Author: bugman
Date: Wed Jan 28 15:02:11 2015
New Revision: 27342
URL: http://svn.gna.org/viewcvs/relax?rev=27342&view=rev
Log:
Created the Test_coordinates.test_common_residues unit test.
This is from the _lib._structure._internal.test_coordinates unit test module.
The test shows that
the lib.structure.internal.coordinates.common_residues() function is working
correctly. However the
printout, which is not caught by the test, is incorrect.
Modified:
trunk/test_suite/unit_tests/_lib/_structure/_internal/test_coordinates.py
Modified:
trunk/test_suite/unit_tests/_lib/_structure/_internal/test_coordinates.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/unit_tests/_lib/_structure/_internal/test_coordinates.py?rev=27342&r1=27341&r2=27342&view=diff
==============================================================================
--- trunk/test_suite/unit_tests/_lib/_structure/_internal/test_coordinates.py
(original)
+++ trunk/test_suite/unit_tests/_lib/_structure/_internal/test_coordinates.py
Wed Jan 28 15:02:11 2015
@@ -19,6 +19,9 @@
# #
###############################################################################
+# Python module imports.
+from numpy import array, int16
+
# relax module imports.
from lib.structure.internal import coordinates
from test_suite.unit_tests.base_classes import UnitTestCase
@@ -27,4 +30,36 @@
class Test_coordinates(UnitTestCase):
"""Unit tests for the functions of the
'lib.structure.internal.coordinates' module."""
+ def test_common_residues(self):
+ """Test the lib.structure.internal.coordinates.common_residues()
function."""
+ # The gap matrices.
+ gap_matrices = [
+ array([
+ [1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1],
+ [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0]
+ ], int16),
+ array([
+ [1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1],
+ [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
+ ], int16)
+ ]
+ seq1 = 'TEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADG**'
+ seq2 =
'ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKM**'
+ seq3 =
'LTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMAR**'
+
+ # Determine the common residues.
+ skip = coordinates.common_residues(gap_matrices=gap_matrices,
one_letter_codes=[seq1, seq2, seq3])
+
+ # The expected skipping matrices.
+ N = len(seq1)
+ skip_real = [
+ [0]*N,
+ [1]*4 + [0]*N + [1]*(len(seq2)-N-4),
+ [1] + [0]*N + [1]*(len(seq3)-N-1)
+ ]
+
+ # Checks.
+ for i in range(3):
+ print("Sequence %i" % (i+1))
+ self.assertEqual(len(skip_real[i]), len(skip[i]))
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