diff options
Diffstat (limited to 'plip/test/test_metal_coordination.py')
| -rw-r--r-- | plip/test/test_metal_coordination.py | 66 |
1 files changed, 33 insertions, 33 deletions
diff --git a/plip/test/test_metal_coordination.py b/plip/test/test_metal_coordination.py index 424b8df..e054735 100644 --- a/plip/test/test_metal_coordination.py +++ b/plip/test/test_metal_coordination.py @@ -22,19 +22,19 @@ class MetalCoordinationTest(unittest.TestCase): """ tmpmol = PDBComplex() - tmpmol.load_pdb('./pdb/1rmd.pdb') - bsid = 'ZN:A:119' + tmpmol.load_pdb("./pdb/1rmd.pdb") + bsid = "ZN:A:119" for ligand in tmpmol.ligands: - if ':'.join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid: + if ":".join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid: tmpmol.characterize_complex(ligand) s = tmpmol.interaction_sets[bsid] # Coordination by three cysteines and one histidine of the protein metalres = [mres.restype for mres in s.metal_complexes] - self.assertEqual(metalres.count('CYS'), 3) - self.assertEqual(metalres.count('HIS'), 1) + self.assertEqual(metalres.count("CYS"), 3) + self.assertEqual(metalres.count("HIS"), 1) # Zn atom with tetrahedral geometry (coordination number 4) self.assertEqual(s.metal_complexes[0].coordination_num, 4) - self.assertEqual(s.metal_complexes[0].geometry, 'tetrahedral') + self.assertEqual(s.metal_complexes[0].geometry, "tetrahedral") def test_1rla(self): """Rat liver arginase, a binuclear manganese metalloenzyme (1rmd) @@ -42,20 +42,20 @@ class MetalCoordinationTest(unittest.TestCase): """ tmpmol = PDBComplex() - tmpmol.load_pdb('./pdb/1rla.pdb') - bsid = 'MN:A:500' + tmpmol.load_pdb("./pdb/1rla.pdb") + bsid = "MN:A:500" for ligand in tmpmol.ligands: - if ':'.join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid: + if ":".join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid: tmpmol.characterize_complex(ligand) s = tmpmol.interaction_sets[bsid] # Coordination by one histidine, three aspartic acid residues, and one water molecule metalres = [mres.restype for mres in s.metal_complexes] - self.assertEqual(metalres.count('HIS'), 1) - self.assertEqual(metalres.count('ASP'), 3) - self.assertEqual(metalres.count('HOH'), 1) + self.assertEqual(metalres.count("HIS"), 1) + self.assertEqual(metalres.count("ASP"), 3) + self.assertEqual(metalres.count("HOH"), 1) # Mn atom with square pyramidal geometry (coordination number 5) self.assertEqual(s.metal_complexes[0].coordination_num, 5) - self.assertEqual(s.metal_complexes[0].geometry, 'square.pyramidal') + self.assertEqual(s.metal_complexes[0].geometry, "square.pyramidal") def test_1het(self): """Liver alcohol deshydrogenase (1het) @@ -63,18 +63,18 @@ class MetalCoordinationTest(unittest.TestCase): """ tmpmol = PDBComplex() - tmpmol.load_pdb('./pdb/1het.pdb') - bsid = 'ZN:A:401' + tmpmol.load_pdb("./pdb/1het.pdb") + bsid = "ZN:A:401" for ligand in tmpmol.ligands: - if ':'.join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid: + if ":".join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid: tmpmol.characterize_complex(ligand) s = tmpmol.interaction_sets[bsid] # Coordination by four cysteines metalres = [mres.restype + str(mres.resnr) for mres in s.metal_complexes] - self.assertEqual(set(metalres), {'CYS97', 'CYS100', 'CYS103', 'CYS111'}) + self.assertEqual(set(metalres), {"CYS97", "CYS100", "CYS103", "CYS111"}) # Zn atom with tetrahedral geometry (coordination number 4) self.assertEqual(s.metal_complexes[0].coordination_num, 4) - self.assertEqual(s.metal_complexes[0].geometry, 'tetrahedral') + self.assertEqual(s.metal_complexes[0].geometry, "tetrahedral") def test_1vfy(self): """Phosphatidylinositol-3-phosphate binding FYVE domain of VPS27P protein (1vfy) @@ -82,18 +82,18 @@ class MetalCoordinationTest(unittest.TestCase): """ tmpmol = PDBComplex() - tmpmol.load_pdb('./pdb/1vfy.pdb') - bsid = 'ZN:A:300' + tmpmol.load_pdb("./pdb/1vfy.pdb") + bsid = "ZN:A:300" for ligand in tmpmol.ligands: - if ':'.join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid: + if ":".join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid: tmpmol.characterize_complex(ligand) s = tmpmol.interaction_sets[bsid] # Coordination by four cysteines metalres = [mres.restype for mres in s.metal_complexes] - self.assertEqual(set(metalres), {'CYS'}) + self.assertEqual(set(metalres), {"CYS"}) # Zn atom with tetrahedral geometry (coordination number 4) self.assertEqual(s.metal_complexes[0].coordination_num, 4) - self.assertEqual(s.metal_complexes[0].geometry, 'tetrahedral') + self.assertEqual(s.metal_complexes[0].geometry, "tetrahedral") def test_2pvb(self): """Pike parvalbumin binding calcium (2pvb) @@ -101,15 +101,15 @@ class MetalCoordinationTest(unittest.TestCase): """ tmpmol = PDBComplex() - tmpmol.load_pdb('./pdb/2pvb.pdb') - bsid = 'CA:A:110' + tmpmol.load_pdb("./pdb/2pvb.pdb") + bsid = "CA:A:110" for ligand in tmpmol.ligands: - if ':'.join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid: + if ":".join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid: tmpmol.characterize_complex(ligand) s = tmpmol.interaction_sets[bsid] # Ca atom with square pyramidal geometry (coordination number 5) self.assertEqual(s.metal_complexes[0].coordination_num, 5) - self.assertEqual(s.metal_complexes[0].geometry, 'square.pyramidal') + self.assertEqual(s.metal_complexes[0].geometry, "square.pyramidal") def test_2q8q(self): """Crystal Structure of S. aureus IsdE complexed with heme (2q8q) @@ -117,16 +117,16 @@ class MetalCoordinationTest(unittest.TestCase): """ tmpmol = PDBComplex() - tmpmol.load_pdb('./pdb/2q8q.pdb') - bsid = 'HEM:A:300' + tmpmol.load_pdb("./pdb/2q8q.pdb") + bsid = "HEM:A:300" for ligand in tmpmol.ligands: - if ':'.join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid: + if ":".join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid: tmpmol.characterize_complex(ligand) s = tmpmol.interaction_sets[bsid] # Coordination by four nitrogens of heme itself and one additional histidine from the protein metalres = [mres.restype for mres in s.metal_complexes] - self.assertEqual(metalres.count('HEM'), 4) - self.assertEqual(metalres.count('HIS'), 1) + self.assertEqual(metalres.count("HEM"), 4) + self.assertEqual(metalres.count("HIS"), 1) # Fe atom with square pyramidal geometry (coordination number 5) self.assertEqual(s.metal_complexes[0].coordination_num, 5) - self.assertEqual(s.metal_complexes[0].geometry, 'square.pyramidal') + self.assertEqual(s.metal_complexes[0].geometry, "square.pyramidal") |