Format code with Blackdeepsource-transform-b65b5545

9 files changed, 274 insertions, 229 deletions

diff --git a/plip/test/test_basic_functions.py b/plip/test/test_basic_functions.py
index 7134f55..ac6a012 100644
--- a/plip/test/test_basic_functions.py
+++ b/plip/test/test_basic_functions.py
@@ -21,13 +21,17 @@ class TestLigandSupport(unittest.TestCase):
     def test_dna_rna(self):
         """Test if DNA and RNA is correctly processed as ligands"""
         tmpmol = PDBComplex()
-        tmpmol.load_pdb('./pdb/1tf6.pdb')
+        tmpmol.load_pdb("./pdb/1tf6.pdb")
         # DNA ligand four times consisting of 31 parts (composite)
-        self.assertEqual([len(ligand.members) for ligand in tmpmol.ligands].count(31), 4)
-        for ligset in [set((x[0] for x in ligand.members)) for ligand in tmpmol.ligands]:
+        self.assertEqual(
+            [len(ligand.members) for ligand in tmpmol.ligands].count(31), 4
+        )
+        for ligset in [
+            set((x[0] for x in ligand.members)) for ligand in tmpmol.ligands
+        ]:
             if len(ligset) == 4:
                 # DNA only contains four bases
-                self.assertEqual(ligset, {'DG', 'DC', 'DA', 'DT'})
+                self.assertEqual(ligset, {"DG", "DC", "DA", "DT"})
 
 
 class TestMapping(unittest.TestCase):
@@ -36,34 +40,34 @@ class TestMapping(unittest.TestCase):
     def test_ids(self):
         """Test if the atom IDs are correctly mapped from internal to original PDB."""
         tmpmol = PDBComplex()
-        tmpmol.load_pdb('./pdb/1vsn.pdb')
-        bsid = 'NFT:A:283'
+        tmpmol.load_pdb("./pdb/1vsn.pdb")
+        bsid = "NFT:A:283"
         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]
         for contact in s.hydrophobic_contacts:
-            if contact.restype == 'ALA' and contact.resnr == 133:
+            if contact.restype == "ALA" and contact.resnr == 133:
                 self.assertEqual(contact.ligatom_orig_idx, 1636)
                 self.assertEqual(contact.bsatom_orig_idx, 994)
-            if contact.restype == 'ASP' and contact.resnr == 61:
+            if contact.restype == "ASP" and contact.resnr == 61:
                 self.assertEqual(contact.ligatom_orig_idx, 1639)
                 self.assertEqual(contact.bsatom_orig_idx, 448)
         for contact in s.hbonds_ldon + s.hbonds_pdon:
-            if contact.restype == 'GLN' and contact.resnr == 19:
+            if contact.restype == "GLN" and contact.resnr == 19:
                 self.assertEqual(contact.a_orig_idx, 1649)
                 self.assertEqual(contact.d_orig_idx, 153)
-            if contact.restype == 'CYS' and contact.resnr == 25:
+            if contact.restype == "CYS" and contact.resnr == 25:
                 self.assertEqual(contact.a_orig_idx, 1649)
                 self.assertEqual(contact.d_orig_idx, 183)
-            if contact.restype == 'ASN' and contact.resnr == 158:
+            if contact.restype == "ASN" and contact.resnr == 158:
                 self.assertEqual(contact.d_orig_idx, 1629)
                 self.assertEqual(contact.a_orig_idx, 1199)
         for contact in s.halogen_bonds:
-            if contact.restype == 'TYR' and contact.resnr == 67:
+            if contact.restype == "TYR" and contact.resnr == 67:
                 self.assertEqual(contact.don.x_orig_idx, 1627)
                 self.assertEqual(contact.acc.o_orig_idx, 485)
-            if contact.restype == 'LEU' and contact.resnr == 157:
+            if contact.restype == "LEU" and contact.resnr == 157:
                 self.assertEqual(contact.don.x_orig_idx, 1628)
                 self.assertEqual(contact.acc.o_orig_idx, 1191)
 
@@ -72,7 +76,7 @@ class GeometryTest(unittest.TestCase):
     """Tests for geometrical calculations in PLIP"""
 
     def vector_magnitude(self, v):
-        return numpy.sqrt(sum(x**2 for x in v))
+        return numpy.sqrt(sum(x ** 2 for x in v))
 
     # noinspection PyUnusedLocal
     def setUp(self):
@@ -132,4 +136,7 @@ class GeometryTest(unittest.TestCase):
     def test_cluster_doubles(self):
         """Tests for mathematics.cluster_doubles"""
         # Are the results correct?
-        self.assertEqual(set(cluster_doubles([(1, 3), (4, 1), (5, 6), (7, 5)])), {(1, 3, 4), (5, 6, 7)})
+        self.assertEqual(
+            set(cluster_doubles([(1, 3), (4, 1), (5, 6), (7, 5)])),
+            {(1, 3, 4), (5, 6, 7)},
+        )
diff --git a/plip/test/test_command_line.py b/plip/test/test_command_line.py
index 5d8e8e5..3e27943 100644
--- a/plip/test/test_command_line.py
+++ b/plip/test/test_command_line.py
@@ -20,29 +20,39 @@ class CommandLineTest(unittest.TestCase):
 
     def test_empty_input_file(self):
         """Input file is empty."""
-        exitcode = subprocess.call(f'{sys.executable} ../plipcmd.py -f ./special/empty.pdb -o {self.tmp_dir.name}',
-                                   shell=True)
+        exitcode = subprocess.call(
+            f"{sys.executable} ../plipcmd.py -f ./special/empty.pdb -o {self.tmp_dir.name}",
+            shell=True,
+        )
         self.assertEqual(exitcode, 1)
 
     def test_invalid_pdb_id(self):
         """A PDB ID with no valid PDB record is provided."""
-        exitcode = subprocess.call(f'{sys.executable} ../plipcmd.py -i xx1x -o {self.tmp_dir.name}', shell=True)
+        exitcode = subprocess.call(
+            f"{sys.executable} ../plipcmd.py -i xx1x -o {self.tmp_dir.name}", shell=True
+        )
         self.assertEqual(exitcode, 1)
 
     def test_invalid_input_file(self):
         """A file is provided which is not a PDB file."""
-        exitcode = subprocess.call(f'{sys.executable} ../plipcmd.py -f ./special/non-pdb.pdb -o {self.tmp_dir.name}',
-                                   shell=True)
+        exitcode = subprocess.call(
+            f"{sys.executable} ../plipcmd.py -f ./special/non-pdb.pdb -o {self.tmp_dir.name}",
+            shell=True,
+        )
         self.assertEqual(exitcode, 1)
 
     def test_pdb_format_not_available(self):
         """A valid PDB ID is provided, but there is no entry in PDB format from wwPDB"""
-        exitcode = subprocess.call(f'{sys.executable} ../plipcmd.py -i 4v59 -o {self.tmp_dir.name}', shell=True)
+        exitcode = subprocess.call(
+            f"{sys.executable} ../plipcmd.py -i 4v59 -o {self.tmp_dir.name}", shell=True
+        )
         self.assertEqual(exitcode, 1)
 
     def test_valid_pdb(self):
         """A PDB ID with no valid PDB record is provided."""
-        exitcode = subprocess.call(f'{sys.executable} ../plipcmd.py -x -f ./pdb/1eve.pdb -o {self.tmp_dir.name}',
-                                   shell=True)
+        exitcode = subprocess.call(
+            f"{sys.executable} ../plipcmd.py -x -f ./pdb/1eve.pdb -o {self.tmp_dir.name}",
+            shell=True,
+        )
         self.assertEqual(len(os.listdir(self.tmp_dir.name)), 2)
         self.assertEqual(exitcode, 0)
diff --git a/plip/test/test_hydrogen_bonds.py b/plip/test/test_hydrogen_bonds.py
index 9d68532..f673c6e 100644
--- a/plip/test/test_hydrogen_bonds.py
+++ b/plip/test/test_hydrogen_bonds.py
@@ -8,31 +8,35 @@ def characterize_complex(pdb_file: str, binding_site_id: str) -> PLInteraction:
     pdb_complex = PDBComplex()
     pdb_complex.load_pdb(pdb_file)
     for ligand in pdb_complex.ligands:
-        if ':'.join([ligand.hetid, ligand.chain, str(ligand.position)]) == binding_site_id:
+        if (
+            ":".join([ligand.hetid, ligand.chain, str(ligand.position)])
+            == binding_site_id
+        ):
             pdb_complex.characterize_complex(ligand)
     return pdb_complex.interaction_sets[binding_site_id]
 
 
 class HydrogenBondTestCase(unittest.TestCase):
-
     def test_4dst_nondeterministic_protonation(self):
         config.NOHYDRO = False
         for i in range(0, 10):
-            interactions = characterize_complex('./pdb/4dst.pdb', 'GCP:A:202')
+            interactions = characterize_complex("./pdb/4dst.pdb", "GCP:A:202")
             all_hbonds = interactions.hbonds_ldon + interactions.hbonds_pdon
             self.assertTrue(len(all_hbonds) == 16 or len(all_hbonds) == 17)
 
     def test_4dst_deterministic_protonation(self):
         config.NOHYDRO = True
         for i in range(0, 10):
-            interactions = characterize_complex('./pdb/4dst_protonated.pdb', 'GCP:A:202')
+            interactions = characterize_complex(
+                "./pdb/4dst_protonated.pdb", "GCP:A:202"
+            )
             all_hbonds = interactions.hbonds_ldon + interactions.hbonds_pdon
             self.assertTrue(len(all_hbonds) == 16)
 
     def test_no_protonation(self):
         config.NOHYDRO = True
-        interactions1 = characterize_complex('./pdb/1x0n_state_1.pdb', 'DTF:A:174')
+        interactions1 = characterize_complex("./pdb/1x0n_state_1.pdb", "DTF:A:174")
         self.assertEqual(len(interactions1.hbonds_ldon), 0)
         config.NOHYDRO = False
-        interactions2 = characterize_complex('./pdb/1x0n_state_1.pdb', 'DTF:A:174')
+        interactions2 = characterize_complex("./pdb/1x0n_state_1.pdb", "DTF:A:174")
         self.assertEqual(len(interactions2.hbonds_ldon), 1)
diff --git a/plip/test/test_literature_validated.py b/plip/test/test_literature_validated.py
index f3f7cbc..d49dba5 100644
--- a/plip/test/test_literature_validated.py
+++ b/plip/test/test_literature_validated.py
@@ -21,10 +21,10 @@ class LiteratureValidatedTest(unittest.TestCase):
         Reference: Chakrabarti et al. Geometry of nonbonded interactions involving planar groups in proteins. (2007)
         """
         tmpmol = PDBComplex()
-        tmpmol.load_pdb('./pdb/1eve.pdb')
-        bsid = 'E20:A:2001'
+        tmpmol.load_pdb("./pdb/1eve.pdb")
+        bsid = "E20:A:2001"
         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]
         # Aromatic stacking with Trp84 and Trp279
@@ -39,10 +39,10 @@ class LiteratureValidatedTest(unittest.TestCase):
         Reference: Chakrabarti et al. Geometry of nonbonded interactions involving planar groups in proteins. (2007)
         """
         tmpmol = PDBComplex()
-        tmpmol.load_pdb('./pdb/1h2t.pdb')
-        bsid = 'GDP:Z:1151'
+        tmpmol.load_pdb("./pdb/1h2t.pdb")
+        bsid = "GDP:Z:1151"
         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]
         # Sandwiched pi-stacking involving Tyr20 and Tyr43
@@ -60,10 +60,10 @@ class LiteratureValidatedTest(unittest.TestCase):
         Reference: Betzi et al. Discovery of a potential allosteric ligand binding site in CDK2 (2012)
         """
         tmpmol = PDBComplex()
-        tmpmol.load_pdb('./pdb/3pxf.pdb')
-        bsids = ['2AN:A:305', '2AN:A:304']
+        tmpmol.load_pdb("./pdb/3pxf.pdb")
+        bsids = ["2AN:A:305", "2AN:A:304"]
         for ligand in tmpmol.ligands:
-            if ':'.join([ligand.hetid, ligand.chain, str(ligand.position)]) in bsids:
+            if ":".join([ligand.hetid, ligand.chain, str(ligand.position)]) in bsids:
                 tmpmol.characterize_complex(ligand)
 
         s = tmpmol.interaction_sets[bsids[0]]  # 2AN:A:305
@@ -91,10 +91,10 @@ class LiteratureValidatedTest(unittest.TestCase):
         from Sinorhizobium meliloti in the liganded and unliganded-closed states. (2008)
         """
         tmpmol = PDBComplex()
-        tmpmol.load_pdb('./pdb/2reg.pdb')
-        bsid = 'CHT:A:1'
+        tmpmol.load_pdb("./pdb/2reg.pdb")
+        bsid = "CHT:A:1"
         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]
         # Cation-pi interactions with Trp43, Trp90, Trp205, and Tyr119
@@ -109,10 +109,10 @@ class LiteratureValidatedTest(unittest.TestCase):
         Reference: Bird et al. Crystal structures of Varicella Zoster Virus Thyrimidine Kinase. (2003)
         """
         tmpmol = PDBComplex()
-        tmpmol.load_pdb('./pdb/1osn.pdb')
-        bsid = 'BVP:A:500'
+        tmpmol.load_pdb("./pdb/1osn.pdb")
+        bsid = "BVP: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]
         # Sandwiched pi-stacking involving Phe93 and Phe139
@@ -128,10 +128,10 @@ class LiteratureValidatedTest(unittest.TestCase):
         has implications for antiviral therapy (2008)
         """
         tmpmol = PDBComplex()
-        tmpmol.load_pdb('./pdb/2w0s.pdb')
-        bsid = 'BVP:B:1207'  # Complex of BVDU with Magnesium Cofactor
+        tmpmol.load_pdb("./pdb/2w0s.pdb")
+        bsid = "BVP:B:1207"  # Complex of BVDU with Magnesium Cofactor
         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]
         # Hydrogen bonding of Tyr101 and Arg72
@@ -152,10 +152,10 @@ class LiteratureValidatedTest(unittest.TestCase):
         Reference: Li et al. Identification of a potent and selective non-basic cathepsin K inhibitor. (2006)
         """
         tmpmol = PDBComplex()
-        tmpmol.load_pdb('./pdb/1vsn.pdb')
-        bsid = 'NFT:A:283'
+        tmpmol.load_pdb("./pdb/1vsn.pdb")
+        bsid = "NFT:A:283"
         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]
         # Hydrogen bonding to Gly66
@@ -167,10 +167,10 @@ class LiteratureValidatedTest(unittest.TestCase):
         Reference: De Moliner et al. Alternative binding modes of an inhibitor to two different kinases. (2003)
         """
         tmpmol = PDBComplex()
-        tmpmol.load_pdb('./pdb/1p5e.pdb')
-        bsid = 'TBS:A:301'
+        tmpmol.load_pdb("./pdb/1p5e.pdb")
+        bsid = "TBS:A:301"
         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]
         # Halogen Bonding of Ile10 and Leu83
@@ -183,10 +183,10 @@ class LiteratureValidatedTest(unittest.TestCase):
         acetylcholinesterase.. (1993)
         """
         tmpmol = PDBComplex()
-        tmpmol.load_pdb('./pdb/1acj.pdb')
-        bsid = 'THA:A:999'
+        tmpmol.load_pdb("./pdb/1acj.pdb")
+        bsid = "THA:A:999"
         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]
         # pi-stacking interaction with Phe330 and Trp84
@@ -199,10 +199,10 @@ class LiteratureValidatedTest(unittest.TestCase):
         glutamicum CgmR in Complex with Inducers and with an Operator. (2010)
         """
         tmpmol = PDBComplex()
-        tmpmol.load_pdb('./pdb/2zoz.pdb')
-        bsid = 'ET:B:184'
+        tmpmol.load_pdb("./pdb/2zoz.pdb")
+        bsid = "ET:B:184"
         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]
         # pi-stacking interaction with Trp63 and Phe147
@@ -219,10 +219,10 @@ class LiteratureValidatedTest(unittest.TestCase):
         RNA editing ligase 1. (2004)
         """
         tmpmol = PDBComplex()
-        tmpmol.load_pdb('./pdb/1xdn.pdb')
-        bsid = 'ATP:A:501'
+        tmpmol.load_pdb("./pdb/1xdn.pdb")
+        bsid = "ATP:A:501"
         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]
         # Hydrogen bonds to Arg111, Ile61 (backbone), Asn92, Val88, Lys87 and Glu86#
@@ -241,10 +241,10 @@ class LiteratureValidatedTest(unittest.TestCase):
         Reference: Peisach et al. Interaction of a Peptidomimetic Aminimide Inhibitor with Elastase. (1995)
         """
         tmpmol = PDBComplex()
-        tmpmol.load_pdb('./pdb/1bma.pdb')
-        bsid = '0QH:A:256'
+        tmpmol.load_pdb("./pdb/1bma.pdb")
+        bsid = "0QH:A:256"
         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]
         # Hydrogen bonds to val224 and Gln200
@@ -265,14 +265,16 @@ class LiteratureValidatedTest(unittest.TestCase):
         and Their Prodrugs As Antimalarial Agents (2004)
         """
         tmpmol = PDBComplex()
-        tmpmol.load_pdb('./pdb/4rao.pdb')
-        bsid = '3L7:B:301'
+        tmpmol.load_pdb("./pdb/4rao.pdb")
+        bsid = "3L7:B:301"
         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]
         # Hydrogen bonds to Val187, Lys165, Thr141, Lys140, Gly139, Thr138, Asp137
-        hbonds = {hbond.resnr for hbond in s.hbonds_pdon}  # res nr 100, 68, 69 and 199 in alternative conformation,
+        hbonds = {
+            hbond.resnr for hbond in s.hbonds_pdon
+        }  # res nr 100, 68, 69 and 199 in alternative conformation,
         self.assertTrue({137, 138, 139, 140, 141, 165, 187}.issubset(hbonds))
         # Water bridges to Asp137, Thr141, Met142, Arg199 and Gly139
         # res nr 199 and 142 in alternative conformation
@@ -286,10 +288,10 @@ class LiteratureValidatedTest(unittest.TestCase):
         Reference:  Bhattacharya et al. Structural basis of HIV-1 capsid recognition by PF74 and CPSF6(2014)
         """
         tmpmol = PDBComplex()
-        tmpmol.load_pdb('./pdb/4qnb.pdb')
-        bsid = '1B0:A:301'
+        tmpmol.load_pdb("./pdb/4qnb.pdb")
+        bsid = "1B0:A:301"
         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]
         # Hydrogen bonds to Asn57 and Lys70
@@ -304,10 +306,10 @@ class LiteratureValidatedTest(unittest.TestCase):
         Reference:  Zaware et al. Structural basis of HIV-1 capsid recognition by PF74 and CPSF6(2014)
         """
         tmpmol = PDBComplex()
-        tmpmol.load_pdb('./pdb/4kya.pdb')
-        bsid = '1UG:E:702'
+        tmpmol.load_pdb("./pdb/4kya.pdb")
+        bsid = "1UG:E:702"
         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]
         # Hydrogen bonds to Ala609
@@ -329,10 +331,10 @@ class LiteratureValidatedTest(unittest.TestCase):
         implications for ligand binding and specificity(2002)
         """
         tmpmol = PDBComplex()
-        tmpmol.load_pdb('./pdb/1n7g.pdb')
-        bsid = 'NDP:A:701'
+        tmpmol.load_pdb("./pdb/1n7g.pdb")
+        bsid = "NDP:A:701"
         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]
         # Hydrogen bonds to Thr37, Gly38, Gln39, Asp40,  Arg60, Leu92, Asp91, Ser63, Leu92, Ala115, Ser117,
@@ -340,7 +342,9 @@ class LiteratureValidatedTest(unittest.TestCase):
         # Publication give the Prediction for Asp91 as hydrogen bond, when this contains two acceptor atoms.
         hbonds = {hbond.resnr for hbond in s.hbonds_pdon}
         # #@todo Hbond to 128 not detected
-        self.assertTrue({37, 38, 39, 40, 92, 63, 92, 115, 117, 185, 189, 215, 220}.issubset(hbonds))
+        self.assertTrue(
+            {37, 38, 39, 40, 92, 63, 92, 115, 117, 185, 189, 215, 220}.issubset(hbonds)
+        )
         # Water bridges to Gly35, Thr37, Gly38, Asp40, Arg60, Arg61, Ser63, Asn66, Ser117, Tyr128, Lys189, Arg220
         waterbridges = {wb.resnr for wb in s.water_bridges}
         # Hydrogen bonds to 35, 37, 38, 40, 63, 117, 128, 189, 220 not detected due to prioritization
@@ -358,10 +362,10 @@ class LiteratureValidatedTest(unittest.TestCase):
         Reference:  Tsuhako et al. The design, synthesis, and biological evaluation of PIM kinase inhibitors.(2012)
         """
         tmpmol = PDBComplex()
-        tmpmol.load_pdb('./pdb/4alw.pdb')
-        bsid = 'HY7:A:1308'
+        tmpmol.load_pdb("./pdb/4alw.pdb")
+        bsid = "HY7:A:1308"
         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]
         # Hydrogen bonds to Asp186
@@ -377,10 +381,10 @@ class LiteratureValidatedTest(unittest.TestCase):
         for TMAO.(2013)
         """
         tmpmol = PDBComplex()
-        tmpmol.load_pdb('./pdb/3o1h.pdb')
-        bsid = 'TMO:B:1'
+        tmpmol.load_pdb("./pdb/3o1h.pdb")
+        bsid = "TMO:B:1"
         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]
         # Hydrogen bonds to Trp45
@@ -396,10 +400,10 @@ class LiteratureValidatedTest(unittest.TestCase):
         Reference:  Shikha et al. Mechanism of mismatch recognition revealed by human MutSβ bound to unpaired DNA loops.(2012)
         """
         tmpmol = PDBComplex()
-        tmpmol.load_pdb('./pdb/3thy.pdb')
-        bsid = 'ADP:A:935'
+        tmpmol.load_pdb("./pdb/3thy.pdb")
+        bsid = "ADP:A:935"
         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]
         # Saltbridge to His295 and Lys675
@@ -414,10 +418,10 @@ class LiteratureValidatedTest(unittest.TestCase):
         Reference:  Ash et al. The structure of an N11A mutant of the G-protein domain of FeoB.(2011)
         """
         tmpmol = PDBComplex()
-        tmpmol.load_pdb('./pdb/3tah.pdb')
-        bsid = 'BGO:A:300'
+        tmpmol.load_pdb("./pdb/3tah.pdb")
+        bsid = "BGO: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]
         # Hydrogen bonds to Ala11, Lys14, Thr15, Ser16, Asp113, Met114, Ala143 and Asp113
@@ -434,10 +438,10 @@ class LiteratureValidatedTest(unittest.TestCase):
         kinase CK2 inhibitors in clinical trials for the treatment of cancer (2011).
         """
         tmpmol = PDBComplex()
-        tmpmol.load_pdb('./pdb/3r0t.pdb')
-        bsid = 'FU9:A:338'
+        tmpmol.load_pdb("./pdb/3r0t.pdb")
+        bsid = "FU9:A:338"
         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]
         # Hydrogen bonds to Val116
@@ -462,10 +466,10 @@ class LiteratureValidatedTest(unittest.TestCase):
         Redox Potentials of DesulfoVibrio Vulgaris Flavodoxin.(2002)
         """
         tmpmol = PDBComplex()
-        tmpmol.load_pdb('./pdb/1aku.pdb')
-        bsid = 'FMN:A:150'
+        tmpmol.load_pdb("./pdb/1aku.pdb")
+        bsid = "FMN:A:150"
         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]
         # Hydrogen bonds to Thr59
@@ -488,10 +492,10 @@ class LiteratureValidatedTest(unittest.TestCase):
         673, a potent inhibitor derived from dihydropyridophthalazinone.(2014)
         """
         tmpmol = PDBComplex()
-        tmpmol.load_pdb('./pdb/4pjt.pdb')
-        bsid = '2YQ:D:1104'
+        tmpmol.load_pdb("./pdb/4pjt.pdb")
+        bsid = "2YQ:D:1104"
         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]
         # Hydrogen bonds to Gly863
@@ -506,15 +510,15 @@ class LiteratureValidatedTest(unittest.TestCase):
         Reference:  Presnell et al. Oxyanion-Mediated Inhibition of Serine Proteases.(1998)
         """
         tmpmol = PDBComplex()
-        tmpmol.load_pdb('./pdb/1bju.pdb')
-        bsid = 'GP6:A:910'
+        tmpmol.load_pdb("./pdb/1bju.pdb")
+        bsid = "GP6:A:910"
         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]
-        #@todo Publication show hydrogen bond interactions for Gly219
+        # @todo Publication show hydrogen bond interactions for Gly219
         # Hydrogen bonds to Ser190, Ser195, Gly219 and Asp189
-        hbonds = {hbond.resnr for hbond in s.hbonds_pdon+s.hbonds_ldon}
+        hbonds = {hbond.resnr for hbond in s.hbonds_pdon + s.hbonds_ldon}
         self.assertTrue({189, 190, 195}.issubset(hbonds))
         # Water bridges to Ser190 and Val227
         # Water bridge to 190 not detected due to prioritization
@@ -532,10 +536,10 @@ class LiteratureValidatedTest(unittest.TestCase):
         Reference:  Wilcken et al. Halogen-Enriched Fragment Libraries as Leads for Drug Rescue of Mutant p53.(2012)
         """
         tmpmol = PDBComplex()
-        tmpmol.load_pdb('./pdb/4agl.pdb')
-        bsid = 'P84:A:400'
+        tmpmol.load_pdb("./pdb/4agl.pdb")
+        bsid = "P84:A:400"
         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]
         # Water bridges to Val147
@@ -554,10 +558,10 @@ class LiteratureValidatedTest(unittest.TestCase):
         Pathway.(2007)
         """
         tmpmol = PDBComplex()
-        tmpmol.load_pdb('./pdb/2efj.pdb')
-        bsid = '37T:A:502'
+        tmpmol.load_pdb("./pdb/2efj.pdb")
+        bsid = "37T:A:502"
         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]
         # Hydrogen bond to Ser237
@@ -573,10 +577,10 @@ class LiteratureValidatedTest(unittest.TestCase):
         inhibitor.(2006)
         """
         tmpmol = PDBComplex()
-        tmpmol.load_pdb('./pdb/2iuz.pdb')
-        bsid = 'D1H:A:1440'
+        tmpmol.load_pdb("./pdb/2iuz.pdb")
+        bsid = "D1H:A:1440"
         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]
         # Hydrogen bonds to Trp137
@@ -597,10 +601,10 @@ class LiteratureValidatedTest(unittest.TestCase):
         phosphodiesterase type 5 (PDE5) inhibitors.(2011)
         """
         tmpmol = PDBComplex()
-        tmpmol.load_pdb('./pdb/3shy.pdb')
-        bsid = '5FO:A:1'
+        tmpmol.load_pdb("./pdb/3shy.pdb")
+        bsid = "5FO:A:1"
         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]
         # Hydrogen bonds to Gln817
@@ -622,10 +626,10 @@ class LiteratureValidatedTest(unittest.TestCase):
         substrate recognition site constructed by rearrangement of hydrogen bond network..(1998)
         """
         tmpmol = PDBComplex()
-        tmpmol.load_pdb('./pdb/1ay8.pdb')
-        bsid = 'PLP:A:413'
+        tmpmol.load_pdb("./pdb/1ay8.pdb")
+        bsid = "PLP:A:413"
         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]
         # Hydrogen bonds to Gly108, Thr109, Asn194 and Ser257
@@ -644,10 +648,10 @@ class LiteratureValidatedTest(unittest.TestCase):
         evolutionary path selected by the Lewis epitope..(2014)
         """
         tmpmol = PDBComplex()
-        tmpmol.load_pdb('./pdb/4rdl.pdb')
-        bsid = 'FUC:A:601'
+        tmpmol.load_pdb("./pdb/4rdl.pdb")
+        bsid = "FUC:A:601"
         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]  # Instead of FUC-A-604 (sugar representative)
         # Water bridges to Asn395
@@ -670,18 +674,22 @@ class LiteratureValidatedTest(unittest.TestCase):
         with CGP 53820, a novel pseudosymmetric inhibitor (1995)
         """
         tmpmol = PDBComplex()
-        tmpmol.load_pdb('./pdb/1hii.pdb')
-        bsid = 'C20:B:101'
+        tmpmol.load_pdb("./pdb/1hii.pdb")
+        bsid = "C20:B:101"
         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]
         # Water bridges
-        waterbridges = {str(wb.resnr)+wb.reschain for wb in s.water_bridges}
-        self.assertTrue({'50A', '50B'}.issubset(waterbridges))  # Bridging Ile-B50 and Ile-A50 with ligand
+        waterbridges = {str(wb.resnr) + wb.reschain for wb in s.water_bridges}
+        self.assertTrue(
+            {"50A", "50B"}.issubset(waterbridges)
+        )  # Bridging Ile-B50 and Ile-A50 with ligand
         # Hydrogen bonds
-        hbonds = {str(hbond.resnr)+hbond.reschain for hbond in s.hbonds_pdon+s.hbonds_ldon}
-        self.assertTrue({'27A', '27B', '29A', '48A', '48B'}.issubset(hbonds))
+        hbonds = {
+            str(hbond.resnr) + hbond.reschain for hbond in s.hbonds_pdon + s.hbonds_ldon
+        }
+        self.assertTrue({"27A", "27B", "29A", "48A", "48B"}.issubset(hbonds))
         # #@todo Publication mentions additional possible hydrogen bond with Asp28B
         # Hydrogen bonds with Asp-A25 are reported as a salt bridge as both partners have (potential) charges
 
@@ -691,22 +699,28 @@ class LiteratureValidatedTest(unittest.TestCase):
          Diol Inhibitors of HIV-1 Protease (1994)
         """
         tmpmol = PDBComplex()
-        tmpmol.load_pdb('./pdb/1hvi.pdb')
-        bsid = 'A77:A:800'
+        tmpmol.load_pdb("./pdb/1hvi.pdb")
+        bsid = "A77:A:800"
         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]
         # Water bridges
-        waterbridges = {str(wb.resnr)+wb.reschain for wb in s.water_bridges}
+        waterbridges = {str(wb.resnr) + wb.reschain for wb in s.water_bridges}
         # #@todo Water bridge with 50B not detected
-        self.assertTrue({'50A'}.issubset(waterbridges))  # Bridging Ile-B50 and Ile-A50 with ligand
+        self.assertTrue(
+            {"50A"}.issubset(waterbridges)
+        )  # Bridging Ile-B50 and Ile-A50 with ligand
         # pi-cation Interactions
         picat = {pication.resnr for pication in s.pication_laro}
-        self.assertEqual({8}, picat)  # Described as weakly polar contact/stacking in paper
+        self.assertEqual(
+            {8}, picat
+        )  # Described as weakly polar contact/stacking in paper
         # Hydrogen bonds
-        hbonds = {str(hbond.resnr)+hbond.reschain for hbond in s.hbonds_pdon+s.hbonds_ldon}
-        self.assertTrue({'25B', '27A', '27B', '48A', '48B'}.issubset(hbonds))
+        hbonds = {
+            str(hbond.resnr) + hbond.reschain for hbond in s.hbonds_pdon + s.hbonds_ldon
+        }
+        self.assertTrue({"25B", "27A", "27B", "48A", "48B"}.issubset(hbonds))
         # #@todo Paper describes additional hydrogen bond with Asp25A
 
     def test_3o7g(self):
@@ -715,16 +729,18 @@ class LiteratureValidatedTest(unittest.TestCase):
         melanoma (2010)
         """
         tmpmol = PDBComplex()
-        tmpmol.load_pdb('./pdb/3og7.pdb')
-        bsid = '032:A:1'
+        tmpmol.load_pdb("./pdb/3og7.pdb")
+        bsid = "032:A:1"
         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]
         # Hydrogen bonds
-        hbonds = {str(hbond.resnr)+hbond.reschain for hbond in s.hbonds_pdon+s.hbonds_ldon}
+        hbonds = {
+            str(hbond.resnr) + hbond.reschain for hbond in s.hbonds_pdon + s.hbonds_ldon
+        }
         # Additional hydrogen bond to residue 530A reported
-        self.assertTrue({'594A'}.issubset(hbonds))
+        self.assertTrue({"594A"}.issubset(hbonds))
 
     def test_1hpx(self):
         """
@@ -735,20 +751,22 @@ class LiteratureValidatedTest(unittest.TestCase):
         For residues in the B chain, the offset is -100 (e.g. Ile 50B in the PDB structure is Ile 150 in the paper).
         """
         tmpmol = PDBComplex()
-        tmpmol.load_pdb('./pdb/1hpx.pdb')
-        bsid = 'KNI:B:900'
+        tmpmol.load_pdb("./pdb/1hpx.pdb")
+        bsid = "KNI:B:900"
         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]
         # Hydrophobic contacts to Val82, Ile84, Ile150 as part of flap (S1, S1' sites)
-        hydroph = {str(hyd.resnr)+hyd.reschain for hyd in s.all_hydrophobic_contacts}
-        self.assertTrue({'82A', '84A', '50B'}.issubset(hydroph))
+        hydroph = {str(hyd.resnr) + hyd.reschain for hyd in s.all_hydrophobic_contacts}
+        self.assertTrue({"82A", "84A", "50B"}.issubset(hydroph))
         # Hydrogen bonds
-        hbonds = {str(hbond.resnr)+hbond.reschain for hbond in s.hbonds_ldon+s.hbonds_pdon}
+        hbonds = {
+            str(hbond.resnr) + hbond.reschain for hbond in s.hbonds_ldon + s.hbonds_pdon
+        }
         # Additional hbond to 25B not detected (low angle?)
-        self.assertTrue({'29B', '48B', '27B', '25A'}.issubset(hbonds))
+        self.assertTrue({"29B", "48B", "27B", "25A"}.issubset(hbonds))
         # Water bridges
-        waterbridges = {str(wb.resnr)+wb.reschain for wb in s.water_bridges}
+        waterbridges = {str(wb.resnr) + wb.reschain for wb in s.water_bridges}
         # Waterbridge with Gly27 is detected instead of Ala28/Asp29
-        self.assertTrue({'50A', '50B', '29A'}.issubset(waterbridges))
+        self.assertTrue({"50A", "50B", "29A"}.issubset(waterbridges))
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")
diff --git a/plip/test/test_pi_stacking.py b/plip/test/test_pi_stacking.py
index bb560a3..16409ef 100644
--- a/plip/test/test_pi_stacking.py
+++ b/plip/test/test_pi_stacking.py
@@ -8,18 +8,22 @@ def characterize_complex(pdb_file: str, binding_site_id: str) -> PLInteraction:
     pdb_complex = PDBComplex()
     pdb_complex.load_pdb(pdb_file)
     for ligand in pdb_complex.ligands:
-        if ':'.join([ligand.hetid, ligand.chain, str(ligand.position)]) == binding_site_id:
+        if (
+            ":".join([ligand.hetid, ligand.chain, str(ligand.position)])
+            == binding_site_id
+        ):
             pdb_complex.characterize_complex(ligand)
     return pdb_complex.interaction_sets[binding_site_id]
 
 
 class RingDetectionTest(unittest.TestCase):
-
     def test_consistent_ring_detection(self):
         config.NOHYDRO = True
         angles = set()
         for i in range(0, 10):
-            interactions = characterize_complex('./pdb/4dst_protonated.pdb', 'GCP:A:202')
+            interactions = characterize_complex(
+                "./pdb/4dst_protonated.pdb", "GCP:A:202"
+            )
             angles.add(interactions.pistacking[0].angle)
         self.assertTrue(len(angles) == 1)
         config.NOHYDRO = False
diff --git a/plip/test/test_remote_services.py b/plip/test/test_remote_services.py
index d52bffc..9cd27b5 100644
--- a/plip/test/test_remote_services.py
+++ b/plip/test/test_remote_services.py
@@ -14,16 +14,16 @@ class TestPDB(unittest.TestCase):
 
     def test_pdb_entry_status(self):
         # 1a0v is an obsolete entry and is replaced by 1y46
-        status, current_pdbid = check_pdb_status('1a0v')
-        self.assertEqual(status, 'OBSOLETE')
-        self.assertEqual(current_pdbid, '1y46')
+        status, current_pdbid = check_pdb_status("1a0v")
+        self.assertEqual(status, "OBSOLETE")
+        self.assertEqual(current_pdbid, "1y46")
 
         # 1vsn is an current entry
-        status, current_pdbid = check_pdb_status('1vsn')
-        self.assertEqual(status, 'CURRENT')
-        self.assertEqual(current_pdbid, '1vsn')
+        status, current_pdbid = check_pdb_status("1vsn")
+        self.assertEqual(status, "CURRENT")
+        self.assertEqual(current_pdbid, "1vsn")
 
         # xxxx is not an PDB entry
-        status, current_pdbid = check_pdb_status('xxxx')
-        self.assertEqual(status, 'UNKNOWN')
-        self.assertEqual(current_pdbid, 'xxxx')
+        status, current_pdbid = check_pdb_status("xxxx")
+        self.assertEqual(status, "UNKNOWN")
+        self.assertEqual(current_pdbid, "xxxx")
diff --git a/plip/test/test_water_bridges.py b/plip/test/test_water_bridges.py
index 24bf128..d820b59 100644
--- a/plip/test/test_water_bridges.py
+++ b/plip/test/test_water_bridges.py
@@ -7,14 +7,16 @@ def characterize_complex(pdb_file: str, binding_site_id: str) -> PLInteraction:
     pdb_complex = PDBComplex()
     pdb_complex.load_pdb(pdb_file)
     for ligand in pdb_complex.ligands:
-        if ':'.join([ligand.hetid, ligand.chain, str(ligand.position)]) == binding_site_id:
+        if (
+            ":".join([ligand.hetid, ligand.chain, str(ligand.position)])
+            == binding_site_id
+        ):
             pdb_complex.characterize_complex(ligand)
     return pdb_complex.interaction_sets[binding_site_id]
 
 
 class WaterBridgeTest(unittest.TestCase):
-
     def test_3ems(self):
-        interactions = characterize_complex('./pdb/3ems.pdb', 'ARG:A:131')
+        interactions = characterize_complex("./pdb/3ems.pdb", "ARG:A:131")
         water_bridges = interactions.water_bridges
         self.assertEqual(len(water_bridges), 4)
diff --git a/plip/test/test_xml_parser.py b/plip/test/test_xml_parser.py
index 1f45daa..da99e50 100644
--- a/plip/test/test_xml_parser.py
+++ b/plip/test/test_xml_parser.py
@@ -13,27 +13,27 @@ class XMLParserTest(unittest.TestCase):
     """Checks if the XML parser is working correctly"""
 
     def setUp(self):
-        self.px = PlipXML('./xml/1vsn.report.xml')
-        self.bsite = self.px.bsites['NFT:A:283']
-        self.smiles = 'CC(C)CC(NC(c1ccc(cc1)c1ccc(cc1)S(N)(=O)=O)C(F)(F)F)C(=O)NCC=N'
+        self.px = PlipXML("./xml/1vsn.report.xml")
+        self.bsite = self.px.bsites["NFT:A:283"]
+        self.smiles = "CC(C)CC(NC(c1ccc(cc1)c1ccc(cc1)S(N)(=O)=O)C(F)(F)F)C(=O)NCC=N"
 
     def test_general_information(self):
         """Test if general information is correctly parsed."""
-        self.assertEqual(self.px.version, '1.4.2')
-        self.assertEqual(self.px.pdbid, '1VSN')
+        self.assertEqual(self.px.version, "1.4.2")
+        self.assertEqual(self.px.pdbid, "1VSN")
         self.assertFalse(self.px.fixed)
-        self.assertEqual(self.px.filename, '1vsn.pdb')
+        self.assertEqual(self.px.filename, "1vsn.pdb")
         self.assertEqual(self.px.excluded, [])
 
     def test_bsite_information(self):
         """Test if the binding site information is correctly parsed."""
-        self.assertEqual(self.bsite.pdbid, '1VSN')
-        self.assertEqual(self.bsite.uniqueid, '1VSN:NFT:A:283')
-        self.assertEqual(self.bsite.hetid, 'NFT')
-        self.assertEqual(self.bsite.longname, 'NFT')
-        self.assertEqual(self.bsite.ligtype, 'SMALLMOLECULE')
+        self.assertEqual(self.bsite.pdbid, "1VSN")
+        self.assertEqual(self.bsite.uniqueid, "1VSN:NFT:A:283")
+        self.assertEqual(self.bsite.hetid, "NFT")
+        self.assertEqual(self.bsite.longname, "NFT")
+        self.assertEqual(self.bsite.ligtype, "SMALLMOLECULE")
         self.assertEqual(self.bsite.smiles, self.smiles)
-        self.assertEqual(self.bsite.members, ['NFT:A:283'])
+        self.assertEqual(self.bsite.members, ["NFT:A:283"])
         self.assertFalse(self.bsite.composite)
 
         # ligand properties
@@ -50,7 +50,7 @@ class XMLParserTest(unittest.TestCase):
         self.assertAlmostEqual(self.bsite.logp, 6, 0)
 
         # Atom mappings (non-exhaustive test)
-        lmap = self.bsite.mappings['pdb_to_smiles']
+        lmap = self.bsite.mappings["pdb_to_smiles"]
         self.assertEqual(lmap[1625], 24)
         self.assertEqual(lmap[1649], 33)
         self.assertEqual(lmap[1617], 14)
@@ -59,7 +59,7 @@ class XMLParserTest(unittest.TestCase):
         self.assertEqual(len(self.bsite.bs_res), 35)
 
         # Interacting chains
-        self.assertEqual(self.bsite.interacting_chains, ['A'])
+        self.assertEqual(self.bsite.interacting_chains, ["A"])
 
         # Has Interactions?
         self.assertTrue(self.bsite.has_interactions, True)
@@ -72,8 +72,8 @@ class XMLParserTest(unittest.TestCase):
         hydrophobic1 = self.bsite.hydrophobics[0]
         self.assertEqual(hydrophobic1.dist, 3.67)
         self.assertEqual(hydrophobic1.resnr, 61)
-        self.assertEqual(hydrophobic1.restype, 'ASP')
-        self.assertEqual(hydrophobic1.reschain, 'A')
+        self.assertEqual(hydrophobic1.restype, "ASP")
+        self.assertEqual(hydrophobic1.reschain, "A")
         self.assertEqual(hydrophobic1.ligcarbonidx, 1639)
         self.assertEqual(hydrophobic1.protcarbonidx, 448)
         self.assertEqual(hydrophobic1.ligcoo, (-7.395, 24.225, 6.614))
@@ -83,17 +83,17 @@ class XMLParserTest(unittest.TestCase):
         self.assertEqual(len(self.bsite.hbonds), 6)
         hbond1 = self.bsite.hbonds[0]
         self.assertEqual(hbond1.resnr, 19)
-        self.assertEqual(hbond1.restype, 'GLN')
-        self.assertEqual(hbond1.reschain, 'A')
+        self.assertEqual(hbond1.restype, "GLN")
+        self.assertEqual(hbond1.reschain, "A")
         self.assertTrue(hbond1.sidechain)
         self.assertEqual(hbond1.dist_h_a, 2.16)
         self.assertEqual(hbond1.dist_d_a, 3.11)
         self.assertEqual(hbond1.don_angle, 160.05)
         self.assertTrue(hbond1.protisdon)
         self.assertEqual(hbond1.donoridx, 153)
-        self.assertEqual(hbond1.donortype, 'Nam')
+        self.assertEqual(hbond1.donortype, "Nam")
         self.assertEqual(hbond1.acceptoridx, 1649)
-        self.assertEqual(hbond1.acceptortype, 'N2')
+        self.assertEqual(hbond1.acceptortype, "N2")
         self.assertEqual(hbond1.ligcoo, (2.820, 18.145, 6.806))
         self.assertEqual(hbond1.protcoo, (3.976, 15.409, 7.712))
 
@@ -101,17 +101,17 @@ class XMLParserTest(unittest.TestCase):
         self.assertEqual(len(self.bsite.wbridges), 1)
         wbridge1 = self.bsite.wbridges[0]
         self.assertEqual(wbridge1.resnr, 159)
-        self.assertEqual(wbridge1.restype, 'HIS')
-        self.assertEqual(wbridge1.reschain, 'A')
+        self.assertEqual(wbridge1.restype, "HIS")
+        self.assertEqual(wbridge1.reschain, "A")
         self.assertEqual(wbridge1.dist_a_w, 3.67)
         self.assertEqual(wbridge1.dist_d_w, 3.13)
         self.assertEqual(wbridge1.don_angle, 126.73)
         self.assertEqual(wbridge1.water_angle, 116.36)
         self.assertTrue(wbridge1.protisdon)
         self.assertEqual(wbridge1.donor_idx, 1210)
-        self.assertEqual(wbridge1.donortype, 'Nar')
+        self.assertEqual(wbridge1.donortype, "Nar")
         self.assertEqual(wbridge1.acceptor_idx, 1649)
-        self.assertEqual(wbridge1.acceptortype, 'N2')
+        self.assertEqual(wbridge1.acceptortype, "N2")
         self.assertEqual(wbridge1.ligcoo, (2.820, 18.145, 6.806))
         self.assertEqual(wbridge1.protcoo, (6.401, 19.307, 4.971))
         self.assertEqual(wbridge1.watercoo, (3.860, 18.563, 3.309))
@@ -129,16 +129,16 @@ class XMLParserTest(unittest.TestCase):
         self.assertEqual(len(self.bsite.halogens), 2)
         hal1 = self.bsite.halogens[0]
         self.assertEqual(hal1.resnr, 67)
-        self.assertEqual(hal1.restype, 'TYR')
-        self.assertEqual(hal1.reschain, 'A')
+        self.assertEqual(hal1.restype, "TYR")
+        self.assertEqual(hal1.reschain, "A")
         self.assertTrue(hal1.sidechain)
         self.assertEqual(hal1.dist, 3.37)
         self.assertEqual(hal1.don_angle, 156.70)
         self.assertEqual(hal1.acc_angle, 100.53)
         self.assertEqual(hal1.don_idx, 1627)
-        self.assertEqual(hal1.donortype, 'F')
+        self.assertEqual(hal1.donortype, "F")
         self.assertEqual(hal1.acc_idx, 485)
-        self.assertEqual(hal1.acceptortype, 'O3')
+        self.assertEqual(hal1.acceptortype, "O3")
         self.assertEqual(hal1.ligcoo, (-1.862, 29.303, 4.507))
         self.assertEqual(hal1.protcoo, (-1.005, 26.276, 3.287))