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Diffstat (limited to 'plip/test/test_metal_coordination.py')
| -rw-r--r-- | plip/test/test_metal_coordination.py | 132 |
1 files changed, 0 insertions, 132 deletions
diff --git a/plip/test/test_metal_coordination.py b/plip/test/test_metal_coordination.py deleted file mode 100644 index 424b8df..0000000 --- a/plip/test/test_metal_coordination.py +++ /dev/null @@ -1,132 +0,0 @@ -# coding=utf-8 -""" -Protein-Ligand Interaction Profiler - Analyze and visualize protein-ligand interactions in PDB files. -test_metal_coordination.py - Unit Tests for Metal Coordination. -""" - - -import unittest -from plip.structure.preparation import PDBComplex - - -class MetalCoordinationTest(unittest.TestCase): - """Checks predictions against literature-validated interactions for metal coordination.""" - - ############################################### - # Literature-validated cases from publication # - ############################################### - - def test_1rmd(self): - """Zinc binding sites in RAG1 dimerization domain (1rmd) - Reference: Harding. The architecture of metal coordination groups in proteins. (2004), Fig. 1a - """ - - tmpmol = PDBComplex() - 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: - 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) - # 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') - - def test_1rla(self): - """Rat liver arginase, a binuclear manganese metalloenzyme (1rmd) - Reference: Harding. The architecture of metal coordination groups in proteins. (2004), Fig. 1b - """ - - tmpmol = PDBComplex() - 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: - 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) - # 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') - - def test_1het(self): - """Liver alcohol deshydrogenase (1het) - Reference: Harding. The architecture of metal coordination groups in proteins. (2004), Fig. 2 - """ - - tmpmol = PDBComplex() - 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: - 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'}) - # 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') - - def test_1vfy(self): - """Phosphatidylinositol-3-phosphate binding FYVE domain of VPS27P protein (1vfy) - Reference: Harding. The architecture of metal coordination groups in proteins. (2004), Fig. 5 - """ - - tmpmol = PDBComplex() - 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: - 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'}) - # 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') - - def test_2pvb(self): - """Pike parvalbumin binding calcium (2pvb) - Reference: Harding. The architecture of metal coordination groups in proteins. (2004), Fig. 6 - """ - - tmpmol = PDBComplex() - 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: - 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') - - def test_2q8q(self): - """Crystal Structure of S. aureus IsdE complexed with heme (2q8q) - Reference: Grigg et al. Heme coordination by Staphylococcus aureus IsdE. (2007) - """ - - tmpmol = PDBComplex() - 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: - 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) - # 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') |