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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/test_basic_functions.py
parent7059ee2a4ced23e467741cc846eb185886ffca38 (diff)
Format code with Blackdeepsource-transform-b65b5545
Diffstat (limited to 'plip/test/test_basic_functions.py')
-rw-r--r--plip/test/test_basic_functions.py39
1 files changed, 23 insertions, 16 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)},
+ )