Repository navigation
Expand file tree
/
Copy pathsgtbx_extra_groups.py
More file actions
211 lines (162 loc) · 5.47 KB
/
Copy pathsgtbx_extra_groups.py
File metadata and controls
211 lines (162 loc) · 5.47 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
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
#!/usr/bin/env python
"""Quick and extremely dirty script for generating code for SpaceGroup
that are defined in cctbx, but not in mmLib. It was used to generate
module sgtbxspacegroups.
This is a utility script that should not be included with code
distribution.
Not to be included with code distributions.
"""
import math
import re
import numpy
from cctbx import sgtbx
from diffpy.structure.spacegroups import SpaceGroup, SymOp, is_space_group_identifier, mmLibSpaceGroupList
def tuple_to_sg_array(tpl):
if not _rtarrays:
import diffpy.structure.SpaceGroups as sgmod
for n in dir(sgmod):
if not n.startswith("Rot_") and not n.startswith("Tr_"):
continue
a = getattr(sgmod, n)
t = tuple(a.flatten())
_rtarrays[t] = a
if len(tpl) == 3:
tpl = tuple([(x - math.floor(x)) for x in tpl])
if tpl not in _rtarrays:
_rtarrays[tpl] = numpy.array(tpl, dtype=float)
return _rtarrays[tpl]
_rtarrays = {}
def mm_space_group_from_symbol(symbol):
"""Construct SpaceGroup instance from a string symbol using sgtbx
data."""
sginfo = sgtbx.space_group_info(symbol)
symop_list = []
symop_list = get_symop_list(sginfo.group())
sgtype = sginfo.type()
uhm = sgtype.lookup_symbol()
sgsmbls = sgtbx.space_group_symbols(uhm)
kw = {}
kw["number"] = sgtype.number()
kw["num_sym_equiv"] = len(symop_list)
kw["num_primitive_sym_equiv"] = count_unique_rotations(symop_list)
kw["short_name"] = sgsmbls.hermann_mauguin().replace(" ", "")
pgt = sgsmbls.point_group_type()
pgn = "PG" + re.sub(r"-(\d)", "\\1bar", pgt)
kw["point_group_name"] = pgn
kw["crystal_system"] = sgsmbls.crystal_system().upper()
kw["pdb_name"] = sgsmbls.hermann_mauguin()
kw["symop_list"] = symop_list
mmsg = SpaceGroup(**kw)
return mmsg
def adjust_mm_space_group_number(mmsg):
sg0 = [x for x in mmLibSpaceGroupList if x.number == mmsg.number]
if sg0 and cmp_space_groups(sg0[0], mmsg):
return
while mmsg.number in sgnumbers:
mmsg.number += 1000
sgnumbers.append(mmsg.number)
def get_symop_list(grp):
symop_list = []
for op in grp:
r_sgtbx = op.r().as_double()
t_sgtbx = op.t().as_double()
R = tuple_to_sg_array(r_sgtbx)
t = tuple_to_sg_array(t_sgtbx)
symop_list.append(SymOp(R, t))
return symop_list
def count_unique_rotations(symop_list):
unique_rotations = set()
for op in symop_list:
tpl = tuple(op.R.flatten())
unique_rotations.add(tpl)
return len(unique_rotations)
def cmp_space_groups(sg0, sg1):
if sg0 is sg1:
return True
s0 = hash_mm_space_group(sg0)
s1 = hash_mm_space_group(sg1)
return s0 == s1
def find_equivalent_mm_space_group(grp):
if not _equivmmsg:
for sgn in mmLibSpaceGroupList:
ssgn = hash_mm_space_group(sgn)
_equivmmsg.setdefault(ssgn, sgn)
ssg = hash_sgtbx_group(grp)
return _equivmmsg.get(ssg)
_equivmmsg = {}
def find_equivalent_sgtbx_space_group(sgmm):
if not _equivsgtbx:
for smbls in sgtbx.space_group_symbol_iterator():
uhm = smbls.universal_hermann_mauguin()
grp = sgtbx.space_group_info(uhm).group()
hgrp = hash_sgtbx_group(grp)
_equivsgtbx.setdefault(hgrp, grp)
hgmm = hash_mm_space_group(sgmm)
return _equivsgtbx.get(hgmm)
_equivsgtbx = {}
def hash_mm_space_group(sg):
lines = [str(sg.number % 1000)] + sorted(map(str, sg.iter_symops()))
s = "\n".join(lines)
return s
def hash_sgtbx_group(grp):
n = grp.type().number()
lines = [str(n)] + sorted(map(str, get_symop_list(grp)))
s = "\n".join(lines)
return s
sgnumbers = [sg.number for sg in mmLibSpaceGroupList]
_SGsrc = """\
sg%(number)i = SpaceGroup(
number = %(number)i,
num_sym_equiv = %(num_sym_equiv)i,
num_primitive_sym_equiv = %(num_sym_equiv)i,
short_name = %(short_name)r,
point_group_name = %(point_group_name)r,
crystal_system = %(crystal_system)r,
pdb_name = %(pdb_name)r,
symop_list = [
@SYMOPS@
]
)
"""
def sg_code(mmsg):
src0 = _SGsrc % mmsg.__dict__
src1 = src0.replace("@SYMOPS@", symops_code(mmsg))
return src1
def symops_code(mmsg):
lst = ["%8s%s," % ("", symop_code(op)) for op in mmsg.iter_symops()]
src = "\n".join(lst).strip()
return src
def symop_code(op):
if not _rtnames:
import diffpy.structure.SpaceGroups as sgmod
for n in dir(sgmod):
if not n.startswith("Rot_") and not n.startswith("Tr_"):
continue
a = getattr(sgmod, n)
at = tuple(a.flatten())
_rtnames[at] = "sgmod." + n
nR = _rtnames[tuple(op.R.flatten())]
nt = _rtnames[tuple(op.t)]
src = "SymOp(%s, %s)" % (nR, nt)
return src
_rtnames = {}
def main():
duplicates = set()
for smbls in sgtbx.space_group_symbol_iterator():
uhm = smbls.universal_hermann_mauguin()
grp = sgtbx.space_group_info(uhm).group()
if find_equivalent_mm_space_group(grp):
continue
shn = smbls.hermann_mauguin().replace(" ", "")
if is_space_group_identifier(shn):
continue
sg = mm_space_group_from_symbol(uhm)
hsg = hash_mm_space_group(sg)
if hsg in duplicates:
continue
adjust_mm_space_group_number(sg)
duplicates.add(hsg)
print(sg_code(sg))
return
if __name__ == "__main__":
main()