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authordeepsource-autofix[bot] <62050782+deepsource-autofix[bot]@users.noreply.github.com>2020-07-07 14:55:17 +0000
committerGitHub <noreply@github.com>2020-07-07 14:55:17 +0000
commit0d135d611506e81d322596c7827b08bbfd3b7c08 (patch)
treea281b8e1f140ad3de77d818747fce03bcfa5b77b /plip/test
parent7059ee2a4ced23e467741cc846eb185886ffca38 (diff)
Format code with Blackdeepsource-transform-b65b5545
Diffstat (limited to 'plip/test')
-rw-r--r--plip/test/test_basic_functions.py39
-rw-r--r--plip/test/test_command_line.py26
-rw-r--r--plip/test/test_hydrogen_bonds.py16
-rw-r--r--plip/test/test_literature_validated.py264
-rw-r--r--plip/test/test_metal_coordination.py66
-rw-r--r--plip/test/test_pi_stacking.py10
-rw-r--r--plip/test/test_remote_services.py18
-rw-r--r--plip/test/test_water_bridges.py8
-rw-r--r--plip/test/test_xml_parser.py56
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 MutSĪ² 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))