diff options
Diffstat (limited to 'plip/test')
| -rw-r--r-- | plip/test/test_command_line.py | 31 | ||||
| -rw-r--r-- | plip/test/test_hydrogen_bonds.py | 18 |
2 files changed, 32 insertions, 17 deletions
diff --git a/plip/test/test_command_line.py b/plip/test/test_command_line.py index d3ab332..b561997 100644 --- a/plip/test/test_command_line.py +++ b/plip/test/test_command_line.py @@ -20,35 +20,46 @@ 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) def test_stdout(self): """A PDB ID with no valid PDB record is provided.""" - exitcode = subprocess.call(f'{sys.executable} ../plipcmd.py -t -f ./pdb/1eve.pdb -O', shell=True) + exitcode = subprocess.call( + f"{sys.executable} ../plipcmd.py -t -f ./pdb/1eve.pdb -O", shell=True + ) self.assertEqual(exitcode, 0) - diff --git a/plip/test/test_hydrogen_bonds.py b/plip/test/test_hydrogen_bonds.py index 75cae6c..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') - self.assertEqual(len(interactions2.hbonds_ldon), 1)
\ No newline at end of file + interactions2 = characterize_complex("./pdb/1x0n_state_1.pdb", "DTF:A:174") + self.assertEqual(len(interactions2.hbonds_ldon), 1) |