Author: bugman
Date: Tue Nov 20 12:03:03 2007
New Revision: 3652
URL: http://svn.gna.org/viewcvs/relax?rev=3652&view=rev
Log:
Created, by copying, the base class for the generic_fns and prompt residue
module unit tests.
Added:
1.3/test_suite/unit_tests/residue_testing_base.py
- copied, changed from r3650,
1.3/test_suite/unit_tests/generic_fns/test_residue.py
Copied: 1.3/test_suite/unit_tests/residue_testing_base.py (from r3650,
1.3/test_suite/unit_tests/generic_fns/test_residue.py)
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/unit_tests/residue_testing_base.py?p2=1.3/test_suite/unit_tests/residue_testing_base.py&p1=1.3/test_suite/unit_tests/generic_fns/test_residue.py&r1=3650&r2=3652&rev=3652&view=diff
==============================================================================
--- 1.3/test_suite/unit_tests/generic_fns/test_residue.py (original)
+++ 1.3/test_suite/unit_tests/residue_testing_base.py Tue Nov 20 12:03:03 2007
@@ -20,18 +20,17 @@
#
#
###############################################################################
-# Python module imports.
-from unittest import TestCase
-
# relax module imports.
from data import Data as relax_data_store
-from data.pipe_container import PipeContainer
-from generic_fns import residue
from relax_errors import RelaxError, RelaxNoPipeError,
RelaxSpinSelectDisallowError
-class Test_residue(TestCase):
- """Unit tests for the functions of the 'generic_fns.residue' module."""
+class Residue_base_class:
+ """Base class for the tests of both the 'prompt.residue' and
'generic_fns.residue' modules.
+
+ This base class also contains many shared unit tests.
+ """
+
def setUp(self):
"""Set up for all the residue unit tests."""
@@ -59,7 +58,7 @@
"""Function for setting up some data for the unit tests."""
# Create the first residue and add some data to its spin container.
- residue.create(1, 'Ala')
+ self.residue_fns.create(1, 'Ala')
relax_data_store['orig'].mol[0].res[0].spin[0].num = 111
relax_data_store['orig'].mol[0].res[0].spin[0].x = 1
relax_data_store['orig'].mol[0].name = 'Old mol'
@@ -68,8 +67,8 @@
relax_data_store['orig'].mol.add_item('New mol')
# Copy the residue to the new molecule.
- residue.copy(res_from=':1', res_to='#New mol')
- residue.copy(res_from='#Old mol:1', res_to='#New mol:5')
+ self.residue_fns.copy(res_from=':1', res_to='#New mol')
+ self.residue_fns.copy(res_from='#Old mol:1', res_to='#New mol:5')
# Change the first residue's data.
relax_data_store['orig'].mol[0].res[0].spin[0].num = 222
@@ -79,7 +78,7 @@
def test_copy_between_molecules(self):
"""Test the copying of the residue data between different molecules.
- The function used is generic_fns.residue.copy().
+ The function tested is both generic_fns.residue.copy() and
prompt.residue.copy().
"""
# Set up some data.
@@ -109,17 +108,17 @@
def test_copy_between_pipes(self):
"""Test the copying of the residue data between different data pipes.
- The function used is generic_fns.residue.copy().
- """
-
- # Create the first residue and add some data to its spin container.
- residue.create(1, 'Ala')
+ The function tested is both generic_fns.residue.copy() and
prompt.residue.copy().
+ """
+
+ # Create the first residue and add some data to its spin container.
+ self.residue_fns.create(1, 'Ala')
relax_data_store['orig'].mol[0].res[0].spin[0].num = 111
relax_data_store['orig'].mol[0].res[0].spin[0].x = 1
# Copy the residue to the second data pipe.
- residue.copy(res_from=':1', pipe_to='test')
- residue.copy(pipe_from='orig', res_from=':1', pipe_to='test',
res_to=':5')
+ self.residue_fns.copy(res_from=':1', pipe_to='test')
+ self.residue_fns.copy(pipe_from='orig', res_from=':1',
pipe_to='test', res_to=':5')
# Change the first residue's data.
relax_data_store['orig'].mol[0].res[0].spin[0].num = 222
@@ -147,39 +146,39 @@
def test_copy_between_pipes_fail_no_pipe(self):
"""Test the copying of the residue data between different data pipes.
- The function used is generic_fns.residue.copy().
- """
-
- # Create the first residue and add some data to its spin container.
- residue.create(1, 'Ala')
+ The function tested is both generic_fns.residue.copy() and
prompt.residue.copy().
+ """
+
+ # Create the first residue and add some data to its spin container.
+ self.residue_fns.create(1, 'Ala')
relax_data_store['orig'].mol[0].res[0].spin[0].num = 111
relax_data_store['orig'].mol[0].res[0].spin[0].x = 1
# Copy the residue to the second data pipe.
- self.assertRaises(RelaxNoPipeError, residue.copy, res_from=':1',
pipe_to='test2')
+ self.assertRaises(RelaxNoPipeError, self.residue_fns.copy,
res_from=':1', pipe_to='test2')
def test_copy_within_molecule(self):
"""Test the copying of the residue data within a single molecule.
- The function used is generic_fns.residue.copy().
- """
-
- # Create the first residue and add some data to its spin container.
- residue.create(1, 'Ala')
+ The function tested is both generic_fns.residue.copy() and
prompt.residue.copy().
+ """
+
+ # Create the first residue and add some data to its spin container.
+ self.residue_fns.create(1, 'Ala')
relax_data_store['orig'].mol[0].res[0].spin[0].num = 111
relax_data_store['orig'].mol[0].res[0].spin[0].x = 1
# Copy the residue a few times.
- residue.copy(res_from=':1', res_to=':2')
- residue.copy(res_from=':1', pipe_to='orig', res_to=':3')
+ self.residue_fns.copy(res_from=':1', res_to=':2')
+ self.residue_fns.copy(res_from=':1', pipe_to='orig', res_to=':3')
# 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
# Copy the residue once more.
- residue.copy(res_from=':1', res_to=':4,Met')
+ self.residue_fns.copy(res_from=':1', res_to=':4,Met')
# Test the original residue.
self.assertEqual(relax_data_store['orig'].mol[0].res[0].num, 1)
@@ -209,41 +208,41 @@
def test_copy_within_molecule_fail1(self):
"""The failure of copying residue data within a molecule of a
non-existent residue.
- The function used is generic_fns.residue.copy().
+ The function tested is both generic_fns.residue.copy() and
prompt.residue.copy().
"""
# Create a few residues.
- residue.create(1, 'Ala')
- residue.create(-1, 'His')
+ self.residue_fns.create(1, 'Ala')
+ self.residue_fns.create(-1, 'His')
# Copy a non-existent residue (1 Met).
- self.assertRaises(RelaxError, residue.copy, res_from=':Met',
res_to=':2,Gly')
+ self.assertRaises(RelaxError, self.residue_fns.copy,
res_from=':Met', res_to=':2,Gly')
def test_copy_within_molecule_fail2(self):
"""The failure of copying residue data within a molecule to a
residue which already exists.
- The function used is generic_fns.residue.copy().
+ The function tested is both generic_fns.residue.copy() and
prompt.residue.copy().
"""
# Create a few residues.
- residue.create(1, 'Ala')
- residue.create(-1, 'His')
+ self.residue_fns.create(1, 'Ala')
+ self.residue_fns.create(-1, 'His')
# Copy a residue to a number which already exists.
- self.assertRaises(RelaxError, residue.copy, res_from=':1',
res_to=':-1,Gly')
+ self.assertRaises(RelaxError, self.residue_fns.copy, res_from=':1',
res_to=':-1,Gly')
def test_creation(self):
"""Test the creation of a residue.
- The function used is generic_fns.residue.create().
+ The function tested is both generic_fns.residue.create() and
prompt.residue.create().
"""
# Create a few new residues.
- residue.create(1, 'Ala')
- residue.create(2, 'Leu')
- residue.create(-3, 'Ser')
+ self.residue_fns.create(1, 'Ala')
+ self.residue_fns.create(2, 'Leu')
+ self.residue_fns.create(-3, 'Ser')
# Test that the residue numbers are correct.
self.assertEqual(relax_data_store['orig'].mol[0].res[0].num, 1)
@@ -259,27 +258,27 @@
def test_creation_fail(self):
"""Test the failure of residue creation (by supplying two residues
with the same number).
- The function used is generic_fns.residue.create().
+ The function tested is both generic_fns.residue.create() and
prompt.residue.create().
"""
# Create the first residue.
- residue.create(1, 'Ala')
+ self.residue_fns.create(1, 'Ala')
# Assert that a RelaxError occurs when the next added residue has
the same sequence number as the first.
- self.assertRaises(RelaxError, residue.create, 1, 'Ala')
+ self.assertRaises(RelaxError, self.residue_fns.create, 1, 'Ala')
def test_delete_name(self):
"""Test residue deletion using residue name identifiers.
- The function used is generic_fns.residue.delete().
+ The function tested is both generic_fns.residue.delete() and
prompt.residue.delete().
"""
# Create some residues and add some data to the spin containers.
- residue.create(1, 'Ala')
- residue.create(2, 'Ala')
- residue.create(3, 'Ala')
- residue.create(4, 'Gly')
+ self.residue_fns.create(1, 'Ala')
+ self.residue_fns.create(2, 'Ala')
+ self.residue_fns.create(3, 'Ala')
+ self.residue_fns.create(4, 'Gly')
relax_data_store['orig'].mol[0].res[3].spin[0].num = 111
relax_data_store['orig'].mol[0].res[3].spin[0].x = 1
@@ -296,14 +295,14 @@
def test_delete_num(self):
"""Test residue deletion using residue number identifiers.
- The function used is generic_fns.residue.delete().
+ The function tested is both generic_fns.residue.delete() and
prompt.residue.delete().
"""
# Create some residues and add some data to the spin containers.
- residue.create(1, 'Ala')
- residue.create(2, 'Ala')
- residue.create(3, 'Ala')
- residue.create(4, 'Gly')
+ self.residue_fns.create(1, 'Ala')
+ self.residue_fns.create(2, 'Ala')
+ self.residue_fns.create(3, 'Ala')
+ self.residue_fns.create(4, 'Gly')
relax_data_store['orig'].mol[0].res[3].spin[0].num = 111
relax_data_store['orig'].mol[0].res[3].spin[0].x = 1
@@ -324,14 +323,14 @@
def test_delete_all(self):
"""Test the deletion of all residues.
- The function used is generic_fns.residue.delete().
+ The function tested is both generic_fns.residue.delete() and
prompt.residue.delete().
"""
# Create some residues and add some data to the spin containers.
- residue.create(1, 'Ala')
- residue.create(2, 'Ala')
- residue.create(3, 'Ala')
- residue.create(4, 'Ala')
+ self.residue_fns.create(1, 'Ala')
+ self.residue_fns.create(2, 'Ala')
+ self.residue_fns.create(3, 'Ala')
+ self.residue_fns.create(4, 'Ala')
relax_data_store['orig'].mol[0].res[3].spin[0].num = 111
relax_data_store['orig'].mol[0].res[3].spin[0].x = 1
@@ -346,14 +345,14 @@
def test_delete_shift(self):
"""Test the deletion of multiple residues.
- The function used is generic_fns.residue.delete().
+ The function tested is both generic_fns.residue.delete() and
prompt.residue.delete().
"""
# Create some residues and add some data to the spin containers.
- residue.create(1, 'Ala')
- residue.create(2, 'Ala')
- residue.create(3, 'Ala')
- residue.create(4, 'Ala')
+ self.residue_fns.create(1, 'Ala')
+ self.residue_fns.create(2, 'Ala')
+ self.residue_fns.create(3, 'Ala')
+ self.residue_fns.create(4, 'Ala')
relax_data_store['orig'].mol[0].res[3].spin[0].num = 111
relax_data_store['orig'].mol[0].res[3].spin[0].x = 1
@@ -370,7 +369,7 @@
def test_delete_fail(self):
"""Test the failure of residue deletion when an atom id is supplied.
- The function used is generic_fns.residue.delete().
+ The function tested is both generic_fns.residue.delete() and
prompt.residue.delete().
"""
# Supply an atom id.
@@ -380,7 +379,7 @@
def test_display(self):
"""Test the display of residue information.
- The function used is generic_fns.residue.display().
+ The function tested is both generic_fns.residue.display() and
prompt.residue.display().
"""
# Set up some data.
@@ -396,7 +395,7 @@
def test_display_fail(self):
"""Test the failure of the display of residue information.
- The function used is generic_fns.residue.display().
+ The function tested is both generic_fns.residue.display() and
prompt.residue.display().
"""
# Set up some data.
@@ -409,11 +408,11 @@
def test_rename(self):
"""Test the renaming of a residue.
- The function tested is generic_fns.residue.rename().
- """
-
- # Create the first residue and add some data to its spin container.
- residue.create(-10, 'His')
+ The function tested is both generic_fns.residue.rename() and
prompt.residue.rename().
+ """
+
+ # Create the first residue and add some data to its spin container.
+ self.residue_fns.create(-10, 'His')
# Rename the residue.
residue.rename(res_id=':-10', new_name='K')
@@ -425,22 +424,22 @@
def test_rename_many(self):
"""Test the renaming of multiple residues.
- The function used is generic_fns.residue.rename().
- """
-
- # Create the first residue and add some data to its spin container.
- residue.create(1, 'Ala')
+ The function tested is both generic_fns.residue.rename() and
prompt.residue.rename().
+ """
+
+ # Create the first residue and add some data to its spin container.
+ self.residue_fns.create(1, 'Ala')
relax_data_store['orig'].mol[0].res[0].spin[0].num = 111
# Copy the residue a few times.
- residue.copy(res_from=':1', res_to=':2')
- residue.copy(res_from=':1', res_to=':3')
+ self.residue_fns.copy(res_from=':1', res_to=':2')
+ self.residue_fns.copy(res_from=':1', res_to=':3')
# Change the first residue's data.
relax_data_store['orig'].mol[0].res[0].name = 'His'
# Copy the residue once more.
- residue.copy(res_from=':1', res_to=':4,Met')
+ self.residue_fns.copy(res_from=':1', res_to=':4,Met')
# Rename all alanines.
residue.rename(res_id=':Ala', new_name='Gln')
@@ -457,7 +456,7 @@
def test_rename_no_spin(self):
"""Test the failure of renaming a residue when a spin id is given.
- The function tested is generic_fns.residue.rename().
+ The function tested is both generic_fns.residue.rename() and
prompt.residue.rename().
"""
# Try renaming using a atom id.
@@ -467,11 +466,11 @@
def test_renumber(self):
"""Test the renumbering of a residue.
- The function tested is generic_fns.residue.renumber().
- """
-
- # Create the first residue and add some data to its spin container.
- residue.create(-10, 'His')
+ The function tested is both generic_fns.residue.renumber() and
prompt.residue.renumber().
+ """
+
+ # Create the first residue and add some data to its spin container.
+ self.residue_fns.create(-10, 'His')
# Rename the residue.
residue.renumber(res_id=':-10', new_number=10)
@@ -483,21 +482,21 @@
def test_renumber_many_fail(self):
"""Test the renaming of multiple residues.
- The function used is generic_fns.residue.renumber().
- """
-
- # Create the first residue and add some data to its spin container.
- residue.create(1, 'Ala')
+ The function tested is both generic_fns.residue.renumber() and
prompt.residue.renumber().
+ """
+
+ # Create the first residue and add some data to its spin container.
+ self.residue_fns.create(1, 'Ala')
# Copy the residue a few times.
- residue.copy(res_from=':1', res_to=':2')
- residue.copy(res_from=':1', res_to=':3')
+ self.residue_fns.copy(res_from=':1', res_to=':2')
+ self.residue_fns.copy(res_from=':1', res_to=':3')
# Change the first residue's data.
relax_data_store['orig'].mol[0].res[0].spin[0].name = 'His'
# Copy the residue once more.
- residue.copy(res_from=':1', res_to=':4,Met')
+ self.residue_fns.copy(res_from=':1', res_to=':4,Met')
# Try renumbering all alanines.
self.assertRaises(RelaxError, residue.renumber, res_id=':Ala',
new_number=10)
@@ -506,7 +505,7 @@
def test_renumber_no_spin(self):
"""Test the failure of renaming a residue when a spin id is given.
- The function tested is generic_fns.residue.renumber().
+ The function tested is both generic_fns.residue.renumber() and
prompt.residue.renumber().
"""
# Try renaming using a atom id.
r3652 - /1.3/test_suite/unit_tests/residue_testing_base.py