Author: bugman
Date: Tue Mar 19 14:50:58 2013
New Revision: 18876
URL: http://svn.gna.org/viewcvs/relax?rev=18876&view=rev
Log:
Created 13 unit tests of the Internal._trim_helix() internal structural
object method.
Modified:
trunk/test_suite/unit_tests/_generic_fns/_structure/test_internal.py
Modified: trunk/test_suite/unit_tests/_generic_fns/_structure/test_internal.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/unit_tests/_generic_fns/_structure/test_internal.py?rev=18876&r1=18875&r2=18876&view=diff
==============================================================================
--- trunk/test_suite/unit_tests/_generic_fns/_structure/test_internal.py
(original)
+++ trunk/test_suite/unit_tests/_generic_fns/_structure/test_internal.py Tue
Mar 19 14:50:58 2013
@@ -60,6 +60,197 @@
# Reset relax.
reset()
+
+
+ def test__trim_helix1(self):
+ """1st test of the Internal._trim_helix() method."""
+
+ # The helix metadata of the internal structural object.
+ helix = [1, 'H1', 'ILE', 'A', 23, None, 'GLU', 'A', 34, None, 1,
None, 12]
+
+ # Residues deleted before the helix.
+ res_data = {1: 'MET', 2: 'GLN', 3: 'ILE', 4: 'PHE', 5: 'VAL', 6:
'LYS', 7: 'THR', 8: 'LEU', 9: 'THR', 10: 'GLY', 11: 'LYS', 12: 'THR', 13:
'ILE', 14: 'THR', 15: 'LEU', 16: 'GLU', 17: 'VAL', 18: 'GLU', 19: 'PRO', 20:
'SER', 21: 'ASP', 22: 'THR', 23: 'ILE', 24: 'GLU', 25: 'ASN', 26: 'VAL', 27:
'LYS', 28: 'ALA', 29: 'LYS', 30: 'ILE', 31: 'GLN', 32: 'ASP', 33: 'LYS', 34:
'GLU'}
+ new_helix = self.data._trim_helix(helix=helix, trim_res_list=[1, 2,
3, 22], res_data=res_data)
+
+ # Test that nothing has happened.
+ self.assertEqual(helix, new_helix)
+
+
+ def test__trim_helix2(self):
+ """2nd test of the Internal._trim_helix() method."""
+
+ # The helix metadata of the internal structural object.
+ helix = [1, 'H1', 'ILE', 'A', 23, None, 'GLU', 'A', 34, None, 1,
None, 12]
+
+ # Residues deleted after the helix.
+ res_data = {1: 'MET', 2: 'GLN', 3: 'ILE', 4: 'PHE', 5: 'VAL', 6:
'LYS', 7: 'THR', 8: 'LEU', 9: 'THR', 10: 'GLY', 11: 'LYS', 12: 'THR', 13:
'ILE', 14: 'THR', 15: 'LEU', 16: 'GLU', 17: 'VAL', 18: 'GLU', 19: 'PRO', 20:
'SER', 21: 'ASP', 22: 'THR', 23: 'ILE', 24: 'GLU', 25: 'ASN', 26: 'VAL', 27:
'LYS', 28: 'ALA', 29: 'LYS', 30: 'ILE', 31: 'GLN', 32: 'ASP', 33: 'LYS', 34:
'GLU'}
+ new_helix = self.data._trim_helix(helix=helix, trim_res_list=[51,
52, 53], res_data=res_data)
+
+ # Test that nothing has happened.
+ self.assertEqual(helix, new_helix)
+
+
+ def test__trim_helix3(self):
+ """3rd test of the Internal._trim_helix() method."""
+
+ # The helix metadata of the internal structural object.
+ helix = [1, 'H1', 'ILE', 'A', 23, None, 'GLU', 'A', 34, None, 1,
None, 12]
+ trimmed_helix = [1, 'H1', 'GLU', 'A', 24, None, 'GLU', 'A', 34,
None, 1, None, 11]
+
+ # Trim the start of the helix.
+ res_data = {1: 'MET', 2: 'GLN', 3: 'ILE', 4: 'PHE', 5: 'VAL', 6:
'LYS', 7: 'THR', 8: 'LEU', 9: 'THR', 10: 'GLY', 11: 'LYS', 12: 'THR', 13:
'ILE', 14: 'THR', 15: 'LEU', 16: 'GLU', 17: 'VAL', 18: 'GLU', 19: 'PRO', 20:
'SER', 21: 'ASP', 22: 'THR', 23: 'ILE', 24: 'GLU', 25: 'ASN', 26: 'VAL', 27:
'LYS', 28: 'ALA', 29: 'LYS', 30: 'ILE', 31: 'GLN', 32: 'ASP', 33: 'LYS', 34:
'GLU'}
+ new_helix = self.data._trim_helix(helix=helix, trim_res_list=[21,
22, 23], res_data=res_data)
+
+ # Test the trimming.
+ self.assertEqual(trimmed_helix, new_helix)
+
+
+ def test__trim_helix4(self):
+ """4th test of the Internal._trim_helix() method."""
+
+ # The helix metadata of the internal structural object.
+ helix = [1, 'H1', 'ILE', 'A', 23, None, 'GLU', 'A', 34, None, 1,
None, 12]
+ trimmed_helix = [1, 'H1', 'VAL', 'A', 26, None, 'GLU', 'A', 34,
None, 1, None, 9]
+
+ # Trim the start of the helix.
+ res_data = {1: 'MET', 2: 'GLN', 3: 'ILE', 4: 'PHE', 5: 'VAL', 6:
'LYS', 7: 'THR', 8: 'LEU', 9: 'THR', 10: 'GLY', 11: 'LYS', 12: 'THR', 13:
'ILE', 14: 'THR', 15: 'LEU', 16: 'GLU', 17: 'VAL', 18: 'GLU', 19: 'PRO', 20:
'SER', 21: 'ASP', 22: 'THR', 23: 'ILE', 24: 'GLU', 25: 'ASN', 26: 'VAL', 27:
'LYS', 28: 'ALA', 29: 'LYS', 30: 'ILE', 31: 'GLN', 32: 'ASP', 33: 'LYS', 34:
'GLU'}
+ new_helix = self.data._trim_helix(helix=helix, trim_res_list=[21,
22, 23, 24, 25], res_data=res_data)
+
+ # Test the trimming.
+ self.assertEqual(trimmed_helix, new_helix)
+
+
+ def test__trim_helix5(self):
+ """5th test of the Internal._trim_helix() method."""
+
+ # The helix metadata of the internal structural object.
+ helix = [1, 'H1', 'ILE', 'A', 23, None, 'GLU', 'A', 34, None, 1,
None, 12]
+ trimmed_helix = [1, 'H1', 'VAL', 'A', 26, None, 'GLU', 'A', 34,
None, 1, None, 9]
+
+ # Trim the start of the helix.
+ res_data = {1: 'MET', 2: 'GLN', 3: 'ILE', 4: 'PHE', 5: 'VAL', 6:
'LYS', 7: 'THR', 8: 'LEU', 9: 'THR', 10: 'GLY', 11: 'LYS', 12: 'THR', 13:
'ILE', 14: 'THR', 15: 'LEU', 16: 'GLU', 17: 'VAL', 18: 'GLU', 19: 'PRO', 20:
'SER', 21: 'ASP', 22: 'THR', 23: 'ILE', 24: 'GLU', 25: 'ASN', 26: 'VAL', 27:
'LYS', 28: 'ALA', 29: 'LYS', 30: 'ILE', 31: 'GLN', 32: 'ASP', 33: 'LYS', 34:
'GLU'}
+ new_helix = self.data._trim_helix(helix=helix, trim_res_list=[21,
22, 23, 24, 25, 30], res_data=res_data)
+
+ # Test the trimming.
+ self.assertEqual(trimmed_helix, new_helix)
+
+
+ def test__trim_helix6(self):
+ """6th test of the Internal._trim_helix() method."""
+
+ # The helix metadata of the internal structural object.
+ helix = [1, 'H1', 'ILE', 'A', 23, None, 'GLU', 'A', 34, None, 1,
None, 12]
+ trimmed_helix = [1, 'H1', 'VAL', 'A', 26, None, 'GLU', 'A', 34,
None, 1, None, 9]
+
+ # Trim the start of the helix.
+ res_data = {1: 'MET', 2: 'GLN', 3: 'ILE', 4: 'PHE', 5: 'VAL', 6:
'LYS', 7: 'THR', 8: 'LEU', 9: 'THR', 10: 'GLY', 11: 'LYS', 12: 'THR', 13:
'ILE', 14: 'THR', 15: 'LEU', 16: 'GLU', 17: 'VAL', 18: 'GLU', 19: 'PRO', 20:
'SER', 21: 'ASP', 22: 'THR', 23: 'ILE', 24: 'GLU', 25: 'ASN', 26: 'VAL', 27:
'LYS', 28: 'ALA', 29: 'LYS', 30: 'ILE', 31: 'GLN', 32: 'ASP', 33: 'LYS', 34:
'GLU'}
+ new_helix = self.data._trim_helix(helix=helix, trim_res_list=[21,
22, 23, 24, 25, 40], res_data=res_data)
+
+ # Test the trimming.
+ self.assertEqual(trimmed_helix, new_helix)
+
+
+ def test__trim_helix7(self):
+ """7th test of the Internal._trim_helix() method."""
+
+ # The helix metadata of the internal structural object.
+ helix = [1, 'H1', 'ILE', 'A', 23, None, 'GLU', 'A', 34, None, 1,
None, 12]
+ trimmed_helix = [1, 'H1', 'ILE', 'A', 23, None, 'LYS', 'A', 33,
None, 1, None, 11]
+
+ # Trim the end of the helix.
+ res_data = {1: 'MET', 2: 'GLN', 3: 'ILE', 4: 'PHE', 5: 'VAL', 6:
'LYS', 7: 'THR', 8: 'LEU', 9: 'THR', 10: 'GLY', 11: 'LYS', 12: 'THR', 13:
'ILE', 14: 'THR', 15: 'LEU', 16: 'GLU', 17: 'VAL', 18: 'GLU', 19: 'PRO', 20:
'SER', 21: 'ASP', 22: 'THR', 23: 'ILE', 24: 'GLU', 25: 'ASN', 26: 'VAL', 27:
'LYS', 28: 'ALA', 29: 'LYS', 30: 'ILE', 31: 'GLN', 32: 'ASP', 33: 'LYS', 34:
'GLU'}
+ new_helix = self.data._trim_helix(helix=helix, trim_res_list=[34,
35, 36], res_data=res_data)
+
+ # Test the trimming.
+ self.assertEqual(trimmed_helix, new_helix)
+
+
+ def test__trim_helix8(self):
+ """8th test of the Internal._trim_helix() method."""
+
+ # The helix metadata of the internal structural object.
+ helix = [1, 'H1', 'ILE', 'A', 23, None, 'GLU', 'A', 34, None, 1,
None, 12]
+
+ # Trim nothing.
+ res_data = {1: 'MET', 2: 'GLN', 3: 'ILE', 4: 'PHE', 5: 'VAL', 6:
'LYS', 7: 'THR', 8: 'LEU', 9: 'THR', 10: 'GLY', 11: 'LYS', 12: 'THR', 13:
'ILE', 14: 'THR', 15: 'LEU', 16: 'GLU', 17: 'VAL', 18: 'GLU', 19: 'PRO', 20:
'SER', 21: 'ASP', 22: 'THR', 23: 'ILE', 24: 'GLU', 25: 'ASN', 26: 'VAL', 27:
'LYS', 28: 'ALA', 29: 'LYS', 30: 'ILE', 31: 'GLN', 32: 'ASP', 33: 'LYS', 34:
'GLU'}
+ new_helix = self.data._trim_helix(helix=helix, trim_res_list=[35,
36], res_data=res_data)
+
+ # Test the trimming.
+ self.assertEqual(helix, new_helix)
+
+
+ def test__trim_helix9(self):
+ """9th test of the Internal._trim_helix() method."""
+
+ # The helix metadata of the internal structural object.
+ helix = [1, 'H1', 'ILE', 'A', 23, None, 'GLU', 'A', 34, None, 1,
None, 12]
+ trimmed_helix = [1, 'H1', 'ILE', 'A', 23, None, 'ILE', 'A', 30,
None, 1, None, 8]
+
+ # Trim the end of the helix.
+ res_data = {1: 'MET', 2: 'GLN', 3: 'ILE', 4: 'PHE', 5: 'VAL', 6:
'LYS', 7: 'THR', 8: 'LEU', 9: 'THR', 10: 'GLY', 11: 'LYS', 12: 'THR', 13:
'ILE', 14: 'THR', 15: 'LEU', 16: 'GLU', 17: 'VAL', 18: 'GLU', 19: 'PRO', 20:
'SER', 21: 'ASP', 22: 'THR', 23: 'ILE', 24: 'GLU', 25: 'ASN', 26: 'VAL', 27:
'LYS', 28: 'ALA', 29: 'LYS', 30: 'ILE', 31: 'GLN', 32: 'ASP', 33: 'LYS', 34:
'GLU'}
+ new_helix = self.data._trim_helix(helix=helix, trim_res_list=[31,
32, 33, 34, 35], res_data=res_data)
+
+ # Test the trimming.
+ self.assertEqual(trimmed_helix, new_helix)
+
+
+ def test__trim_helix10(self):
+ """10th test of the Internal._trim_helix() method."""
+
+ # The helix metadata of the internal structural object.
+ helix = [1, 'H1', 'ILE', 'A', 23, None, 'GLU', 'A', 34, None, 1,
None, 12]
+ trimmed_helix = [1, 'H1', 'ILE', 'A', 23, None, 'GLN', 'A', 31,
None, 1, None, 9]
+
+ # Trim the end of the helix.
+ res_data = {1: 'MET', 2: 'GLN', 3: 'ILE', 4: 'PHE', 5: 'VAL', 6:
'LYS', 7: 'THR', 8: 'LEU', 9: 'THR', 10: 'GLY', 11: 'LYS', 12: 'THR', 13:
'ILE', 14: 'THR', 15: 'LEU', 16: 'GLU', 17: 'VAL', 18: 'GLU', 19: 'PRO', 20:
'SER', 21: 'ASP', 22: 'THR', 23: 'ILE', 24: 'GLU', 25: 'ASN', 26: 'VAL', 27:
'LYS', 28: 'ALA', 29: 'LYS', 30: 'ILE', 31: 'GLN', 32: 'ASP', 33: 'LYS', 34:
'GLU'}
+ new_helix = self.data._trim_helix(helix=helix, trim_res_list=[24,
32, 33, 34, 35], res_data=res_data)
+
+ # Test the trimming.
+ self.assertEqual(trimmed_helix, new_helix)
+
+
+ def test__trim_helix11(self):
+ """11th test of the Internal._trim_helix() method."""
+
+ # The helix metadata of the internal structural object.
+ helix = [1, 'H1', 'ILE', 'A', 23, None, 'GLU', 'A', 34, None, 1,
None, 12]
+ trimmed_helix = [1, 'H1', 'ASN', 'A', 25, None, 'GLN', 'A', 31,
None, 1, None, 6]
+
+ # Trim the both ends of the helix.
+ res_data = {1: 'MET', 2: 'GLN', 3: 'ILE', 4: 'PHE', 5: 'VAL', 6:
'LYS', 7: 'THR', 8: 'LEU', 9: 'THR', 10: 'GLY', 11: 'LYS', 12: 'THR', 13:
'ILE', 14: 'THR', 15: 'LEU', 16: 'GLU', 17: 'VAL', 18: 'GLU', 19: 'PRO', 20:
'SER', 21: 'ASP', 22: 'THR', 23: 'ILE', 24: 'GLU', 25: 'ASN', 26: 'VAL', 27:
'LYS', 28: 'ALA', 29: 'LYS', 30: 'ILE', 31: 'GLN', 32: 'ASP', 33: 'LYS', 34:
'GLU'}
+ new_helix = self.data._trim_helix(helix=helix, trim_res_list=[22,
23, 24, 32, 33, 34, 35], res_data=res_data)
+
+ # Test the trimming.
+ self.assertEqual(trimmed_helix, new_helix)
+
+
+ def test__trim_helix12(self):
+ """12th test of the Internal._trim_helix() method."""
+
+ # The helix metadata of the internal structural object.
+ helix = [1, 'H1', 'ILE', 'A', 23, None, 'GLU', 'A', 34, None, 1,
None, 12]
+ trimmed_helix = [1, 'H1', 'ASN', 'A', 25, None, 'GLN', 'A', 31,
None, 1, None, 6]
+
+ # Trim the both ends of the helix.
+ res_data = {1: 'MET', 2: 'GLN', 3: 'ILE', 4: 'PHE', 5: 'VAL', 6:
'LYS', 7: 'THR', 8: 'LEU', 9: 'THR', 10: 'GLY', 11: 'LYS', 12: 'THR', 13:
'ILE', 14: 'THR', 15: 'LEU', 16: 'GLU', 17: 'VAL', 18: 'GLU', 19: 'PRO', 20:
'SER', 21: 'ASP', 22: 'THR', 23: 'ILE', 24: 'GLU', 25: 'ASN', 26: 'VAL', 27:
'LYS', 28: 'ALA', 29: 'LYS', 30: 'ILE', 31: 'GLN', 32: 'ASP', 33: 'LYS', 34:
'GLU'}
+ new_helix = self.data._trim_helix(helix=helix, trim_res_list=[22,
23, 24, 27, 32, 33, 34, 35], res_data=res_data)
+
+ # Test the trimming.
+ self.assertEqual(trimmed_helix, new_helix)
+
+
+ def test__trim_helix13(self):
+ """13th test of the Internal._trim_helix() method."""
+
+ # The helix metadata of the internal structural object.
+ helix = [1, 'H1', 'ILE', 'A', 23, None, 'GLU', 'A', 34, None, 1,
None, 12]
+
+ # Trim everything.
+ res_data = {1: 'MET', 2: 'GLN', 3: 'ILE', 4: 'PHE', 5: 'VAL', 6:
'LYS', 7: 'THR', 8: 'LEU', 9: 'THR', 10: 'GLY', 11: 'LYS', 12: 'THR', 13:
'ILE', 14: 'THR', 15: 'LEU', 16: 'GLU', 17: 'VAL', 18: 'GLU', 19: 'PRO', 20:
'SER', 21: 'ASP', 22: 'THR', 23: 'ILE', 24: 'GLU', 25: 'ASN', 26: 'VAL', 27:
'LYS', 28: 'ALA', 29: 'LYS', 30: 'ILE', 31: 'GLN', 32: 'ASP', 33: 'LYS', 34:
'GLU'}
+ new_helix = self.data._trim_helix(helix=helix, trim_res_list=[1, 2,
3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23,
24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35], res_data=res_data)
+
+ # Test the trimming.
+ self.assertEqual(None, new_helix)
def test_atom_loop(self):
r18876 - /trunk/test_suite/unit_tests/_generic_fns/_structure/test_internal.py