def exercise_sucrose(flipping_type, anomalous_flag, d_min, verbose=False, amplitude_type="quasi-E"):
from smtbx import development
target_structure = development.sucrose()
print "Sucrose"
exercise_one_structure(
target_structure,
flipping_type,
anomalous_flag,
d_min,
grid_resolution_factor=1 / 2,
verbose=verbose,
amplitude_type=amplitude_type,
)
def __init__(self, m):
test_case.__init__(self, m)
self.xray_structure = development.sucrose()
self.t_celsius = 20
self.shall_refine_thermal_displacements = True
self.constraints = [
_.scalar_scaled_u(range(len(self.xray_structure.scatterers())))
]
self.expected_reparametrisation_for_hydrogen_named = {}
xs = self.xray_structure
# Make one O atom isotropic to exercise scalar_scaled_u_iso on a non-H atom
sc1 = xs.scatterers()[1]
sc1.u_iso = sc1.u_iso_or_equiv(xs.unit_cell())
sc1.set_use_u_iso_only()
self.expected_mapping_to_grad_fc = tuple(range(271,
271 + 155)) # There are
def exercise_connectivity_table():
xs = development.sucrose()
connectivity = utils.connectivity_table(xs)
pair_counts = [
2, 2, 1, 2, 1, 2, 1, 2, 1, 2, 2, 1, 2, 1, 2, 1, 2, 1, 2, 4, 1, 4, 1,
4, 1, 4, 1, 1, 4, 1, 4, 1, 4, 4, 1, 1, 4, 1, 4, 1, 4, 1, 4, 1, 1]
assert approx_equal(connectivity.pair_asu_table.pair_counts(), pair_counts)
connectivity.add_bond(0, 1)
assert approx_equal(
connectivity.pair_asu_table.pair_counts(),
[3, 3, 1, 2, 1, 2, 1, 2, 1, 2, 2, 1, 2, 1, 2, 1, 2, 1, 2, 4, 1, 4, 1,
4, 1, 4, 1, 1, 4, 1, 4, 1, 4, 4, 1, 1, 4, 1, 4, 1, 4, 1, 4, 1, 1])
connectivity.add_bond(5, 5, rt_mx_ji=sgtbx.rt_mx("x+1,y,z"))
assert connectivity.pair_asu_table.pair_counts()[5] == 4
connectivity.remove_bond(0, 1)
connectivity.remove_bond(5,5, rt_mx_ji=sgtbx.rt_mx("x+1,y,z"))
assert approx_equal(connectivity.pair_asu_table.pair_counts(), pair_counts)
def exercise_sucrose(flipping_type,
anomalous_flag,
d_min,
verbose=False,
amplitude_type='quasi-E'):
from smtbx import development
target_structure = development.sucrose()
print "Sucrose"
exercise_one_structure(
target_structure,
flipping_type,
anomalous_flag,
d_min,
grid_resolution_factor=1 / 2,
verbose=verbose,
amplitude_type=amplitude_type,
)
def test_connectivity_table():
xs = development.sucrose()
connectivity = utils.connectivity_table(xs)
pair_counts = [
2, 2, 1, 2, 1, 2, 1, 2, 1, 2, 2, 1, 2, 1, 2, 1, 2, 1, 2, 4, 1, 4, 1, 4,
1, 4, 1, 1, 4, 1, 4, 1, 4, 4, 1, 1, 4, 1, 4, 1, 4, 1, 4, 1, 1
]
assert approx_equal(connectivity.pair_asu_table.pair_counts(), pair_counts)
connectivity.add_bond(0, 1)
assert approx_equal(connectivity.pair_asu_table.pair_counts(), [
3, 3, 1, 2, 1, 2, 1, 2, 1, 2, 2, 1, 2, 1, 2, 1, 2, 1, 2, 4, 1, 4, 1, 4,
1, 4, 1, 1, 4, 1, 4, 1, 4, 4, 1, 1, 4, 1, 4, 1, 4, 1, 4, 1, 1
])
connectivity.add_bond(5, 5, rt_mx_ji=sgtbx.rt_mx("x+1,y,z"))
assert connectivity.pair_asu_table.pair_counts()[5] == 4
connectivity.remove_bond(0, 1)
connectivity.remove_bond(5, 5, rt_mx_ji=sgtbx.rt_mx("x+1,y,z"))
assert approx_equal(connectivity.pair_asu_table.pair_counts(), pair_counts)
def exercise_rigid_bond():
xray_structure = development.sucrose()
pair_sym_table = get_pair_sym_table(xray_structure)
for table in (None,pair_sym_table):
if table is None: xs = xray_structure
else: xs = None
restraints = \
adp_restraints.rigid_bond_restraints(
xray_structure=xs,
pair_sym_table=table)
assert restraints.proxies.size() == 60
i_seqs = (9,14,28,32,36,38)
restraints = \
adp_restraints.rigid_bond_restraints(
xray_structure=xs,
pair_sym_table=table,
i_seqs=i_seqs)
expected_i_seqs = (
(9,32),(9,36),(14,36),(14,32),(14,38),(32,36),(32,38),(36,38))
expected_weights = [10000]*len(expected_i_seqs)
proxies = restraints.proxies
assert proxies.size() == len(expected_i_seqs)
for i in range(proxies.size()):
assert approx_equal(proxies[i].i_seqs, expected_i_seqs[i])
assert approx_equal(proxies[i].weight, expected_weights[i])
# add more restraints to same shared proxy
i_seqs = (10,40,42)
restraints = \
adp_restraints.rigid_bond_restraints(
xray_structure=xs,
pair_sym_table=table,
proxies=proxies,
i_seqs=i_seqs)
expected_i_seqs = (
(9,32),(9,36),(14,36),(14,32),(14,38),(32,36),
(32,38),(36,38),(10,42),(10,40),(40,42))
expected_weights = [10000]*len(expected_i_seqs)
proxies = restraints.proxies
assert proxies.size() == len(expected_i_seqs)
for i in range(proxies.size()):
assert approx_equal(proxies[i].i_seqs, expected_i_seqs[i])
assert approx_equal(proxies[i].weight, expected_weights[i])
def test_adp_similarity():
xray_structure = development.sucrose()
pair_sym_table = get_pair_sym_table(xray_structure)
for table in (None,pair_sym_table):
if table is None: xs = xray_structure
else: xs = None
restraints = \
adp_restraints.adp_similarity_restraints(
xray_structure=xs,
pair_sym_table=table)
assert restraints.proxies.size() == 24
i_seqs = (9,14,28,32,36,38)
restraints = \
adp_restraints.adp_similarity_restraints(
xray_structure=xs,
pair_sym_table=table,
i_seqs=i_seqs)
expected_i_seqs = ((9,32),(14,36),(32,36),(36,38))
expected_weights = (625,156.25,625,625)
proxies = restraints.proxies
assert proxies.size() == len(expected_i_seqs)
for i in range(proxies.size()):
assert approx_equal(proxies[i].i_seqs, expected_i_seqs[i])
assert approx_equal(proxies[i].weight, expected_weights[i])
# add more restraints to same shared proxy
i_seqs = (3,23,40,42)
restraints = \
adp_restraints.adp_similarity_restraints(
xray_structure=xs,
pair_sym_table=table,
proxies=proxies,
i_seqs=i_seqs)
expected_i_seqs = (
(9,32),(14,36),(32,36),(36,38),(3,23),(40,42))
expected_weights = (625,156.25,625,625,156.25,625)
proxies = restraints.proxies
assert proxies.size() == len(expected_i_seqs)
for i in range(proxies.size()):
assert approx_equal(proxies[i].i_seqs, expected_i_seqs[i])
assert approx_equal(proxies[i].weight, expected_weights[i])
def exercise_isotropic_adp():
xray_structure = development.sucrose()
xray_structure.scatterers()[10].set_use_u_iso_only()
pair_sym_table = get_pair_sym_table(xray_structure)
for table in (None,pair_sym_table):
restraints = \
adp_restraints.isotropic_adp_restraints(
xray_structure=xray_structure,
pair_sym_table=table)
assert restraints.proxies.size() == 22
i_seqs = (9,14,28,32,36,38)
expected_weights = (100,25,100,100,100,100)
restraints = \
adp_restraints.isotropic_adp_restraints(
xray_structure=xray_structure,
pair_sym_table=table,
i_seqs=i_seqs)
proxies = restraints.proxies
assert proxies.size() == len(i_seqs)
for i in range(proxies.size()):
assert approx_equal(proxies[i].i_seqs[0], i_seqs[i])
assert approx_equal(proxies[i].weight, expected_weights[i])
# add more restraints to same shared proxy
i_seqs = (3,5,42)
restraints = \
adp_restraints.isotropic_adp_restraints(
xray_structure=xray_structure,
pair_sym_table=table,
proxies=proxies,
i_seqs=i_seqs)
expected_i_seqs = (9,14,28,32,36,38,3,5,42)
expected_weights = (100,25,100,100,100,100,25,25,100)
proxies = restraints.proxies
assert proxies.size() == len(expected_i_seqs)
for i in range(proxies.size()):
assert approx_equal(proxies[i].i_seqs[0], expected_i_seqs[i])
assert approx_equal(proxies[i].weight, expected_weights[i])
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 = []
self.expected_mapping_to_grad_fc = (
0,
1,
2,
3,
4,
5,
6,
7,
8,
9,
10,
11,
12,
13,
14,
15,
16,
17,
18,
19,
20,
21 # that was easy
)
self.expected_reparametrisation_for_hydrogen_named = {}
self.fp_refinement_tolerance = 1e-6
self.fdp_refinement_tolerance = 1e-6
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
