blob: f673c6e17db94a9964f212b9ee733e30c2ae5cce (
plain)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
|
import unittest
from plip.basic import config
from plip.structure.preparation import PDBComplex, PLInteraction
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
):
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")
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"
)
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")
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)
|
