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
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
|
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2017 Stanford University and the Authors
#
# Authors: Robert McGibbon
# Contributors:
#
# MDTraj is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as
# published by the Free Software Foundation, either version 2.1
# of the License, or (at your option) any later version.
#
# This library is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with MDTraj. If not, see <http://www.gnu.org/licenses/>.
##############################################################################
import mdtraj as md
from mdtraj.geometry.pi_stacking import pi_stacking
def test_pi_stacking(get_fn):
"""Test that pi-stacking is being detected correctly."""
t: md.Trajectory = md.load(get_fn("4BFQ.pdb"))
lig_aromatic_atms_to_test = [
("C16", "C17", "C18", "C19", "C20", "C21"), # pi-stacking
("N4", "C9", "C15", "C16", "C21", "C8"), # pi-stacking
("N5", "C10", "C11", "C12", "C13", "C14"), # NOT pi-stacking
]
lig_grps = []
for lig_grp in lig_aromatic_atms_to_test:
lig_grps.append(
tuple(
int(idx)
for idx in t.top.select(
f"chainid 5 and resSeq 301 and (name {lig_grp[0]} or name {' or name '.join(lig_grp[1:])})",
)
),
)
protein_grps = []
# TYR186
protein_stacking_atms = [("CE2", "CD2", "CG", "CD1", "CE1", "CZ")]
for protein_grp in protein_stacking_atms:
protein_grps.append(
tuple(
int(idx)
for idx in t.top.select(
f"chainid 0 and resSeq 186 and (name {protein_grp[0]} or name {' or name '.join(protein_grp[1:])})", # noqa
)
),
)
stacking_interactions = pi_stacking(t, lig_grps, protein_grps)
# Since it returns per-frame, just get the 'first'
stacking_interactions = stacking_interactions[0]
assert len(stacking_interactions) == 2
assert (lig_grps[0], protein_grps[0]) in stacking_interactions
assert (lig_grps[1], protein_grps[0]) in stacking_interactions
assert (lig_grps[2], protein_grps[0]) not in stacking_interactions
def test_t_stacking_more_relaxed_radius(get_fn):
"""Test that t-stacking version of pi-stacking is being detected correctly."""
t: md.Trajectory = md.load(get_fn("4BFQ.pdb"))
lig_aromatic_atms_to_test = [
("C2", "C3", "C4", "N1", "C6", "N6"), # t-stacking
("N5", "C10", "C11", "C12", "C13", "C14"), # NOT pi-stacking
]
lig_grps = []
for lig_grp in lig_aromatic_atms_to_test:
lig_grps.append(
tuple(
int(idx)
for idx in t.top.select(
f"chainid 5 and resSeq 302 and (name {lig_grp[0]} or name {' or name '.join(lig_grp[1:])})",
)
),
)
protein_grps = []
# TYR91
protein_stacking_atms = [("CE2", "CD2", "CG", "CD1", "CE1", "CZ")]
for protein_grp in protein_stacking_atms:
protein_grps.append(
tuple(
int(idx)
for idx in t.top.select(
f"chainid 0 and resSeq 91 and (name {protein_grp[0]} or name {' or name '.join(protein_grp[1:])})",
)
),
)
# More permissive edge intersection radius for t-stack
stacking_interactions = pi_stacking(t, lig_grps, protein_grps, edge_intersection_radius=0.21)
stacking_interactions = stacking_interactions[0]
assert len(stacking_interactions) == 1
assert (lig_grps[0], protein_grps[0]) in stacking_interactions
assert (lig_grps[1], protein_grps[0]) not in stacking_interactions
def test_t_stacking_default_settings(get_fn):
"""Test that t-stacking version of pi-stacking is being detected correctly."""
t: md.Trajectory = md.load(get_fn("6A22.pdb"))
lig_aromatic_atms_to_test = [
("S10", "C9", "C8", "N7", "C6"), # t-stacking
("C14", "C15", "C16", "C17", "C18", "C19"), # NOT pi-stacking
]
lig_grps = []
for lig_grp in lig_aromatic_atms_to_test:
lig_grps.append(
tuple(
int(idx)
for idx in t.top.select(
f"chainid 9 and resSeq 9000 and (name {lig_grp[0]} or name {' or name '.join(lig_grp[1:])})",
)
),
)
protein_grps = []
# PHR118/378
protein_stacking_atms = [("CE2", "CD2", "CG", "CD1", "CE1", "CZ")]
for protein_grp in protein_stacking_atms:
protein_grps.append(
tuple(
int(idx)
for idx in t.top.select(
f"chainid 2 and resSeq 378 and (name {protein_grp[0]} or name {' or name '.join(protein_grp[1:])})", # noqa
)
),
)
stacking_interactions = pi_stacking(t, lig_grps, protein_grps)
stacking_interactions = stacking_interactions[0]
assert len(stacking_interactions) == 1
assert (lig_grps[0], protein_grps[0]) in stacking_interactions
assert (lig_grps[1], protein_grps[0]) not in stacking_interactions
|
