def __init__(self, m):
test_case.__init__(self, m)
self.xray_structure = xray.structure(
crystal_symmetry=crystal.symmetry(
unit_cell=(17.0216, 8.4362, 10.2248, 90, 102.79, 90),
space_group_symbol='hall: -C 2yc'),
scatterers=flex.xray_scatterer((
xray.scatterer( #0
label='S1',
site=(0.525736, 0.737492, 0.619814),
u=(0.000084, 0.000243, 0.000191,
0.000021, 0.000026, -0.000035)),
xray.scatterer( #1
label='C1',
site=(0.500000, 0.868009, 0.750000),
u=(0.000061, 0.000181, 0.000164,
0.000000, 0.000025, 0.000000)),
xray.scatterer( #2
label='C2',
site=(0.533017, 0.552825, 0.710913),
u=(0.000161, 0.000241, 0.000348,
0.000041, 0.000039, -0.000020)),
xray.scatterer( #3
label='H2A',
site=(0.525986, 0.462184, 0.647894),
u=0.041420),
xray.scatterer( #4
label='H2B',
site=(0.586473, 0.543642, 0.772877),
u=0.038360),
xray.scatterer( #5
label='C3',
site=(0.425914, 0.971290, 0.682589),
u=(0.000058, 0.000199, 0.000164,
-0.000003, 0.000017, -0.000007)),
xray.scatterer( #6
label='H3',
site=(0.441258, 1.029902, 0.606966),
u=0.023950),
xray.scatterer( #7
label='C4',
site=(0.349971, 0.874741, 0.622481),
u=(0.000064, 0.000236, 0.000219,
-0.000015, 0.000011, -0.000014)),
xray.scatterer( #8
label='H4B',
site=(0.362228, 0.799281, 0.555566),
u=0.026970),
xray.scatterer( #9
label='H4A',
site=(0.333906, 0.812566, 0.694426),
u=0.025070),
xray.scatterer( #10
label='C5',
site=(0.279832, 0.981636, 0.555089),
u=(0.000064, 0.000307, 0.000222,
-0.000007, 0.000003, -0.000021)),
xray.scatterer( #11
label='H5B',
site=(0.294150, 1.037327, 0.478372),
u=0.026970),
xray.scatterer( #12
label='H5A',
site=(0.231706, 0.915594, 0.519984),
u=0.034720),
xray.scatterer( #13
label='C6',
site=(0.259978, 1.103478, 0.653453),
u=(0.000061, 0.000335, 0.000246,
0.000016, 0.000021, -0.000001)),
xray.scatterer( #14
label='H6B',
site=(0.216403, 1.174193, 0.606307),
u=0.037560),
xray.scatterer( #15
label='H6A',
site=(0.240791, 1.048477, 0.726038),
u=0.024860),
xray.scatterer( #16
label='C7',
site=(0.334517, 1.201490, 0.713404),
u=(0.000071, 0.000265, 0.000251,
0.000019, 0.000019, -0.000029)),
xray.scatterer( #17
label='H7B',
site=(0.349843, 1.265431, 0.641770),
u=0.031500),
xray.scatterer( #18
label='H7A',
site=(0.321733, 1.275376, 0.780996),
u=0.030620),
xray.scatterer( #19
label='C8',
site=(0.405687, 1.096392, 0.779637),
u=(0.000064, 0.000247, 0.000187,
0.000009, 0.000015, -0.000033)),
xray.scatterer( #20
label='H8A',
site=(0.392638, 1.042204, 0.858057),
u=0.026000),
xray.scatterer( #21
label='H8B',
site=(0.453574, 1.163891, 0.812432),
u=0.027360)
)))
self.t_celsius = -153
self.shall_refine_thermal_displacements = True
self.constraints = [
_.secondary_xh2_sites(
pivot=2,
constrained_site_indices=(3,4)),
_.u_iso_proportional_to_pivot_u_eq(
u_eq_scatterer_idx=2,
u_iso_scatterer_idx=3,
multiplier=1.5),
_.u_iso_proportional_to_pivot_u_eq(
u_eq_scatterer_idx=2,
u_iso_scatterer_idx=4,
multiplier=1.5),
_.tertiary_xh_site(
pivot=5,
constrained_site_indices=(6,)),
_.u_iso_proportional_to_pivot_u_eq(
u_eq_scatterer_idx=5,
u_iso_scatterer_idx=6,
multiplier=1.5),
_.secondary_xh2_sites(
pivot=7,
constrained_site_indices=(8, 9)),
_.u_iso_proportional_to_pivot_u_eq(
u_eq_scatterer_idx=7,
u_iso_scatterer_idx=8,
multiplier=1.5),
_.u_iso_proportional_to_pivot_u_eq(
u_eq_scatterer_idx=7,
u_iso_scatterer_idx=9,
multiplier=1.5),
_.secondary_xh2_sites(
pivot=10,
constrained_site_indices=(11, 12)),
_.u_iso_proportional_to_pivot_u_eq(
u_eq_scatterer_idx=10,
u_iso_scatterer_idx=11,
multiplier=1.5),
_.u_iso_proportional_to_pivot_u_eq(
u_eq_scatterer_idx=10,
u_iso_scatterer_idx=12,
multiplier=1.5),
_.secondary_xh2_sites(
pivot=13,
constrained_site_indices=(14, 15)),
_.u_iso_proportional_to_pivot_u_eq(
u_eq_scatterer_idx=13,
u_iso_scatterer_idx=14,
multiplier=1.5),
_.u_iso_proportional_to_pivot_u_eq(
u_eq_scatterer_idx=13,
u_iso_scatterer_idx=15,
multiplier=1.5),
_.secondary_xh2_sites(
pivot=16,
constrained_site_indices=(17, 18)),
_.u_iso_proportional_to_pivot_u_eq(
u_eq_scatterer_idx=16,
u_iso_scatterer_idx=17,
multiplier=1.5),
_.u_iso_proportional_to_pivot_u_eq(
u_eq_scatterer_idx=16,
u_iso_scatterer_idx=18,
multiplier=1.5),
_.secondary_xh2_sites(
pivot=19,
constrained_site_indices=(20, 21)),
_.u_iso_proportional_to_pivot_u_eq(
u_eq_scatterer_idx=19,
u_iso_scatterer_idx=20,
multiplier=1.5),
_.u_iso_proportional_to_pivot_u_eq(
u_eq_scatterer_idx=19,
u_iso_scatterer_idx=21,
multiplier=1.5),
]
self.expected_reparametrisation_for_hydrogen_named = {
"H2A": (core.secondary_xh2_sites, 'C2'),
"H2B": (core.secondary_xh2_sites, 'C2'),
"H3" : (core.tertiary_xh_site , 'C3'),
"H4A": (core.secondary_xh2_sites, 'C4'),
"H4B": (core.secondary_xh2_sites, 'C4'),
"H5A": (core.secondary_xh2_sites, 'C5'),
"H5B": (core.secondary_xh2_sites, 'C5'),
"H6A": (core.secondary_xh2_sites, 'C6'),
"H6B": (core.secondary_xh2_sites, 'C6'),
"H7A": (core.secondary_xh2_sites, 'C7'),
"H7B": (core.secondary_xh2_sites, 'C7'),
"H8A": (core.secondary_xh2_sites, 'C8'),
"H8B": (core.secondary_xh2_sites, 'C8'),
}
self.site_refinement_tolerance = 0.01
self.u_star_refinement_tolerance = 5e-7
def __init__(self, m):
test_case.__init__(self, m)
self.xray_structure = xray.structure(
crystal_symmetry=crystal.symmetry(
unit_cell=(17.0216, 8.4362, 10.2248, 90, 102.79, 90),
space_group_symbol='hall: -C 2yc'),
scatterers=flex.xray_scatterer((
xray.scatterer( #0
label='S1',
site=(0.525736, 0.737492, 0.619814),
u=(0.000084, 0.000243, 0.000191, 0.000021, 0.000026,
-0.000035)),
xray.scatterer( #1
label='C1',
site=(0.500000, 0.868009, 0.750000),
u=(0.000061, 0.000181, 0.000164, 0.000000, 0.000025,
0.000000)),
xray.scatterer( #2
label='C2',
site=(0.533017, 0.552825, 0.710913),
u=(0.000161, 0.000241, 0.000348, 0.000041, 0.000039,
-0.000020)),
xray.scatterer( #3
label='H2A',
site=(0.525986, 0.462184, 0.647894),
u=0.041420),
xray.scatterer( #4
label='H2B',
site=(0.586473, 0.543642, 0.772877),
u=0.038360),
xray.scatterer( #5
label='C3',
site=(0.425914, 0.971290, 0.682589),
u=(0.000058, 0.000199, 0.000164, -0.000003, 0.000017,
-0.000007)),
xray.scatterer( #6
label='H3',
site=(0.441258, 1.029902, 0.606966),
u=0.023950),
xray.scatterer( #7
label='C4',
site=(0.349971, 0.874741, 0.622481),
u=(0.000064, 0.000236, 0.000219, -0.000015, 0.000011,
-0.000014)),
xray.scatterer( #8
label='H4B',
site=(0.362228, 0.799281, 0.555566),
u=0.026970),
xray.scatterer( #9
label='H4A',
site=(0.333906, 0.812566, 0.694426),
u=0.025070),
xray.scatterer( #10
label='C5',
site=(0.279832, 0.981636, 0.555089),
u=(0.000064, 0.000307, 0.000222, -0.000007, 0.000003,
-0.000021)),
xray.scatterer( #11
label='H5B',
site=(0.294150, 1.037327, 0.478372),
u=0.026970),
xray.scatterer( #12
label='H5A',
site=(0.231706, 0.915594, 0.519984),
u=0.034720),
xray.scatterer( #13
label='C6',
site=(0.259978, 1.103478, 0.653453),
u=(0.000061, 0.000335, 0.000246, 0.000016, 0.000021,
-0.000001)),
xray.scatterer( #14
label='H6B',
site=(0.216403, 1.174193, 0.606307),
u=0.037560),
xray.scatterer( #15
label='H6A',
site=(0.240791, 1.048477, 0.726038),
u=0.024860),
xray.scatterer( #16
label='C7',
site=(0.334517, 1.201490, 0.713404),
u=(0.000071, 0.000265, 0.000251, 0.000019, 0.000019,
-0.000029)),
xray.scatterer( #17
label='H7B',
site=(0.349843, 1.265431, 0.641770),
u=0.031500),
xray.scatterer( #18
label='H7A',
site=(0.321733, 1.275376, 0.780996),
u=0.030620),
xray.scatterer( #19
label='C8',
site=(0.405687, 1.096392, 0.779637),
u=(0.000064, 0.000247, 0.000187, 0.000009, 0.000015,
-0.000033)),
xray.scatterer( #20
label='H8A',
site=(0.392638, 1.042204, 0.858057),
u=0.026000),
xray.scatterer( #21
label='H8B',
site=(0.453574, 1.163891, 0.812432),
u=0.027360))))
self.t_celsius = -153
self.shall_refine_thermal_displacements = True
self.constraints = [
_.secondary_xh2_sites(pivot=2, constrained_site_indices=(3, 4)),
_.u_iso_proportional_to_pivot_u_eq(u_eq_scatterer_idx=2,
u_iso_scatterer_idx=3,
multiplier=1.5),
_.u_iso_proportional_to_pivot_u_eq(u_eq_scatterer_idx=2,
u_iso_scatterer_idx=4,
multiplier=1.5),
_.tertiary_xh_site(pivot=5, constrained_site_indices=(6, )),
_.u_iso_proportional_to_pivot_u_eq(u_eq_scatterer_idx=5,
u_iso_scatterer_idx=6,
multiplier=1.5),
_.secondary_xh2_sites(pivot=7, constrained_site_indices=(8, 9)),
_.u_iso_proportional_to_pivot_u_eq(u_eq_scatterer_idx=7,
u_iso_scatterer_idx=8,
multiplier=1.5),
_.u_iso_proportional_to_pivot_u_eq(u_eq_scatterer_idx=7,
u_iso_scatterer_idx=9,
multiplier=1.5),
_.secondary_xh2_sites(pivot=10, constrained_site_indices=(11, 12)),
_.u_iso_proportional_to_pivot_u_eq(u_eq_scatterer_idx=10,
u_iso_scatterer_idx=11,
multiplier=1.5),
_.u_iso_proportional_to_pivot_u_eq(u_eq_scatterer_idx=10,
u_iso_scatterer_idx=12,
multiplier=1.5),
_.secondary_xh2_sites(pivot=13, constrained_site_indices=(14, 15)),
_.u_iso_proportional_to_pivot_u_eq(u_eq_scatterer_idx=13,
u_iso_scatterer_idx=14,
multiplier=1.5),
_.u_iso_proportional_to_pivot_u_eq(u_eq_scatterer_idx=13,
u_iso_scatterer_idx=15,
multiplier=1.5),
_.secondary_xh2_sites(pivot=16, constrained_site_indices=(17, 18)),
_.u_iso_proportional_to_pivot_u_eq(u_eq_scatterer_idx=16,
u_iso_scatterer_idx=17,
multiplier=1.5),
_.u_iso_proportional_to_pivot_u_eq(u_eq_scatterer_idx=16,
u_iso_scatterer_idx=18,
multiplier=1.5),
_.secondary_xh2_sites(pivot=19, constrained_site_indices=(20, 21)),
_.u_iso_proportional_to_pivot_u_eq(u_eq_scatterer_idx=19,
u_iso_scatterer_idx=20,
multiplier=1.5),
_.u_iso_proportional_to_pivot_u_eq(u_eq_scatterer_idx=19,
u_iso_scatterer_idx=21,
multiplier=1.5),
]
self.expected_reparametrisation_for_hydrogen_named = {
"H2A": (core.secondary_xh2_sites, 'C2'),
"H2B": (core.secondary_xh2_sites, 'C2'),
"H3": (core.tertiary_xh_site, 'C3'),
"H4A": (core.secondary_xh2_sites, 'C4'),
"H4B": (core.secondary_xh2_sites, 'C4'),
"H5A": (core.secondary_xh2_sites, 'C5'),
"H5B": (core.secondary_xh2_sites, 'C5'),
"H6A": (core.secondary_xh2_sites, 'C6'),
"H6B": (core.secondary_xh2_sites, 'C6'),
"H7A": (core.secondary_xh2_sites, 'C7'),
"H7B": (core.secondary_xh2_sites, 'C7'),
"H8A": (core.secondary_xh2_sites, 'C8'),
"H8B": (core.secondary_xh2_sites, 'C8'),
}
self.site_refinement_tolerance = 0.01
self.u_star_refinement_tolerance = 5e-7
def __init__(self, m):
test_case.__init__(self, m)
self.xray_structure = development.sucrose()
self.t_celsius = 20
self.shall_refine_thermal_displacements = False
self.constraints = [
_.terminal_tetrahedral_xh_site(
rotating=True,
pivot=1,
constrained_site_indices=(2,)),
_.terminal_tetrahedral_xh_site(
rotating=True,
pivot=3,
constrained_site_indices=(4,)),
_.terminal_tetrahedral_xh_site(
rotating=True,
pivot=5,
constrained_site_indices=(6,)),
_.terminal_tetrahedral_xh_site(
rotating=True,
pivot=7,
constrained_site_indices=(8,)),
_.terminal_tetrahedral_xh_site(
rotating=True,
pivot=10,
constrained_site_indices=(11,)),
_.terminal_tetrahedral_xh_site(
rotating=True,
pivot=12,
constrained_site_indices=(13,)),
_.terminal_tetrahedral_xh_site(
rotating=True,
pivot=14,
constrained_site_indices=(15,)),
_.terminal_tetrahedral_xh_site(
rotating=True,
pivot=16,
constrained_site_indices=(17,)),
_.tertiary_xh_site(
pivot=19,
constrained_site_indices=(20,)),
_.secondary_xh2_sites(
pivot=21,
flapping = True,
constrained_site_indices=(26, 22)),
_.tertiary_xh_site(
pivot=23,
constrained_site_indices=(24,)),
_.tertiary_xh_site(
pivot=25,
constrained_site_indices=(27,)),
_.tertiary_xh_site(
pivot=28,
constrained_site_indices=(29,)),
_.tertiary_xh_site(
pivot=30,
constrained_site_indices=(31,)),
_.secondary_xh2_sites(
pivot=33,
flapping = True,
constrained_site_indices=(35, 34)),
_.tertiary_xh_site(
pivot=36,
constrained_site_indices=(37,)),
_.tertiary_xh_site(
pivot=38,
constrained_site_indices=(39,)),
_.tertiary_xh_site(
pivot=40,
constrained_site_indices=(41,)),
_.secondary_xh2_sites(
pivot=42,
flapping = True,
constrained_site_indices=(43, 44)),
]
self.expected_reparametrisation_for_hydrogen_named = {
"H2": (core.terminal_tetrahedral_xh_site, 'O2'),
"H3": (core.terminal_tetrahedral_xh_site, 'O3'),
"H4": (core.terminal_tetrahedral_xh_site, 'O4'),
"H5": (core.terminal_tetrahedral_xh_site, 'O5'),
"H7": (core.terminal_tetrahedral_xh_site, 'O7'),
"H8": (core.terminal_tetrahedral_xh_site, 'O8'),
"H9": (core.terminal_tetrahedral_xh_site, 'O9'),
"H10": (core.terminal_tetrahedral_xh_site, 'O10'),
"H1": (core.tertiary_xh_site, 'C1'),
"H2A": (core.secondary_xh2_sites, 'C2'),
"H2B": (core.secondary_xh2_sites, 'C2'),
"H3B": (core.tertiary_xh_site, 'C3'),
"H4B": (core.tertiary_xh_site, 'C4'),
"H5B": (core.tertiary_xh_site, 'C5'),
"H6": (core.tertiary_xh_site, 'C6'),
"H8A": (core.secondary_xh2_sites, 'C8'),
"H8B": (core.secondary_xh2_sites, 'C8'),
"H9B": (core.tertiary_xh_site, 'C9'),
"H10B": (core.tertiary_xh_site, 'C10'),
"H11": (core.tertiary_xh_site, 'C11'),
"H12A": (core.secondary_xh2_sites, 'C12'),
"H12B": (core.secondary_xh2_sites, 'C12'),
}
self.expected_mapping_to_grad_fc = (
59,60,61 , # O1.site
80,81,82,83,84,85 , # O1.u
0,1,2 , # O2.site
86,87,88,89,90,91 , # O2.u
304,305,306 , # H2.site
92 , # H2.u
7,8,9 , # O3.site
93,94,95,96,97,98 , # O3.u
307,308,309 , # H3.site
99 , # H3.u
14,15,16 , # O4.site
100,101,102,103,104,105 , # O4.u
310,311,312 , # H4.site
106 , # H4.u
21,22,23 , # O5.site
107,108,109,110,111,112 , # O5.u
313,314,315 , # H5.site
113 , # H5.u
76,77,78 , # O6.site
114,115,116,117,118,119 , # O6.u
28,29,30 , # O7.site
120,121,122,123,124,125 , # O7.u
316,317,318 , # H7.site
126 , # H7.u
35,36,37 , # O8.site
127,128,129,130,131,132 , # O8.u
319,320,321 , # H8.site
133 , # H8.u
42,43,44 , # O9.site
134,135,136,137,138,139 , # O9.u
322,323,324 , # H9.site
140 , # H9.u
49,50,51 , # O10.site
141,142,143,144,145,146 , # O10.u
325,326,327 , # H10.site
147 , # H10.u
66,67,68 , # O11.site
148,149,150,151,152,153 , # O11.u
56,57,58 , # C1.site
154,155,156,157,158,159 , # C1.u
328,329,330 , # H1.site
160 , # H1.u
3,4,5 , # C2.site
161,162,163,164,165,166 , # C2.u
334,335,336 , # H2B.site
167 , # H2B.u
10,11,12 , # C3.site
168,169,170,171,172,173 , # C3.u
337,338,339 , # H3B.site
174 , # H3B.u
17,18,19 , # C4.site
175,176,177,178,179,180 , # C4.u
331,332,333 , # H2A.site
181 , # H2A.u
340,341,342 , # H4B.site
182 , # H4B.u
24,25,26 , # C5.site
183,184,185,186,187,188 , # C5.u
343,344,345 , # H5B.site
189 , # H5B.u
63,64,65 , # C6.site
190,191,192,193,194,195 , # C6.u
346,347,348 , # H6.site
196 , # H6.u
69,70,71 , # C7.site
197,198,199,200,201,202 , # C7.u
52,53,54 , # C8.site
203,204,205,206,207,208 , # C8.u
352,353,354 , # H8A.site
209 , # H8A.u
349,350,351 , # H8B.site
210 , # H8B.u
45,46,47 , # C9.site
211,212,213,214,215,216 , # C9.u
355,356,357 , # H9B.site
217 , # H9B.u
38,39,40 , # C10.site
218,219,220,221,222,223 , # C10.u
358,359,360 , # H10B.site
224 , # H10B.u
73,74,75 , # C11.site
225,226,227,228,229,230 , # C11.u
361,362,363 , # H11.site
231 , # H11.u
31,32,33 , # C12.site
232,233,234,235,236,237 , # C12.u
364,365,366 , # H12B.site
238 , # H12B.u
367,368,369 , # H12A.site
239 , # H12A.u
)
self.site_refinement_tolerance = 1e-4
def __init__(self, m):
test_case.__init__(self, m)
self.xray_structure = development.sucrose()
self.t_celsius = 20
self.shall_refine_thermal_displacements = False
self.constraints = [
_.terminal_tetrahedral_xh_site(rotating=True,
pivot=1,
constrained_site_indices=(2, )),
_.terminal_tetrahedral_xh_site(rotating=True,
pivot=3,
constrained_site_indices=(4, )),
_.terminal_tetrahedral_xh_site(rotating=True,
pivot=5,
constrained_site_indices=(6, )),
_.terminal_tetrahedral_xh_site(rotating=True,
pivot=7,
constrained_site_indices=(8, )),
_.terminal_tetrahedral_xh_site(rotating=True,
pivot=10,
constrained_site_indices=(11, )),
_.terminal_tetrahedral_xh_site(rotating=True,
pivot=12,
constrained_site_indices=(13, )),
_.terminal_tetrahedral_xh_site(rotating=True,
pivot=14,
constrained_site_indices=(15, )),
_.terminal_tetrahedral_xh_site(rotating=True,
pivot=16,
constrained_site_indices=(17, )),
_.tertiary_xh_site(pivot=19, constrained_site_indices=(20, )),
_.secondary_xh2_sites(pivot=21,
flapping=True,
constrained_site_indices=(26, 22)),
_.tertiary_xh_site(pivot=23, constrained_site_indices=(24, )),
_.tertiary_xh_site(pivot=25, constrained_site_indices=(27, )),
_.tertiary_xh_site(pivot=28, constrained_site_indices=(29, )),
_.tertiary_xh_site(pivot=30, constrained_site_indices=(31, )),
_.secondary_xh2_sites(pivot=33,
flapping=True,
constrained_site_indices=(35, 34)),
_.tertiary_xh_site(pivot=36, constrained_site_indices=(37, )),
_.tertiary_xh_site(pivot=38, constrained_site_indices=(39, )),
_.tertiary_xh_site(pivot=40, constrained_site_indices=(41, )),
_.secondary_xh2_sites(pivot=42,
flapping=True,
constrained_site_indices=(43, 44)),
]
self.expected_reparametrisation_for_hydrogen_named = {
"H2": (core.terminal_tetrahedral_xh_site, 'O2'),
"H3": (core.terminal_tetrahedral_xh_site, 'O3'),
"H4": (core.terminal_tetrahedral_xh_site, 'O4'),
"H5": (core.terminal_tetrahedral_xh_site, 'O5'),
"H7": (core.terminal_tetrahedral_xh_site, 'O7'),
"H8": (core.terminal_tetrahedral_xh_site, 'O8'),
"H9": (core.terminal_tetrahedral_xh_site, 'O9'),
"H10": (core.terminal_tetrahedral_xh_site, 'O10'),
"H1": (core.tertiary_xh_site, 'C1'),
"H2A": (core.secondary_xh2_sites, 'C2'),
"H2B": (core.secondary_xh2_sites, 'C2'),
"H3B": (core.tertiary_xh_site, 'C3'),
"H4B": (core.tertiary_xh_site, 'C4'),
"H5B": (core.tertiary_xh_site, 'C5'),
"H6": (core.tertiary_xh_site, 'C6'),
"H8A": (core.secondary_xh2_sites, 'C8'),
"H8B": (core.secondary_xh2_sites, 'C8'),
"H9B": (core.tertiary_xh_site, 'C9'),
"H10B": (core.tertiary_xh_site, 'C10'),
"H11": (core.tertiary_xh_site, 'C11'),
"H12A": (core.secondary_xh2_sites, 'C12'),
"H12B": (core.secondary_xh2_sites, 'C12'),
}
self.expected_mapping_to_grad_fc = (
59,
60,
61, # O1.site
80,
81,
82,
83,
84,
85, # O1.u
0,
1,
2, # O2.site
86,
87,
88,
89,
90,
91, # O2.u
304,
305,
306, # H2.site
92, # H2.u
7,
8,
9, # O3.site
93,
94,
95,
96,
97,
98, # O3.u
307,
308,
309, # H3.site
99, # H3.u
14,
15,
16, # O4.site
100,
101,
102,
103,
104,
105, # O4.u
310,
311,
312, # H4.site
106, # H4.u
21,
22,
23, # O5.site
107,
108,
109,
110,
111,
112, # O5.u
313,
314,
315, # H5.site
113, # H5.u
76,
77,
78, # O6.site
114,
115,
116,
117,
118,
119, # O6.u
28,
29,
30, # O7.site
120,
121,
122,
123,
124,
125, # O7.u
316,
317,
318, # H7.site
126, # H7.u
35,
36,
37, # O8.site
127,
128,
129,
130,
131,
132, # O8.u
319,
320,
321, # H8.site
133, # H8.u
42,
43,
44, # O9.site
134,
135,
136,
137,
138,
139, # O9.u
322,
323,
324, # H9.site
140, # H9.u
49,
50,
51, # O10.site
141,
142,
143,
144,
145,
146, # O10.u
325,
326,
327, # H10.site
147, # H10.u
66,
67,
68, # O11.site
148,
149,
150,
151,
152,
153, # O11.u
56,
57,
58, # C1.site
154,
155,
156,
157,
158,
159, # C1.u
328,
329,
330, # H1.site
160, # H1.u
3,
4,
5, # C2.site
161,
162,
163,
164,
165,
166, # C2.u
334,
335,
336, # H2B.site
167, # H2B.u
10,
11,
12, # C3.site
168,
169,
170,
171,
172,
173, # C3.u
337,
338,
339, # H3B.site
174, # H3B.u
17,
18,
19, # C4.site
175,
176,
177,
178,
179,
180, # C4.u
331,
332,
333, # H2A.site
181, # H2A.u
340,
341,
342, # H4B.site
182, # H4B.u
24,
25,
26, # C5.site
183,
184,
185,
186,
187,
188, # C5.u
343,
344,
345, # H5B.site
189, # H5B.u
63,
64,
65, # C6.site
190,
191,
192,
193,
194,
195, # C6.u
346,
347,
348, # H6.site
196, # H6.u
69,
70,
71, # C7.site
197,
198,
199,
200,
201,
202, # C7.u
52,
53,
54, # C8.site
203,
204,
205,
206,
207,
208, # C8.u
352,
353,
354, # H8A.site
209, # H8A.u
349,
350,
351, # H8B.site
210, # H8B.u
45,
46,
47, # C9.site
211,
212,
213,
214,
215,
216, # C9.u
355,
356,
357, # H9B.site
217, # H9B.u
38,
39,
40, # C10.site
218,
219,
220,
221,
222,
223, # C10.u
358,
359,
360, # H10B.site
224, # H10B.u
73,
74,
75, # C11.site
225,
226,
227,
228,
229,
230, # C11.u
361,
362,
363, # H11.site
231, # H11.u
31,
32,
33, # C12.site
232,
233,
234,
235,
236,
237, # C12.u
364,
365,
366, # H12B.site
238, # H12B.u
367,
368,
369, # H12A.site
239, # H12A.u
)
self.site_refinement_tolerance = 1e-4
