-
Notifications
You must be signed in to change notification settings - Fork 3
Expand file tree
/
Copy path__init__.py
More file actions
143 lines (112 loc) · 3.83 KB
/
__init__.py
File metadata and controls
143 lines (112 loc) · 3.83 KB
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
138
139
140
141
142
143
######################################################################
# SOMD2: GPU accelerated alchemical free-energy engine.
#
# Copyright: 2023-2026
#
# Authors: The OpenBioSim Team <team@openbiosim.org>
#
# SOMD2 is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# SOMD2 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 General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with SOMD2. If not, see <http://www.gnu.org/licenses/>.
#####################################################################
import sys as _sys
try:
"λΔ°".encode(_sys.stdout.encoding or "utf-8")
_lam_sym = "λ"
_delta_sym = "ΔE"
_degree_sym = "°"
except (UnicodeEncodeError, LookupError):
_lam_sym = "lambda"
_delta_sym = "delta"
_degree_sym = "deg"
del _sys
def _has_ghost(mol, idxs, is_lambda1=False):
"""
Internal function to check whether any atom is a ghost.
Parameters
----------
mol : sire.legacy.Mol.Molecule
The molecule.
idxs : [sire.legacy.Mol.AtomIdx]
A list of atom indices.
is_lambda1 : bool
Whether to check the lambda = 1 state.
Returns
-------
has_ghost : bool
Whether a ghost atom is present.
"""
import sire.legacy.Mol as _SireMol
# We need to check by ambertype too since this molecule may have been
# created via sire.morph.create_from_pertfile, in which case the element
# property will have been set to the end state with the largest mass, i.e.
# may no longer by a ghost.
if is_lambda1:
element_prop = "element1"
ambertype_prop = "ambertype1"
else:
element_prop = "element0"
ambertype_prop = "ambertype0"
element_ghost = _SireMol.Element(0)
ambertype_ghost = "du"
# Check whether an of the atoms is a ghost.
for idx in idxs:
if (
mol.atom(idx).property(element_prop) == element_ghost
or mol.atom(idx).property(ambertype_prop) == ambertype_ghost
):
return True
return False
def _is_ghost(mol, idxs, is_lambda1=False):
"""
Internal function to return whether each atom is a ghost.
Parameters
----------
mol : sire.legacy.Mol.Molecule
The molecule.
idxs : [sire.legacy.Mol.AtomIdx]
A list of atom indices.
is_lambda1 : bool
Whether to check the lambda = 1 state.
Returns
-------
is_ghost : [bool]
Whether each atom is a ghost.
"""
import sire.legacy.Mol as _SireMol
# We need to check by ambertype too since this molecule may have been
# created via sire.morph.create_from_pertfile, in which case the element
# property will have been set to the end state with the largest mass, i.e.
# may no longer by a ghost.
if is_lambda1:
element_prop = "element1"
ambertype_prop = "ambertype1"
else:
element_prop = "element0"
ambertype_prop = "ambertype0"
if is_lambda1:
element_prop = "element1"
ambertype_prop = "ambertype1"
else:
element_prop = "element0"
ambertype_prop = "ambertype0"
element_ghost = _SireMol.Element(0)
ambertype_ghost = "du"
# Initialise a list to store the state of each atom.
is_ghost = []
# Check whether each of the atoms is a ghost.
for idx in idxs:
is_ghost.append(
mol.atom(idx).property(element_prop) == element_ghost
or mol.atom(idx).property(ambertype_prop) == ambertype_ghost
)
return is_ghost