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Merging improvements from https://github.com/rdk/funpdbe-validator rdk@github - "more specific information in mismatch messages"

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This commit is contained in:
Mihaly Varadi 2019-02-20 15:08:30 +00:00
parent b37b155bfc
commit 89ac85e304
2 changed files with 32 additions and 24 deletions
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18
tests/test_residue_index.py
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@ -42,7 +42,7 @@ def mock_get_residue_numbering_true(self):
return True
def mock_compare_residue_number(self, foo, bar):
def mock_compare_residue_number(self, foo, bar, asd):
return False
@ -67,16 +67,16 @@ class TestCheckResidueIndices(TestCase):
self.assertIsNone(bad_cri._set_pdb_id())
def test_check_numbering(self):
result = self.cri._check_numbering({}, {})
result = self.cri._check_numbering({}, {}, "A")
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"}]})
result = self.cri._check_numbering({}, {"residues": [{"pdb_res_label": 0, "aa_type": "ALA"}]}, "A")
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
self.cri._check_numbering = lambda x, y, z : True
result = self.cri._get_residue_numbering(mock_data)
self.assertTrue(result)
self.cri.pdb_id = "2H58"
@ -84,7 +84,7 @@ class TestCheckResidueIndices(TestCase):
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, "A")
self.assertFalse(result)
def test_with_bad_numbering(self):
@ -94,16 +94,16 @@ class TestCheckResidueIndices(TestCase):
def test_process_residues(self):
result = self.cri._process_residues(
[{"author_residue_number": 1, "residue_name": "ALA", "author_insertion_code": ""}], "1", "ALA")
[{"author_residue_number": 1, "residue_name": "ALA", "author_insertion_code": ""}], "1", "ALA", "A")
self.assertTrue(result)
result = self.cri._process_residues(
[{"author_residue_number": 1, "residue_name": "ALA", "author_insertion_code": "C"}], "1C", "ALA")
[{"author_residue_number": 1, "residue_name": "ALA", "author_insertion_code": "C"}], "1C", "ALA", "A")
self.assertTrue(result)
result = self.cri._process_residues(
[{"author_residue_number": 2, "residue_name": "ALA", "author_insertion_code": ""}], "1", "ALA")
[{"author_residue_number": 2, "residue_name": "ALA", "author_insertion_code": ""}], "1", "ALA", "A")
self.assertFalse(result)
result = self.cri._process_residues(
[{"author_residue_number": 1, "residue_name": "ALA", "author_insertion_code": ""}], "1", "HIS")
[{"author_residue_number": 1, "residue_name": "ALA", "author_insertion_code": ""}], "1", "HIS", "A")
self.assertFalse(result)
def test_with_multichain(self):