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+# 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')