenise2(self):
+ """Test the generic_fns.selection.tokenise() function on the string
':-4'."""
+
+ # Tokenise.
+ mol_token, res_token, spin_token = selection.tokenise(':-4')
+
+ # Check the tokens.
+ self.assertEqual(mol_token, None)
+ self.assertEqual(res_token, '-4')
+ self.assertEqual(spin_token, None)
+
+
+ def test_tokenise3(self):
+ """Test the generic_fns.selection.tokenise() function on the string
'#CaM'."""
+
+ # Tokenise.
+ mol_token, res_token, spin_token = selection.tokenise('#CaM')
+
+ # Check the tokens.
+ self.assertEqual(mol_token, 'CaM')
+ self.assertEqual(res_token, None)
+ self.assertEqual(spin_token, None)
+
+
+ def test_tokenise4(self):
+ """Test the generic_fns.selection.tokenise() function on the string
':G@N3'."""
+
+ # Tokenise.
+ mol_token, res_token, spin_token = selection.tokenise(':G@N3')
+
+ # Check the tokens.
+ self.assertEqual(mol_token, None)
+ self.assertEqual(res_token, 'G')
+ self.assertEqual(spin_token, 'N3')
+
+
+ def test_tokenise5(self):
+ """Test the generic_fns.selection.tokenise() function on the string
'#OMP@NH'."""
+
+ # Tokenise.
+ mol_token, res_token, spin_token = selection.tokenise('#OMP@NH')
+
+ # Check the tokens.
+ self.assertEqual(mol_token, 'OMP')
+ self.assertEqual(res_token, None)
+ self.assertEqual(spin_token, 'NH')
+
+
+ def test_tokenise6(self):
+ """Test the generic_fns.selection.tokenise() function on the string
'#Lyso:20-50'."""
+
+ # Tokenise.
+ mol_token, res_token, spin_token = selection.tokenise('#Lyso:20-50')
+
+ # Check the tokens.
+ self.assertEqual(mol_token, 'Lyso')
+ self.assertEqual(res_token, '20-50')
+ self.assertEqual(spin_token, None)
+
+
+ def test_tokenise7(self):
+ """Test the generic_fns.selection.tokenise() function on the string
'#Ap4Aase:*@N,CA'."""
+
+ # Tokenise.
+ mol_token, res_token, spin_token =
selection.tokenise('#Ap4Aase:*@N,CA')
+
+ # Check the tokens.
+ self.assertEqual(mol_token, 'Ap4Aase')
+ self.assertEqual(res_token, '*')
+ self.assertEqual(spin_token, 'N,CA')
+
+
+ def test_tokenise_dup_atom_id_fail1(self):
+ """Test failure of the generic_fns.selection.tokenise() function on
the string '@N@1'.
+
+ This tests for a duplicated atom identifier.
+ """
+
+ # Tokenise an invalid string.
+ self.assertRaises(RelaxError, selection.tokenise, '@N@1')
+
+
+ def test_tokenise_dup_atom_id_fail2(self):
+ """Test failure of the generic_fns.selection.tokenise() function on
the string ':*@N@1'.
+
+ This tests for a duplicated atom identifier.
+ """
+
+ # Tokenise an invalid string.
+ self.assertRaises(RelaxError, selection.tokenise, ':*@N@1')
+
+
+ def test_tokenise_dup_atom_id_fail3(self):
+ """Test failure of the generic_fns.selection.tokenise() function on
the string '@N:*@1'.
+
+ This tests for a duplicated atom identifier.
+ """
+
+ # Tokenise an invalid string.
+ self.assertRaises(RelaxError, selection.tokenise, '@N:*@1')
+
+
+ def test_tokenise_dup_res_id_fail1(self):
+ """Test failure of the generic_fns.selection.tokenise() function on
the string ':1:2'.
+
+ This tests for a duplicated residue identifier.
+ """
+
+ # Tokenise an invalid string.
+ self.assertRaises(RelaxError, selection.tokenise, ':1:2')
+
+
+ def test_tokenise_dup_res_id_fail2(self):
+ """Test failure of the generic_fns.selection.tokenise() function on
the string '#None:1:Ala'.
+
+ This tests for a duplicated residue identifier.
+ """
+
+ # Tokenise an invalid string.
+ self.assertRaises(RelaxError, selection.tokenise, '#None:1:Ala')
+
+
+ def test_tokenise_dup_res_id_fail3(self):
+ """Test failure of the generic_fns.selection.tokenise() function on
the string ':1:Ala@N'.
+
+ This tests for a duplicated residue identifier.
+ """
+
+ # Tokenise an invalid string.
+ self.assertRaises(RelaxError, selection.tokenise, ':1:Ala@N')
+
+
+ def test_tokenise_dup_mol_id_fail1(self):
+ """Test failure of the generic_fns.selection.tokenise() function on
the string '#A#B'.
+
+ This tests for a duplicated molecule identifier.
+ """
+
+ # Tokenise an invalid string.
+ self.assertRaises(RelaxError, selection.tokenise, '#A#B')
+
+
+ def test_tokenise_dup_mol_id_fail2(self):
+ """Test failure of the generic_fns.selection.tokenise() function on
the string '#A#B:Leu'.
+
+ This tests for a duplicated molecule identifier.
+ """
+
+ # Tokenise an invalid string.
+ self.assertRaises(RelaxError, selection.tokenise, '#A#B:Leu')
+
+
+ def test_tokenise_dup_mol_id_fail3(self):
+ """Test failure of the generic_fns.selection.tokenise() function on
the string '#A#C@CA'.
+
+ This tests for a duplicated molecule identifier.
+ """
+
+ # Tokenise an invalid string.
+ self.assertRaises(RelaxError, selection.tokenise, '#A#C@CA')
+
+
+ def test_tokenise_out_of_order_atom_id_fail1(self):
+ """Test failure of the generic_fns.selection.tokenise() function on
the string '@CA#A'.
+
+ This tests for an out of order '@' identifier.
+ """
+
+ # Tokenise an invalid string.
+ self.assertRaises(RelaxError, selection.tokenise, '@CA#A')
+
+
+ def test_tokenise_out_of_order_atom_id_fail2(self):
+ """Test failure of the generic_fns.selection.tokenise() function on
the string '@CA:Pro'.
+
+ This tests for an out of order '@' identifier.
+ """
+
+ # Tokenise an invalid string.
+ self.assertRaises(RelaxError, selection.tokenise, '@CA:Pro')
+
+
+ def test_tokenise_out_of_order_atom_id_fail3(self):
+ """Test failure of the generic_fns.selection.tokenise() function on
the string '@CA#Z:Pro'.
+
+ This tests for an out of order '@' identifier.
+ """
+
+ # Tokenise an invalid string.
+ self.assertRaises(RelaxError, selection.tokenise, '@CA#Z:Pro')
+
+
+ def test_tokenise_out_of_order_res_id_fail1(self):
+ """Test failure of the generic_fns.selection.tokenise() function on
the string '@CA:Pro'.
+
+ This tests for an out of order ':' identifier.
+ """
+
+ # Tokenise an invalid string.
+ self.assertRaises(RelaxError, selection.tokenise, '@CA:Pro')
+
+
+ def test_tokenise_out_of_order_res_id_fail2(self):
+ """Test failure of the generic_fns.selection.tokenise() function on
the string ':Glu#X'.
+
+ This tests for an out of order ':' identifier.
+ """
+
+ # Tokenise an invalid string.
+ self.assertRaises(RelaxError, selection.tokenise, ':Glu#X')
+
+
+ def test_tokenise_out_of_order_res_id_fail3(self):
+ """Test failure of the generic_fns.selection.tokenise() function on
the string '#1@12423:Glu'.
+
+ This tests for an out of order ':' identifier.
+ """
+
+ # Tokenise an invalid string.
+ self.assertRaises(RelaxError, selection.tokenise, ':Glu#X')
+
+
+ def test_tokenise_out_of_order_mol_id_fail1(self):
+ """Test failure of the generic_fns.selection.tokenise() function on
the string ':1-160#A'.
+
+ This tests for an out of order '#' identifier.
+ """
+
+ # Tokenise an invalid string.
+ self.assertRaises(RelaxError, selection.tokenise, ':1-160#A')
+
+
+ def test_tokenise_out_of_order_mol_id_fail2(self):
+ """Test failure of the generic_fns.selection.tokenise() function on
the string '@N,CA#A'.
+
+ This tests for an out of order '#' identifier.
+ """
+
+ # Tokenise an invalid string.
+ self.assertRaises(RelaxError, selection.tokenise, '@N,CA#A')
+
+
+ def test_tokenise_out_of_order_mol_id_fail3(self):
+ """Test failure of the generic_fns.selection.tokenise() function on
the string '@N:-10#Zip'.
+
+ This tests for an out of order '#' identifier.
+ """
+
+ # Tokenise an invalid string.
+ self.assertRaises(RelaxError, selection.tokenise, '@N:-10#Zip')
+
+
+ def test_tokenise_bad_string_fail1(self):
+ """Test failure of the generic_fns.selection.tokenise() function on
the string '13'.
+
+ This tests for an improper selection string.
+ """
+
+ # Tokenise an invalid string.
+ self.assertRaises(RelaxError, selection.tokenise, '13')
+
+
+ def test_tokenise_bad_string_fail2(self):
+ """Test failure of the generic_fns.selection.tokenise() function on
the string 'XXX'.
+
+ This tests for an improper selection string.
+ """
+
+ # Tokenise an invalid string.
+ self.assertRaises(RelaxError, selection.tokenise, 'XXX')
+
+
+ def test_tokenise_bad_string_fail3(self):
+ """Test failure of the generic_fns.selection.tokenise() function on
the string ''.
+
+ This tests for an improper selection string.
+ """
+
+ # Tokenise an invalid string.
+ self.assertRaises(RelaxError, selection.tokenise, '')
r3229 - in /1.3: generic_fns/selection.py test_suite/unit_tests/generic_fns/test_selection.py