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Minor refactoring and adding more docs

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This commit is contained in:
mvaradi 2018-10-14 10:37:14 +01:00
parent 7d89f1131b
commit 33b484085f
2 changed files with 66 additions and 44 deletions
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38
tests/test_residue_index.py
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@ -49,56 +49,56 @@ class TestCheckResidueIndices(TestCase):
self.cri = CheckResidueIndices(mock_data)
def test_loop_chains(self):
self.cri.get_residue_numbering = mock_get_residue_numbering_false
result = self.cri.loop_chains()
self.cri._get_residue_numbering = mock_get_residue_numbering_false
result = self.cri.check_every_residue()
self.assertFalse(result)
self.cri.get_residue_numbering = mock_get_residue_numbering_true
result = self.cri.loop_chains()
self.cri._get_residue_numbering = mock_get_residue_numbering_true
result = self.cri.check_every_residue()
self.assertTrue(result)
self.cri.pdb_id = None
self.assertFalse(self.cri.loop_chains())
self.assertFalse(self.cri.check_every_residue())
def test_set_pdb_id(self):
self.assertIsNotNone(self.cri.set_pdb_id())
self.assertIsNotNone(self.cri._set_pdb_id())
bad_cri = CheckResidueIndices(mock_data_no_pdb_id)
self.assertIsNone(bad_cri.set_pdb_id())
self.assertIsNone(bad_cri._set_pdb_id())
def test_check_numbering(self):
result = self.cri.check_numbering({}, {})
result = self.cri._check_numbering({}, {})
self.assertFalse(result)
self.cri.compare_residue_number = mock_compare_residue_number
result = self.cri.check_numbering({}, {"residues": [{"pdb_res_label": 0, "aa_type": "ALA"}]})
self.cri._compare_residue_number = mock_compare_residue_number
result = self.cri._check_numbering({}, {"residues": [{"pdb_res_label": 0, "aa_type": "ALA"}]})
self.assertFalse(result)
def test_get_residue_numbering(self):
mock_data = {"chain_label": "A"}
self.cri.pdb_id = "1CBS"
self.cri.check_numbering = lambda x, y : True
result = self.cri.get_residue_numbering(mock_data)
self.cri._check_numbering = lambda x, y : True
result = self.cri._get_residue_numbering(mock_data)
self.assertTrue(result)
self.cri.pdb_id = "2H58"
result = self.cri.get_residue_numbering(mock_data)
result = self.cri._get_residue_numbering(mock_data)
self.assertFalse(result)
def test_recursive_loop(self):
result = self.cri.recursive_loop([{"foo": "bar"}], "foo", None, None)
result = self.cri._recursive_loop([{"foo": "bar"}], "foo", None, None)
self.assertFalse(result)
def test_with_bad_numbering(self):
cri_with_bad_numbering = CheckResidueIndices(mock_data_bad_numbering)
result = cri_with_bad_numbering.loop_chains()
result = cri_with_bad_numbering.check_every_residue()
self.assertFalse(result)
def test_process_residues(self):
result = self.cri.process_residues(
result = self.cri._process_residues(
[{"author_residue_number": 1, "residue_name": "ALA", "author_insertion_code": ""}], "1", "ALA")
self.assertTrue(result)
result = self.cri.process_residues(
result = self.cri._process_residues(
[{"author_residue_number": 1, "residue_name": "ALA", "author_insertion_code": "C"}], "1C", "ALA")
self.assertTrue(result)
result = self.cri.process_residues(
result = self.cri._process_residues(
[{"author_residue_number": 2, "residue_name": "ALA", "author_insertion_code": ""}], "1", "ALA")
self.assertFalse(result)
result = self.cri.process_residues(
result = self.cri._process_residues(
[{"author_residue_number": 1, "residue_name": "ALA", "author_insertion_code": ""}], "1", "HIS")
self.assertFalse(result)