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23 from os import path, sep
24
25
26 from data_store import Relax_data_store; ds = Relax_data_store()
27 from pipe_control.reset import reset
28 from lib.io import file_root
29 from lib.structure.internal.molecules import MolContainer
30 from lib.structure.internal.object import Internal
31 from status import Status; status = Status()
32 from test_suite.unit_tests.base_classes import UnitTestCase
33
34
36 """Unit tests for the functions of the 'pipe_control.structure.internal' module."""
37
39 """Set up for all the internal relax structural object unit tests."""
40
41
42 self.test_pdb_path = status.install_path+sep+'test_suite'+sep+'shared_data'+sep+'structures'+sep+'Ap4Aase_res1-12.pdb'
43 expanded = path.split(self.test_pdb_path)
44 self.test_pdb_dir = expanded[0]
45 self.test_pdb_file_name = expanded[1]
46 self.test_pdb_root = file_root(self.test_pdb_path)
47
48
49 self.data = Internal()
50
51
52 self.mol_cont = MolContainer()
53
54
56 """Reset the relax data storage object."""
57
58
59 del self.data
60
61
62 reset()
63
64
66 """1st test of the Internal._trim_helix() method."""
67
68
69 helix = ['H1', 'A', 'ILE', 23, 'A', 'GLU', 34, 1, 12]
70
71
72 res_data = {1: 'MET', 2: 'GLN', 3: 'ILE', 4: 'PHE', 5: 'VAL', 6: 'LYS', 7: 'THR', 8: 'LEU', 9: 'THR', 10: 'GLY', 11: 'LYS', 12: 'THR', 13: 'ILE', 14: 'THR', 15: 'LEU', 16: 'GLU', 17: 'VAL', 18: 'GLU', 19: 'PRO', 20: 'SER', 21: 'ASP', 22: 'THR', 23: 'ILE', 24: 'GLU', 25: 'ASN', 26: 'VAL', 27: 'LYS', 28: 'ALA', 29: 'LYS', 30: 'ILE', 31: 'GLN', 32: 'ASP', 33: 'LYS', 34: 'GLU'}
73 new_helix = self.data._trim_helix(helix=helix, trim_res_list=[1, 2, 3, 22], res_data=res_data)
74
75
76 self.assertEqual(helix, new_helix)
77
78
80 """2nd test of the Internal._trim_helix() method."""
81
82
83 helix = ['H1', 'A', 'ILE', 23, 'A', 'GLU', 34, 1, 12]
84
85
86 res_data = {1: 'MET', 2: 'GLN', 3: 'ILE', 4: 'PHE', 5: 'VAL', 6: 'LYS', 7: 'THR', 8: 'LEU', 9: 'THR', 10: 'GLY', 11: 'LYS', 12: 'THR', 13: 'ILE', 14: 'THR', 15: 'LEU', 16: 'GLU', 17: 'VAL', 18: 'GLU', 19: 'PRO', 20: 'SER', 21: 'ASP', 22: 'THR', 23: 'ILE', 24: 'GLU', 25: 'ASN', 26: 'VAL', 27: 'LYS', 28: 'ALA', 29: 'LYS', 30: 'ILE', 31: 'GLN', 32: 'ASP', 33: 'LYS', 34: 'GLU'}
87 new_helix = self.data._trim_helix(helix=helix, trim_res_list=[51, 52, 53], res_data=res_data)
88
89
90 self.assertEqual(helix, new_helix)
91
92
94 """3rd test of the Internal._trim_helix() method."""
95
96
97 helix = ['H1', 'A', 'ILE', 23, 'A', 'GLU', 34, 1, 12]
98 trimmed_helix = ['H1', 'A', 'GLU', 24, 'A', 'GLU', 34, 1, 11]
99
100
101 res_data = {1: 'MET', 2: 'GLN', 3: 'ILE', 4: 'PHE', 5: 'VAL', 6: 'LYS', 7: 'THR', 8: 'LEU', 9: 'THR', 10: 'GLY', 11: 'LYS', 12: 'THR', 13: 'ILE', 14: 'THR', 15: 'LEU', 16: 'GLU', 17: 'VAL', 18: 'GLU', 19: 'PRO', 20: 'SER', 21: 'ASP', 22: 'THR', 23: 'ILE', 24: 'GLU', 25: 'ASN', 26: 'VAL', 27: 'LYS', 28: 'ALA', 29: 'LYS', 30: 'ILE', 31: 'GLN', 32: 'ASP', 33: 'LYS', 34: 'GLU'}
102 new_helix = self.data._trim_helix(helix=helix, trim_res_list=[21, 22, 23], res_data=res_data)
103
104
105 self.assertEqual(trimmed_helix, new_helix)
106
107
109 """4th test of the Internal._trim_helix() method."""
110
111
112 helix = ['H1', 'A', 'ILE', 23, 'A', 'GLU', 34, 1, 12]
113 trimmed_helix = ['H1', 'A', 'VAL', 26, 'A', 'GLU', 34, 1, 9]
114
115
116 res_data = {1: 'MET', 2: 'GLN', 3: 'ILE', 4: 'PHE', 5: 'VAL', 6: 'LYS', 7: 'THR', 8: 'LEU', 9: 'THR', 10: 'GLY', 11: 'LYS', 12: 'THR', 13: 'ILE', 14: 'THR', 15: 'LEU', 16: 'GLU', 17: 'VAL', 18: 'GLU', 19: 'PRO', 20: 'SER', 21: 'ASP', 22: 'THR', 23: 'ILE', 24: 'GLU', 25: 'ASN', 26: 'VAL', 27: 'LYS', 28: 'ALA', 29: 'LYS', 30: 'ILE', 31: 'GLN', 32: 'ASP', 33: 'LYS', 34: 'GLU'}
117 new_helix = self.data._trim_helix(helix=helix, trim_res_list=[21, 22, 23, 24, 25], res_data=res_data)
118
119
120 self.assertEqual(trimmed_helix, new_helix)
121
122
124 """5th test of the Internal._trim_helix() method."""
125
126
127 helix = ['H1', 'A', 'ILE', 23, 'A', 'GLU', 34, 1, 12]
128 trimmed_helix = ['H1', 'A', 'VAL', 26, 'A', 'GLU', 34, 1, 9]
129
130
131 res_data = {1: 'MET', 2: 'GLN', 3: 'ILE', 4: 'PHE', 5: 'VAL', 6: 'LYS', 7: 'THR', 8: 'LEU', 9: 'THR', 10: 'GLY', 11: 'LYS', 12: 'THR', 13: 'ILE', 14: 'THR', 15: 'LEU', 16: 'GLU', 17: 'VAL', 18: 'GLU', 19: 'PRO', 20: 'SER', 21: 'ASP', 22: 'THR', 23: 'ILE', 24: 'GLU', 25: 'ASN', 26: 'VAL', 27: 'LYS', 28: 'ALA', 29: 'LYS', 30: 'ILE', 31: 'GLN', 32: 'ASP', 33: 'LYS', 34: 'GLU'}
132 new_helix = self.data._trim_helix(helix=helix, trim_res_list=[21, 22, 23, 24, 25, 30], res_data=res_data)
133
134
135 self.assertEqual(trimmed_helix, new_helix)
136
137
139 """6th test of the Internal._trim_helix() method."""
140
141
142 helix = ['H1', 'A', 'ILE', 23, 'A', 'GLU', 34, 1, 12]
143 trimmed_helix = ['H1', 'A', 'VAL', 26, 'A', 'GLU', 34, 1, 9]
144
145
146 res_data = {1: 'MET', 2: 'GLN', 3: 'ILE', 4: 'PHE', 5: 'VAL', 6: 'LYS', 7: 'THR', 8: 'LEU', 9: 'THR', 10: 'GLY', 11: 'LYS', 12: 'THR', 13: 'ILE', 14: 'THR', 15: 'LEU', 16: 'GLU', 17: 'VAL', 18: 'GLU', 19: 'PRO', 20: 'SER', 21: 'ASP', 22: 'THR', 23: 'ILE', 24: 'GLU', 25: 'ASN', 26: 'VAL', 27: 'LYS', 28: 'ALA', 29: 'LYS', 30: 'ILE', 31: 'GLN', 32: 'ASP', 33: 'LYS', 34: 'GLU'}
147 new_helix = self.data._trim_helix(helix=helix, trim_res_list=[21, 22, 23, 24, 25, 40], res_data=res_data)
148
149
150 self.assertEqual(trimmed_helix, new_helix)
151
152
154 """7th test of the Internal._trim_helix() method."""
155
156
157 helix = ['H1', 'A', 'ILE', 23, 'A', 'GLU', 34, 1, 12]
158 trimmed_helix = ['H1', 'A', 'ILE', 23, 'A', 'LYS', 33, 1, 11]
159
160
161 res_data = {1: 'MET', 2: 'GLN', 3: 'ILE', 4: 'PHE', 5: 'VAL', 6: 'LYS', 7: 'THR', 8: 'LEU', 9: 'THR', 10: 'GLY', 11: 'LYS', 12: 'THR', 13: 'ILE', 14: 'THR', 15: 'LEU', 16: 'GLU', 17: 'VAL', 18: 'GLU', 19: 'PRO', 20: 'SER', 21: 'ASP', 22: 'THR', 23: 'ILE', 24: 'GLU', 25: 'ASN', 26: 'VAL', 27: 'LYS', 28: 'ALA', 29: 'LYS', 30: 'ILE', 31: 'GLN', 32: 'ASP', 33: 'LYS', 34: 'GLU'}
162 new_helix = self.data._trim_helix(helix=helix, trim_res_list=[34, 35, 36], res_data=res_data)
163
164
165 self.assertEqual(trimmed_helix, new_helix)
166
167
169 """8th test of the Internal._trim_helix() method."""
170
171
172 helix = ['H1', 'A', 'ILE', 23, 'A', 'GLU', 34, 1, 12]
173
174
175 res_data = {1: 'MET', 2: 'GLN', 3: 'ILE', 4: 'PHE', 5: 'VAL', 6: 'LYS', 7: 'THR', 8: 'LEU', 9: 'THR', 10: 'GLY', 11: 'LYS', 12: 'THR', 13: 'ILE', 14: 'THR', 15: 'LEU', 16: 'GLU', 17: 'VAL', 18: 'GLU', 19: 'PRO', 20: 'SER', 21: 'ASP', 22: 'THR', 23: 'ILE', 24: 'GLU', 25: 'ASN', 26: 'VAL', 27: 'LYS', 28: 'ALA', 29: 'LYS', 30: 'ILE', 31: 'GLN', 32: 'ASP', 33: 'LYS', 34: 'GLU'}
176 new_helix = self.data._trim_helix(helix=helix, trim_res_list=[35, 36], res_data=res_data)
177
178
179 self.assertEqual(helix, new_helix)
180
181
183 """9th test of the Internal._trim_helix() method."""
184
185
186 helix = ['H1', 'A', 'ILE', 23, 'A', 'GLU', 34, 1, 12]
187 trimmed_helix = ['H1', 'A', 'ILE', 23, 'A', 'ILE', 30, 1, 8]
188
189
190 res_data = {1: 'MET', 2: 'GLN', 3: 'ILE', 4: 'PHE', 5: 'VAL', 6: 'LYS', 7: 'THR', 8: 'LEU', 9: 'THR', 10: 'GLY', 11: 'LYS', 12: 'THR', 13: 'ILE', 14: 'THR', 15: 'LEU', 16: 'GLU', 17: 'VAL', 18: 'GLU', 19: 'PRO', 20: 'SER', 21: 'ASP', 22: 'THR', 23: 'ILE', 24: 'GLU', 25: 'ASN', 26: 'VAL', 27: 'LYS', 28: 'ALA', 29: 'LYS', 30: 'ILE', 31: 'GLN', 32: 'ASP', 33: 'LYS', 34: 'GLU'}
191 new_helix = self.data._trim_helix(helix=helix, trim_res_list=[31, 32, 33, 34, 35], res_data=res_data)
192
193
194 self.assertEqual(trimmed_helix, new_helix)
195
196
198 """10th test of the Internal._trim_helix() method."""
199
200
201 helix = ['H1', 'A', 'ILE', 23, 'A', 'GLU', 34, 1, 12]
202 trimmed_helix = ['H1', 'A', 'ILE', 23, 'A', 'GLN', 31, 1, 9]
203
204
205 res_data = {1: 'MET', 2: 'GLN', 3: 'ILE', 4: 'PHE', 5: 'VAL', 6: 'LYS', 7: 'THR', 8: 'LEU', 9: 'THR', 10: 'GLY', 11: 'LYS', 12: 'THR', 13: 'ILE', 14: 'THR', 15: 'LEU', 16: 'GLU', 17: 'VAL', 18: 'GLU', 19: 'PRO', 20: 'SER', 21: 'ASP', 22: 'THR', 23: 'ILE', 24: 'GLU', 25: 'ASN', 26: 'VAL', 27: 'LYS', 28: 'ALA', 29: 'LYS', 30: 'ILE', 31: 'GLN', 32: 'ASP', 33: 'LYS', 34: 'GLU'}
206 new_helix = self.data._trim_helix(helix=helix, trim_res_list=[24, 32, 33, 34, 35], res_data=res_data)
207
208
209 self.assertEqual(trimmed_helix, new_helix)
210
211
213 """11th test of the Internal._trim_helix() method."""
214
215
216 helix = ['H1', 'A', 'ILE', 23, 'A', 'GLU', 34, 1, 12]
217 trimmed_helix = ['H1', 'A', 'ASN', 25, 'A', 'GLN', 31, 1, 7]
218
219
220 res_data = {1: 'MET', 2: 'GLN', 3: 'ILE', 4: 'PHE', 5: 'VAL', 6: 'LYS', 7: 'THR', 8: 'LEU', 9: 'THR', 10: 'GLY', 11: 'LYS', 12: 'THR', 13: 'ILE', 14: 'THR', 15: 'LEU', 16: 'GLU', 17: 'VAL', 18: 'GLU', 19: 'PRO', 20: 'SER', 21: 'ASP', 22: 'THR', 23: 'ILE', 24: 'GLU', 25: 'ASN', 26: 'VAL', 27: 'LYS', 28: 'ALA', 29: 'LYS', 30: 'ILE', 31: 'GLN', 32: 'ASP', 33: 'LYS', 34: 'GLU'}
221 new_helix = self.data._trim_helix(helix=helix, trim_res_list=[22, 23, 24, 32, 33, 34, 35], res_data=res_data)
222
223
224 self.assertEqual(trimmed_helix, new_helix)
225
226
228 """12th test of the Internal._trim_helix() method."""
229
230
231 helix = ['H1', 'A', 'ILE', 23, 'A', 'GLU', 34, 1, 12]
232 trimmed_helix = ['H1', 'A', 'ASN', 25, 'A', 'GLN', 31, 1, 7]
233
234
235 res_data = {1: 'MET', 2: 'GLN', 3: 'ILE', 4: 'PHE', 5: 'VAL', 6: 'LYS', 7: 'THR', 8: 'LEU', 9: 'THR', 10: 'GLY', 11: 'LYS', 12: 'THR', 13: 'ILE', 14: 'THR', 15: 'LEU', 16: 'GLU', 17: 'VAL', 18: 'GLU', 19: 'PRO', 20: 'SER', 21: 'ASP', 22: 'THR', 23: 'ILE', 24: 'GLU', 25: 'ASN', 26: 'VAL', 27: 'LYS', 28: 'ALA', 29: 'LYS', 30: 'ILE', 31: 'GLN', 32: 'ASP', 33: 'LYS', 34: 'GLU'}
236 new_helix = self.data._trim_helix(helix=helix, trim_res_list=[22, 23, 24, 27, 32, 33, 34, 35], res_data=res_data)
237
238
239 self.assertEqual(trimmed_helix, new_helix)
240
241
243 """13th test of the Internal._trim_helix() method."""
244
245
246 helix = ['H1', 'A', 'ILE', 23, 'A', 'GLU', 34, 1, 12]
247
248
249 res_data = {1: 'MET', 2: 'GLN', 3: 'ILE', 4: 'PHE', 5: 'VAL', 6: 'LYS', 7: 'THR', 8: 'LEU', 9: 'THR', 10: 'GLY', 11: 'LYS', 12: 'THR', 13: 'ILE', 14: 'THR', 15: 'LEU', 16: 'GLU', 17: 'VAL', 18: 'GLU', 19: 'PRO', 20: 'SER', 21: 'ASP', 22: 'THR', 23: 'ILE', 24: 'GLU', 25: 'ASN', 26: 'VAL', 27: 'LYS', 28: 'ALA', 29: 'LYS', 30: 'ILE', 31: 'GLN', 32: 'ASP', 33: 'LYS', 34: 'GLU'}
250 new_helix = self.data._trim_helix(helix=helix, trim_res_list=[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], res_data=res_data)
251
252
253 self.assertEqual(None, new_helix)
254
255
257 """1st test of the Internal._trim_sheet() method."""
258
259
260 sheet = [1, 'BET', 5, 'GLY', 'A', 10, None, 'VAL', 'A', 17, None, 0, None, None, None, None, None, None, None, None, None, None]
261
262
263 res_data = {1: 'MET', 2: 'GLN', 3: 'ILE', 4: 'PHE', 5: 'VAL', 6: 'LYS', 7: 'THR', 8: 'LEU', 9: 'THR', 10: 'GLY', 11: 'LYS', 12: 'THR', 13: 'ILE', 14: 'THR', 15: 'LEU', 16: 'GLU', 17: 'VAL', 18: 'GLU', 19: 'PRO', 20: 'SER', 21: 'ASP', 22: 'THR', 23: 'ILE', 24: 'GLU', 25: 'ASN', 26: 'VAL', 27: 'LYS', 28: 'ALA', 29: 'LYS', 30: 'ILE', 31: 'GLN', 32: 'ASP', 33: 'LYS', 34: 'GLU'}
264 new_sheet = self.data._trim_sheet(sheet=sheet, trim_res_list=[1, 2, 3, 22], res_data=res_data)
265
266
267 self.assertEqual(sheet, new_sheet)
268
269
271 """2nd test of the Internal._trim_sheet() method."""
272
273
274 sheet = [1, 'BET', 5, 'GLY', 'A', 10, None, 'VAL', 'A', 17, None, 0, None, None, None, None, None, None, None, None, None, None]
275
276
277 res_data = {1: 'MET', 2: 'GLN', 3: 'ILE', 4: 'PHE', 5: 'VAL', 6: 'LYS', 7: 'THR', 8: 'LEU', 9: 'THR', 10: 'GLY', 11: 'LYS', 12: 'THR', 13: 'ILE', 14: 'THR', 15: 'LEU', 16: 'GLU', 17: 'VAL', 18: 'GLU', 19: 'PRO', 20: 'SER', 21: 'ASP', 22: 'THR', 23: 'ILE', 24: 'GLU', 25: 'ASN', 26: 'VAL', 27: 'LYS', 28: 'ALA', 29: 'LYS', 30: 'ILE', 31: 'GLN', 32: 'ASP', 33: 'LYS', 34: 'GLU'}
278 new_sheet = self.data._trim_sheet(sheet=sheet, trim_res_list=[51, 52, 53], res_data=res_data)
279
280
281 self.assertEqual(sheet, new_sheet)
282
283
285 """3rd test of the Internal._trim_sheet() method."""
286
287
288 sheet = [1, 'BET', 5, 'GLY', 'A', 10, None, 'VAL', 'A', 17, None, 0, None, None, None, None, None, None, None, None, None, None]
289 trimmed_sheet = [1, 'BET', 5, 'LYS', 'A', 11, None, 'VAL', 'A', 17, None, 0, None, None, None, None, None, None, None, None, None, None]
290
291
292 res_data = {1: 'MET', 2: 'GLN', 3: 'ILE', 4: 'PHE', 5: 'VAL', 6: 'LYS', 7: 'THR', 8: 'LEU', 9: 'THR', 10: 'GLY', 11: 'LYS', 12: 'THR', 13: 'ILE', 14: 'THR', 15: 'LEU', 16: 'GLU', 17: 'VAL', 18: 'GLU', 19: 'PRO', 20: 'SER', 21: 'ASP', 22: 'THR', 23: 'ILE', 24: 'GLU', 25: 'ASN', 26: 'VAL', 27: 'LYS', 28: 'ALA', 29: 'LYS', 30: 'ILE', 31: 'GLN', 32: 'ASP', 33: 'LYS', 34: 'GLU'}
293 new_sheet = self.data._trim_sheet(sheet=sheet, trim_res_list=[8, 9, 10], res_data=res_data)
294
295
296 self.assertEqual(trimmed_sheet, new_sheet)
297
298
300 """4th test of the Internal._trim_sheet() method."""
301
302
303 sheet = [1, 'BET', 5, 'GLY', 'A', 10, None, 'VAL', 'A', 17, None, 0, None, None, None, None, None, None, None, None, None, None]
304 trimmed_sheet = [1, 'BET', 5, 'ILE', 'A', 13, None, 'VAL', 'A', 17, None, 0, None, None, None, None, None, None, None, None, None, None]
305
306
307 res_data = {1: 'MET', 2: 'GLN', 3: 'ILE', 4: 'PHE', 5: 'VAL', 6: 'LYS', 7: 'THR', 8: 'LEU', 9: 'THR', 10: 'GLY', 11: 'LYS', 12: 'THR', 13: 'ILE', 14: 'THR', 15: 'LEU', 16: 'GLU', 17: 'VAL', 18: 'GLU', 19: 'PRO', 20: 'SER', 21: 'ASP', 22: 'THR', 23: 'ILE', 24: 'GLU', 25: 'ASN', 26: 'VAL', 27: 'LYS', 28: 'ALA', 29: 'LYS', 30: 'ILE', 31: 'GLN', 32: 'ASP', 33: 'LYS', 34: 'GLU'}
308 new_sheet = self.data._trim_sheet(sheet=sheet, trim_res_list=[8, 9, 10, 11, 12], res_data=res_data)
309
310
311 self.assertEqual(trimmed_sheet, new_sheet)
312
313
315 """5th test of the Internal._trim_sheet() method."""
316
317
318 sheet = [1, 'BET', 5, 'GLY', 'A', 10, None, 'VAL', 'A', 17, None, 0, None, None, None, None, None, None, None, None, None, None]
319 trimmed_sheet = [1, 'BET', 5, 'ILE', 'A', 13, None, 'VAL', 'A', 17, None, 0, None, None, None, None, None, None, None, None, None, None]
320
321
322 res_data = {1: 'MET', 2: 'GLN', 3: 'ILE', 4: 'PHE', 5: 'VAL', 6: 'LYS', 7: 'THR', 8: 'LEU', 9: 'THR', 10: 'GLY', 11: 'LYS', 12: 'THR', 13: 'ILE', 14: 'THR', 15: 'LEU', 16: 'GLU', 17: 'VAL', 18: 'GLU', 19: 'PRO', 20: 'SER', 21: 'ASP', 22: 'THR', 23: 'ILE', 24: 'GLU', 25: 'ASN', 26: 'VAL', 27: 'LYS', 28: 'ALA', 29: 'LYS', 30: 'ILE', 31: 'GLN', 32: 'ASP', 33: 'LYS', 34: 'GLU'}
323 new_sheet = self.data._trim_sheet(sheet=sheet, trim_res_list=[8, 9, 10, 11, 12, 15], res_data=res_data)
324
325
326 self.assertEqual(trimmed_sheet, new_sheet)
327
328
330 """6th test of the Internal._trim_sheet() method."""
331
332
333 sheet = [1, 'BET', 5, 'GLY', 'A', 10, None, 'VAL', 'A', 17, None, 0, None, None, None, None, None, None, None, None, None, None]
334 trimmed_sheet = [1, 'BET', 5, 'ILE', 'A', 13, None, 'VAL', 'A', 17, None, 0, None, None, None, None, None, None, None, None, None, None]
335
336
337 res_data = {1: 'MET', 2: 'GLN', 3: 'ILE', 4: 'PHE', 5: 'VAL', 6: 'LYS', 7: 'THR', 8: 'LEU', 9: 'THR', 10: 'GLY', 11: 'LYS', 12: 'THR', 13: 'ILE', 14: 'THR', 15: 'LEU', 16: 'GLU', 17: 'VAL', 18: 'GLU', 19: 'PRO', 20: 'SER', 21: 'ASP', 22: 'THR', 23: 'ILE', 24: 'GLU', 25: 'ASN', 26: 'VAL', 27: 'LYS', 28: 'ALA', 29: 'LYS', 30: 'ILE', 31: 'GLN', 32: 'ASP', 33: 'LYS', 34: 'GLU'}
338 new_sheet = self.data._trim_sheet(sheet=sheet, trim_res_list=[8, 9, 10, 11, 12, 30], res_data=res_data)
339
340
341 self.assertEqual(trimmed_sheet, new_sheet)
342
343
345 """7th test of the Internal._trim_sheet() method."""
346
347
348 sheet = [1, 'BET', 5, 'GLY', 'A', 10, None, 'VAL', 'A', 17, None, 0, None, None, None, None, None, None, None, None, None, None]
349 trimmed_sheet = [1, 'BET', 5, 'GLY', 'A', 10, None, 'GLU', 'A', 16, None, 0, None, None, None, None, None, None, None, None, None, None]
350
351
352 res_data = {1: 'MET', 2: 'GLN', 3: 'ILE', 4: 'PHE', 5: 'VAL', 6: 'LYS', 7: 'THR', 8: 'LEU', 9: 'THR', 10: 'GLY', 11: 'LYS', 12: 'THR', 13: 'ILE', 14: 'THR', 15: 'LEU', 16: 'GLU', 17: 'VAL', 18: 'GLU', 19: 'PRO', 20: 'SER', 21: 'ASP', 22: 'THR', 23: 'ILE', 24: 'GLU', 25: 'ASN', 26: 'VAL', 27: 'LYS', 28: 'ALA', 29: 'LYS', 30: 'ILE', 31: 'GLN', 32: 'ASP', 33: 'LYS', 34: 'GLU'}
353 new_sheet = self.data._trim_sheet(sheet=sheet, trim_res_list=[17, 18, 19], res_data=res_data)
354
355
356 self.assertEqual(trimmed_sheet, new_sheet)
357
358
360 """8th test of the Internal._trim_sheet() method."""
361
362
363 sheet = [1, 'BET', 5, 'GLY', 'A', 10, None, 'VAL', 'A', 17, None, 0, None, None, None, None, None, None, None, None, None, None]
364
365
366 res_data = {1: 'MET', 2: 'GLN', 3: 'ILE', 4: 'PHE', 5: 'VAL', 6: 'LYS', 7: 'THR', 8: 'LEU', 9: 'THR', 10: 'GLY', 11: 'LYS', 12: 'THR', 13: 'ILE', 14: 'THR', 15: 'LEU', 16: 'GLU', 17: 'VAL', 18: 'GLU', 19: 'PRO', 20: 'SER', 21: 'ASP', 22: 'THR', 23: 'ILE', 24: 'GLU', 25: 'ASN', 26: 'VAL', 27: 'LYS', 28: 'ALA', 29: 'LYS', 30: 'ILE', 31: 'GLN', 32: 'ASP', 33: 'LYS', 34: 'GLU'}
367 new_sheet = self.data._trim_sheet(sheet=sheet, trim_res_list=[18, 19], res_data=res_data)
368
369
370 self.assertEqual(sheet, new_sheet)
371
372
374 """9th test of the Internal._trim_sheet() method."""
375
376
377 sheet = [1, 'BET', 5, 'GLY', 'A', 10, None, 'VAL', 'A', 17, None, 0, None, None, None, None, None, None, None, None, None, None]
378 trimmed_sheet = [1, 'BET', 5, 'GLY', 'A', 10, None, 'THR', 'A', 14, None, 0, None, None, None, None, None, None, None, None, None, None]
379
380
381 res_data = {1: 'MET', 2: 'GLN', 3: 'ILE', 4: 'PHE', 5: 'VAL', 6: 'LYS', 7: 'THR', 8: 'LEU', 9: 'THR', 10: 'GLY', 11: 'LYS', 12: 'THR', 13: 'ILE', 14: 'THR', 15: 'LEU', 16: 'GLU', 17: 'VAL', 18: 'GLU', 19: 'PRO', 20: 'SER', 21: 'ASP', 22: 'THR', 23: 'ILE', 24: 'GLU', 25: 'ASN', 26: 'VAL', 27: 'LYS', 28: 'ALA', 29: 'LYS', 30: 'ILE', 31: 'GLN', 32: 'ASP', 33: 'LYS', 34: 'GLU'}
382 new_sheet = self.data._trim_sheet(sheet=sheet, trim_res_list=[15, 16, 17, 18, 19], res_data=res_data)
383
384
385 self.assertEqual(trimmed_sheet, new_sheet)
386
387
389 """10th test of the Internal._trim_sheet() method."""
390
391
392 sheet = [1, 'BET', 5, 'GLY', 'A', 10, None, 'VAL', 'A', 17, None, 0, None, None, None, None, None, None, None, None, None, None]
393 trimmed_sheet = [1, 'BET', 5, 'GLY', 'A', 10, None, 'THR', 'A', 14, None, 0, None, None, None, None, None, None, None, None, None, None]
394
395
396 res_data = {1: 'MET', 2: 'GLN', 3: 'ILE', 4: 'PHE', 5: 'VAL', 6: 'LYS', 7: 'THR', 8: 'LEU', 9: 'THR', 10: 'GLY', 11: 'LYS', 12: 'THR', 13: 'ILE', 14: 'THR', 15: 'LEU', 16: 'GLU', 17: 'VAL', 18: 'GLU', 19: 'PRO', 20: 'SER', 21: 'ASP', 22: 'THR', 23: 'ILE', 24: 'GLU', 25: 'ASN', 26: 'VAL', 27: 'LYS', 28: 'ALA', 29: 'LYS', 30: 'ILE', 31: 'GLN', 32: 'ASP', 33: 'LYS', 34: 'GLU'}
397 new_sheet = self.data._trim_sheet(sheet=sheet, trim_res_list=[11, 15, 16, 17, 18, 19], res_data=res_data)
398
399
400 self.assertEqual(trimmed_sheet, new_sheet)
401
402
404 """11th test of the Internal._trim_sheet() method."""
405
406
407 sheet = [1, 'BET', 5, 'GLY', 'A', 10, None, 'VAL', 'A', 17, None, 0, None, None, None, None, None, None, None, None, None, None]
408 trimmed_sheet = [1, 'BET', 5, 'LYS', 'A', 11, None, 'LEU', 'A', 15, None, 0, None, None, None, None, None, None, None, None, None, None]
409
410
411 res_data = {1: 'MET', 2: 'GLN', 3: 'ILE', 4: 'PHE', 5: 'VAL', 6: 'LYS', 7: 'THR', 8: 'LEU', 9: 'THR', 10: 'GLY', 11: 'LYS', 12: 'THR', 13: 'ILE', 14: 'THR', 15: 'LEU', 16: 'GLU', 17: 'VAL', 18: 'GLU', 19: 'PRO', 20: 'SER', 21: 'ASP', 22: 'THR', 23: 'ILE', 24: 'GLU', 25: 'ASN', 26: 'VAL', 27: 'LYS', 28: 'ALA', 29: 'LYS', 30: 'ILE', 31: 'GLN', 32: 'ASP', 33: 'LYS', 34: 'GLU'}
412 new_sheet = self.data._trim_sheet(sheet=sheet, trim_res_list=[9, 10, 16, 17, 18, 19], res_data=res_data)
413
414
415 self.assertEqual(trimmed_sheet, new_sheet)
416
417
419 """12th test of the Internal._trim_sheet() method."""
420
421
422 sheet = [1, 'BET', 5, 'GLY', 'A', 10, None, 'VAL', 'A', 17, None, 0, None, None, None, None, None, None, None, None, None, None]
423 trimmed_sheet = [1, 'BET', 5, 'LYS', 'A', 11, None, 'LEU', 'A', 15, None, 0, None, None, None, None, None, None, None, None, None, None]
424
425
426 res_data = {1: 'MET', 2: 'GLN', 3: 'ILE', 4: 'PHE', 5: 'VAL', 6: 'LYS', 7: 'THR', 8: 'LEU', 9: 'THR', 10: 'GLY', 11: 'LYS', 12: 'THR', 13: 'ILE', 14: 'THR', 15: 'LEU', 16: 'GLU', 17: 'VAL', 18: 'GLU', 19: 'PRO', 20: 'SER', 21: 'ASP', 22: 'THR', 23: 'ILE', 24: 'GLU', 25: 'ASN', 26: 'VAL', 27: 'LYS', 28: 'ALA', 29: 'LYS', 30: 'ILE', 31: 'GLN', 32: 'ASP', 33: 'LYS', 34: 'GLU'}
427 new_sheet = self.data._trim_sheet(sheet=sheet, trim_res_list=[9, 10, 13, 16, 17, 18, 19], res_data=res_data)
428
429
430 self.assertEqual(trimmed_sheet, new_sheet)
431
432
434 """13th test of the Internal._trim_sheet() method."""
435
436
437 sheet = [1, 'BET', 5, 'GLY', 'A', 10, None, 'VAL', 'A', 17, None, 0, None, None, None, None, None, None, None, None, None, None]
438
439
440 res_data = {1: 'MET', 2: 'GLN', 3: 'ILE', 4: 'PHE', 5: 'VAL', 6: 'LYS', 7: 'THR', 8: 'LEU', 9: 'THR', 10: 'GLY', 11: 'LYS', 12: 'THR', 13: 'ILE', 14: 'THR', 15: 'LEU', 16: 'GLU', 17: 'VAL', 18: 'GLU', 19: 'PRO', 20: 'SER', 21: 'ASP', 22: 'THR', 23: 'ILE', 24: 'GLU', 25: 'ASN', 26: 'VAL', 27: 'LYS', 28: 'ALA', 29: 'LYS', 30: 'ILE', 31: 'GLN', 32: 'ASP', 33: 'LYS', 34: 'GLU'}
441 new_sheet = self.data._trim_sheet(sheet=sheet, trim_res_list=[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], res_data=res_data)
442
443
444 self.assertEqual(None, new_sheet)
445
446
448 """Test the Internal.atom_loop() method."""
449
450
451 self.data.load_pdb(self.test_pdb_path)
452
453
454 atom_count = 0
455 for atom in self.data.atom_loop():
456 atom_count = atom_count + 1
457
458
459 self.assertEqual(atom_count, 150)
460
461
463 """Test the Internal.atom_loop() method with the '#XXX' mol selection."""
464
465
466 self.data.load_pdb(self.test_pdb_path)
467
468
469 atom_count = 0
470 for atom in self.data.atom_loop(atom_id='#XXX'):
471 atom_count = atom_count + 1
472
473
474 self.assertEqual(atom_count, 0)
475
476
478 """Test the Internal.atom_loop() method with the ':8' res selection."""
479
480
481 self.data.load_pdb(self.test_pdb_path)
482
483
484 atom_count = 0
485 for res_num, res_name in self.data.atom_loop(atom_id=':8', res_num_flag=True, res_name_flag=True):
486
487 self.assertEqual(res_num, 8)
488 self.assertEqual(res_name, 'SER')
489
490
491 atom_count = atom_count + 1
492
493
494 self.assertEqual(atom_count, 11)
495
496
498 """Test the Internal.atom_loop() method with the ':PRO' res selection."""
499
500
501 self.data.load_pdb(self.test_pdb_path)
502
503
504 atom_count = 0
505 for atom in self.data.atom_loop(atom_id=':PRO', res_name_flag=True):
506
507 self.assertEqual(atom, 'PRO')
508
509
510 atom_count = atom_count + 1
511
512
513 self.assertEqual(atom_count, 42)
514
515
517 """Test the Internal.atom_loop() method with the '@CA' spin selection."""
518
519
520 self.data.load_pdb(self.test_pdb_path)
521
522
523 atom_count = 0
524 for spin_name in self.data.atom_loop(atom_id='@CA', atom_name_flag=True):
525
526 self.assertEqual(spin_name, 'CA')
527
528
529 atom_count = atom_count + 1
530
531
532 self.assertEqual(atom_count, 12)
533
534
536 """Test the Internal.atom_loop() method with the '@163' spin selection."""
537
538
539 self.data.load_pdb(self.test_pdb_path)
540
541
542 atom_count = 0
543 for mol_name, res_num, res_name, spin_num, spin_name, element, pos in self.data.atom_loop(atom_id='@140', mol_name_flag=True, res_num_flag=True, res_name_flag=True, atom_num_flag=True, atom_name_flag=True, element_flag=True, pos_flag=True):
544
545 self.assertEqual(mol_name, self.test_pdb_root+'_mol1')
546 self.assertEqual(res_num, 11)
547 self.assertEqual(res_name, 'GLU')
548 self.assertEqual(spin_num, 140)
549 self.assertEqual(spin_name, 'OE1')
550 self.assertEqual(element, 'O')
551 self.assertEqual(pos.shape, (1, 3))
552 self.assertEqual(pos[0, 0], float('10.055'))
553 self.assertEqual(pos[0, 1], float('-2.74'))
554 self.assertEqual(pos[0, 2], float('-13.193'))
555
556
557 atom_count = atom_count + 1
558
559
560 self.assertEqual(atom_count, 1)
561
562
564 """Load a PDB file using Internal.load_pdb()."""
565
566
567 self.data.load_pdb(self.test_pdb_path)
568
569
570 model = self.data.structural_data[0]
571 mol = model.mol[0]
572
573
574 self.assertEqual(len(self.data.structural_data), 1)
575 self.assertEqual(len(model.mol), 1)
576 self.assertEqual(model.num, 1)
577 self.assertEqual(mol.mol_name, self.test_pdb_root+'_mol1')
578 self.assertEqual(mol.file_name, self.test_pdb_file_name)
579 self.assertEqual(mol.file_path, self.test_pdb_dir)
580 self.assertEqual(mol.file_model, 1)
581 self.assertEqual(mol.file_mol_num, 1)
582
583
584 atom_name = ['N', 'CA', '1HA', '2HA', 'C', 'O', '1HT', '2HT', '3HT', 'N', 'CD', 'CA', 'HA', 'CB', '1HB', '2HB', 'CG', '1HG', '2HG', '1HD', '2HD', 'C', 'O', 'N', 'H', 'CA', 'HA', 'CB', '1HB', '2HB', 'CG', 'HG', 'CD1', '1HD1', '2HD1', '3HD1', 'CD2', '1HD2', '2HD2', '3HD2', 'C', 'O', 'N', 'H', 'CA', '1HA', '2HA', 'C', 'O', 'N', 'H', 'CA', 'HA', 'CB', '1HB', '2HB', 'OG', 'HG', 'C', 'O', 'N', 'H', 'CA', 'HA', 'CB', '1HB', '2HB', 'CG', '1HG', '2HG', 'SD', 'CE', '1HE', '2HE', '3HE', 'C', 'O', 'N', 'H', 'CA', 'HA', 'CB', '1HB', '2HB', 'CG', 'OD1', 'OD2', 'C', 'O', 'N', 'H', 'CA', 'HA', 'CB', '1HB', '2HB', 'OG', 'HG', 'C', 'O', 'N', 'CD', 'CA', 'HA', 'CB', '1HB', '2HB', 'CG', '1HG', '2HG', '1HD', '2HD', 'C', 'O', 'N', 'CD', 'CA', 'HA', 'CB', '1HB', '2HB', 'CG', '1HG', '2HG', '1HD', '2HD', 'C', 'O', 'N', 'H', 'CA', 'HA', 'CB', '1HB', '2HB', 'CG', '1HG', '2HG', 'CD', 'OE1', 'OE2', 'C', 'O', 'N', 'H', 'CA', '1HA', '2HA', 'C', 'O']
585 bonded = [[]]*174
586 chain_id = [None]*174
587 element = ['N', 'C', 'H', 'H', 'C', 'O', 'H', 'H', 'H', 'N', 'C', 'C', 'H', 'C', 'H', 'H', 'C', 'H', 'H', 'H', 'H', 'C', 'O', 'N', 'H', 'C', 'H', 'C', 'H', 'H', 'C', 'H', 'C', 'H', 'H', 'H', 'C', 'H', 'H', 'H', 'C', 'O', 'N', 'H', 'C', 'H', 'H', 'C', 'O', 'N', 'H', 'C', 'H', 'C', 'H', 'H', 'O', 'H', 'C', 'O', 'N', 'H', 'C', 'H', 'C', 'H', 'H', 'C', 'H', 'H', 'S', 'C', 'H', 'H', 'H', 'C', 'O', 'N', 'H', 'C', 'H', 'C', 'H', 'H', 'C', 'O', 'O', 'C', 'O', 'N', 'H', 'C', 'H', 'C', 'H', 'H', 'O', 'H', 'C', 'O', 'N', 'C', 'C', 'H', 'C', 'H', 'H', 'C', 'H', 'H', 'H', 'H', 'C', 'O', 'N', 'C', 'C', 'H', 'C', 'H', 'H', 'C', 'H', 'H', 'H', 'H', 'C', 'O', 'N', 'H', 'C', 'H', 'C', 'H', 'H', 'C', 'H', 'H', 'C', 'O', 'O', 'C', 'O', 'N', 'H', 'C', 'H', 'H', 'C', 'O']
588 pdb_record = ['ATOM']*174
589 res_name = ['GLY', 'GLY', 'GLY', 'GLY', 'GLY', 'GLY', 'GLY', 'GLY', 'GLY', 'PRO', 'PRO', 'PRO', 'PRO', 'PRO', 'PRO', 'PRO', 'PRO', 'PRO', 'PRO', 'PRO', 'PRO', 'PRO', 'PRO', 'LEU', 'LEU', 'LEU', 'LEU', 'LEU', 'LEU', 'LEU', 'LEU', 'LEU', 'LEU', 'LEU', 'LEU', 'LEU', 'LEU', 'LEU', 'LEU', 'LEU', 'LEU', 'LEU', 'GLY', 'GLY', 'GLY', 'GLY', 'GLY', 'GLY', 'GLY', 'SER', 'SER', 'SER', 'SER', 'SER', 'SER', 'SER', 'SER', 'SER', 'SER', 'SER', 'MET', 'MET', 'MET', 'MET', 'MET', 'MET', 'MET', 'MET', 'MET', 'MET', 'MET', 'MET', 'MET', 'MET', 'MET', 'MET', 'MET', 'ASP', 'ASP', 'ASP', 'ASP', 'ASP', 'ASP', 'ASP', 'ASP', 'ASP', 'ASP', 'ASP', 'ASP', 'SER', 'SER', 'SER', 'SER', 'SER', 'SER', 'SER', 'SER', 'SER', 'SER', 'SER', 'PRO', 'PRO', 'PRO', 'PRO', 'PRO', 'PRO', 'PRO', 'PRO', 'PRO', 'PRO', 'PRO', 'PRO', 'PRO', 'PRO', 'PRO', 'PRO', 'PRO', 'PRO', 'PRO', 'PRO', 'PRO', 'PRO', 'PRO', 'PRO', 'PRO', 'PRO', 'PRO', 'PRO', 'GLU', 'GLU', 'GLU', 'GLU', 'GLU', 'GLU', 'GLU', 'GLU', 'GLU', 'GLU', 'GLU', 'GLU', 'GLU', 'GLU', 'GLU', 'GLY', 'GLY', 'GLY', 'GLY', 'GLY', 'GLY', 'GLY']
590 res_num = [1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 12, 12, 12, 12, 12, 12, 12]
591 seg_id = [None]*174
592 x = [8.442, 7.469, 8.013, 6.825, 6.610, 6.827, 9.398, 8.180, 8.448, 5.613, 5.281, 4.714, 5.222, 3.646, 3.332, 2.800, 4.319, 4.853, 3.587, 6.162, 4.805, 4.075, 3.593, 4.074, 4.475, 3.498, 3.572, 2.025, 1.965, 1.609, 1.176, 1.823, 0.176, 0.096, 0.509, -0.789, 0.474, 0.809, -0.595, 0.707, 4.264, 4.364, 4.809, 4.697, 5.561, 6.220, 6.156, 4.659, 4.746, 3.786, 3.770, 2.851, 2.368, 1.785, 1.177, 1.165, 2.360, 1.690, 3.546, 3.804, 3.814, 3.563, 4.442, 4.984, 5.411, 6.192, 4.872, 6.068, 6.868, 5.332, 6.747, 6.155, 5.409, 6.977, 5.721, 3.369, 2.255, 3.703, 4.604, 2.753, 1.851, 3.329, 4.182, 3.644, 2.319, 1.992, 1.854, 2.419, 1.251, 3.451, 4.359, 3.267, 2.246, 4.223, 4.054, 4.040, 5.573, 6.142, 3.488, 4.276, 2.795, 1.828, 2.929, 2.810, 1.772, 0.912, 2.067, 1.505, 0.464, 2.138, 0.938, 2.273, 4.268, 4.585, 5.076, 4.776, 6.392, 6.925, 7.120, 7.968, 7.464, 6.130, 6.384, 6.135, 4.210, 4.246, 6.325, 5.263, 7.477, 8.281, 7.587, 7.039, 9.047, 9.133, 9.654, 9.590, 10.670, 9.215, 9.190, 10.055, 8.012, 7.007, 7.361, 6.144, 5.925, 5.555, 6.329, 4.814, 4.894, 4.761]
593 y = [10.188, 9.889, 9.712, 10.745, 8.674, 7.991, 10.291, 11.073, 9.416, 8.385, 9.152, 7.243, 6.302, 7.443, 6.483, 7.963, 8.253, 7.605, 8.842, 9.327, 10.088, 7.251, 8.285, 6.099, 5.309, 5.986, 4.953, 6.396, 7.471, 6.106, 5.775, 5.225, 4.796, 4.954, 3.787, 4.949, 6.853, 7.828, 6.775, 6.720, 6.853, 8.068, 6.222, 5.251, 6.956, 6.273, 7.706, 7.634, 8.841, 6.847, 5.889, 7.360, 6.511, 8.230, 7.620, 8.669, 9.269, 9.652, 8.174, 9.362, 7.546, 6.604, 8.253, 9.095, 7.354, 7.976, 6.886, 6.258, 5.824, 5.499, 6.846, 5.570, 5.985, 5.190, 4.766, 8.771, 8.245, 9.789, 10.161, 10.351, 10.605, 11.610, 11.341, 12.287, 12.322, 11.787, 13.410, 9.322, 9.015, 8.776, 9.052, 7.758, 7.826, 7.990, 8.977, 7.248, 7.894, 8.285, 6.370, 6.214, 5.342, 5.431, 3.973, 3.943, 3.230, 3.234, 2.212, 3.991, 3.892, 3.624, 5.960, 5.908, 3.339, 3.179, 2.980, 3.150, 2.375, 2.876, 2.616, 3.262, 1.675, 3.264, 4.305, 2.758, 4.055, 2.299, 0.876, 0.258, 0.312, 0.871, -1.106, -1.253, -1.489, -2.564, -1.049, -1.041, -1.011, -0.052, -1.970, -2.740, -1.931, -2.037, -1.962, -2.949, -2.983, -3.917, -4.588, -4.488, -3.289, -3.932]
594 z = [6.302, 7.391, 8.306, 7.526, 7.089, 6.087, 6.697, 5.822, 5.604, 7.943, 9.155, 7.752, 7.908, 8.829, 9.212, 8.407, 9.880, 10.560, 10.415, 9.754, 8.900, 6.374, 5.909, 5.719, 6.139, 4.391, 4.081, 4.415, 4.326, 5.367, 3.307, 2.640, 3.889, 4.956, 3.700, 3.430, 2.493, 2.814, 2.633, 1.449, 3.403, 3.572, 2.369, 2.281, 1.371, 0.855, 1.868, 0.359, 0.149, -0.269, -0.055, -1.268, -1.726, -0.608, 0.037, -1.377, 0.162, 0.731, -2.354, -2.175, -3.496, -3.603, -4.606, -4.199, -5.387, -5.803, -6.196, -4.563, -5.146, -4.350, -3.001, -1.895, -1.241, -1.307, -2.472, -5.551, -5.582, -6.328, -6.269, -7.274, -6.735, -7.913, -8.518, -7.133, -8.791, -9.871, -8.395, -8.346, -8.584, -8.977, -8.732, -10.002, -10.355, -11.174, -11.584, -11.936, -10.759, -11.425, -9.403, -8.469, -9.921, -11.030, -9.410, -8.336, -10.080, -9.428, -10.291, -11.333, -11.606, -12.128, -10.723, -11.893, -9.781, -10.959, -8.768, -7.344, -8.971, -9.765, -7.642, -7.816, -7.251, -6.715, -6.584, -5.765, -7.175, -6.955, -9.288, -9.222, -9.654, -9.696, -10.009, -10.928, -10.249, -10.194, -9.475, -11.596, -11.540, -11.813, -12.724, -13.193, -13.137, -8.947, -7.774, -9.383, -10.338, -8.477, -8.138, -9.017, -7.265, -6.226]
595
596
597 for i in range(len(mol.atom_name)):
598 self.assertEqual(mol.atom_name[i], atom_name[i])
599 self.assertEqual(mol.bonded[i], bonded[i])
600 self.assertEqual(mol.chain_id[i], chain_id[i])
601 self.assertEqual(mol.element[i], element[i])
602 self.assertEqual(mol.pdb_record[i], pdb_record[i])
603 self.assertEqual(mol.res_name[i], res_name[i])
604 self.assertEqual(mol.res_num[i], res_num[i])
605 self.assertEqual(mol.seg_id[i], seg_id[i])
606 self.assertEqual(mol.x[i], x[i])
607 self.assertEqual(mol.y[i], y[i])
608 self.assertEqual(mol.z[i], z[i])
609