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23 from math import sqrt
24 from numpy import float64, zeros
25 from os import sep
26 from tempfile import mktemp
27
28
29 from data_store import Relax_data_store; ds = Relax_data_store()
30 from pipe_control.mol_res_spin import count_spins, return_spin, spin_loop
31 from lib.geometry.rotations import euler_to_R_zyz
32 from lib.errors import RelaxError
33 from lib.io import DummyFileObject
34 from status import Status; status = Status()
35 from test_suite.system_tests.base_classes import SystemTestCase
36
37
39 """Class for testing the structural objects."""
40
46
47
49 """Strip out all PDB remark lines.
50
51 @param lines: The list of PDB lines.
52 @type lines: list of str
53 """
54
55
56 lines[:] = [x for x in lines if x[:6] != 'REMARK']
57
58
60 """Test that a RelaxError occurs when the alternate location indicator is present but not specified."""
61
62
63 path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'structures'
64
65
66 self.assertRaises(RelaxError, self.interpreter.structure.read_pdb, '1OGT_trunc.pdb', dir=path)
67
68
70 """Test the bug reported as the U{support request #2998<https://web.archive.org/web/https://gna.org/support/?2998>}, the broken CONECT records."""
71
72
73 path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'structures'
74
75
76 self.interpreter.structure.read_pdb('1RTE_trunc.pdb', dir=path)
77
78
89
90
107
108
110 """Catch U{bug #21522<https://web.archive.org/web/https://gna.org/bugs/?21522>}, the structure.write_pdb user function creating an incorrect MASTER record.
111
112 This also triggers U{bug #21520<https://web.archive.org/web/https://gna.org/bugs/?21520>}, the failure of the structure.write_pdb user function when creating the MASTER record due to too many ATOM and HETATM records being present.
113 """
114
115
116 self.interpreter.structure.add_model(model_num=1)
117 self.interpreter.structure.add_model(model_num=2)
118
119
120 self.interpreter.structure.add_atom(atom_name='N', res_name='Pro', res_num=2, pos=[1., 2., 3.], element='N')
121
122
123 file = DummyFileObject()
124 self.interpreter.structure.write_pdb(file=file, force=True)
125
126
127 contents = [
128 "MODEL 1 \n",
129 "ATOM 1 N Pro A 2 1.000 2.000 3.000 1.00 0.00 N \n",
130 "TER 2 Pro A 2 \n",
131 "ENDMDL \n",
132 "MODEL 2 \n",
133 "ATOM 1 N Pro A 2 1.000 2.000 3.000 1.00 0.00 N \n",
134 "TER 2 Pro A 2 \n",
135 "ENDMDL \n",
136 "MASTER 0 0 0 0 0 0 0 0 1 1 0 0 \n",
137 "END \n"
138 ]
139
140
141 lines = file.readlines()
142 self.strip_remarks(lines)
143 for i in range(len(lines)):
144 self.assertEqual(contents[i], lines[i])
145
146
148 """Catch U{bug #21814<https://web.archive.org/web/https://gna.org/bugs/?21814>}, the PDB reading failure when not padded to 80 spaces."""
149
150
151 path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'structures'
152
153
154 self.interpreter.structure.read_pdb('SpUreE_dimer_H_new', dir=path)
155
156
158 """Catch U{bug #22041<https://web.archive.org/web/https://gna.org/bugs/?22041>}, the atom serial number not being sequential from 1 onwards."""
159
160
161 path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'structures'
162
163
164 self.interpreter.structure.read_pdb('1RTE_trunc.pdb', dir=path, set_mol_name='N-dom')
165 self.interpreter.structure.read_pdb('1RTE_trunc.pdb', dir=path, set_mol_name='C-dom')
166
167
168 file = DummyFileObject()
169 self.interpreter.structure.write_pdb(file=file, force=True)
170
171
172 contents = [
173 "HET CYN A 445 1 \n",
174 "HET CYN B 445 1 \n",
175 "HETNAM CYN UNKNOWN \n",
176 "FORMUL 1 CYN C1 \n",
177 "ATOM 1 N LEU A 3 49.617 4.693 46.426 1.00 0.00 N \n",
178 "ATOM 2 CA LEU A 3 49.432 5.476 45.190 1.00 0.00 C \n",
179 "ATOM 3 C LEU A 3 50.346 4.980 44.055 1.00 0.00 C \n",
180 "ATOM 4 O LEU A 3 49.924 4.868 42.889 1.00 0.00 O \n",
181 "ATOM 5 CB LEU A 3 49.673 6.968 45.457 1.00 0.00 C \n",
182 "ATOM 6 CG LEU A 3 49.804 7.863 44.222 1.00 0.00 C \n",
183 "ATOM 7 CD1 LEU A 3 48.564 7.837 43.327 1.00 0.00 C \n",
184 "ATOM 8 CD2 LEU A 3 50.075 9.282 44.625 1.00 0.00 C \n",
185 "TER 9 LEU A 3 \n",
186 "HETATM 10 C CYN A 445 29.160 13.127 62.533 1.00 0.00 C \n",
187 "ATOM 11 N LEU B 3 49.617 4.693 46.426 1.00 0.00 N \n",
188 "ATOM 12 CA LEU B 3 49.432 5.476 45.190 1.00 0.00 C \n",
189 "ATOM 13 C LEU B 3 50.346 4.980 44.055 1.00 0.00 C \n",
190 "ATOM 14 O LEU B 3 49.924 4.868 42.889 1.00 0.00 O \n",
191 "ATOM 15 CB LEU B 3 49.673 6.968 45.457 1.00 0.00 C \n",
192 "ATOM 16 CG LEU B 3 49.804 7.863 44.222 1.00 0.00 C \n",
193 "ATOM 17 CD1 LEU B 3 48.564 7.837 43.327 1.00 0.00 C \n",
194 "ATOM 18 CD2 LEU B 3 50.075 9.282 44.625 1.00 0.00 C \n",
195 "TER 19 LEU B 3 \n",
196 "HETATM 20 C CYN B 445 29.160 13.127 62.533 1.00 0.00 C \n",
197 "MASTER 0 0 2 0 0 0 0 0 18 2 0 0 \n",
198 "END \n"
199 ]
200
201
202 lines = file.readlines()
203 self.strip_remarks(lines)
204 for i in range(len(lines)):
205 self.assertEqual(contents[i], lines[i])
206
207
209 """Catch U{bug #22069<https://web.archive.org/web/https://gna.org/bugs/?22069>}, the failure of the structure.delete user function with helix attribute errors."""
210
211
212 path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'frame_order'+sep+'cam'
213
214
215 self.interpreter.structure.read_pdb('1J7P_1st_NH_rot.pdb', dir=path)
216
217
218 self.interpreter.structure.delete(atom_id='@CA')
219
220
222 """Catch U{bug #22070<https://web.archive.org/web/https://gna.org/bugs/?22070>}, the failure of the structure.superimpose user function after deleting atoms with structure.delete."""
223
224
225 path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'frame_order'+sep+'cam'
226
227
228 self.interpreter.structure.read_pdb('1J7P_1st_NH.pdb', dir=path, set_mol_name='C-dom', set_model_num=1)
229 self.interpreter.structure.read_pdb('1J7P_1st_NH_rot.pdb', dir=path, set_mol_name='C-dom', set_model_num=2)
230
231
232 self.interpreter.structure.delete(atom_id='@CA')
233
234
235 for i in range(2):
236 print("Checking the last atom of model %s." % i)
237 self.assertEqual(cdp.structure.structural_data[i].mol[0].atom_name[-1], 'H')
238
239
240 self.interpreter.structure.superimpose(method='fit to first', centre_type='CoM')
241
242
248
249
251 """Test the deletion of structural data in only one pipe."""
252
253
254 self.interpreter.structure.add_atom(atom_name='PIV', res_name='M1', res_num=1, pos=[0., 1., 2.], element='S')
255
256
257 self.interpreter.pipe.create('new', 'N-state')
258
259
260 self.interpreter.structure.add_atom(atom_name='PIV', res_name='M1', res_num=2, pos=[4., 5., 6.], element='S')
261
262
263 self.interpreter.structure.delete()
264
265
266 self.assert_(hasattr(cdp, 'structure'))
267 self.assertEqual(len(cdp.structure.structural_data), 0)
268 self.interpreter.pipe.switch('mf')
269 self.assert_(hasattr(cdp, 'structure'))
270 self.assertEqual(len(cdp.structure.structural_data), 1)
271
272
274 """Test of the structure.displacement user function."""
275
276
277 path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'structures'
278
279
280 self.interpreter.structure.read_pdb('Ap4Aase_res1-12.pdb', dir=path, set_model_num=1)
281 self.interpreter.structure.read_pdb('Ap4Aase_res1-12.pdb', dir=path, set_model_num=2)
282
283
284 R = zeros((3, 3), float64)
285 euler_to_R_zyz(1.3, 0.4, 4.5, R)
286
287
288 self.interpreter.structure.rotate(R, model=2)
289
290
291 self.interpreter.structure.displacement()
292
293
294 self.interpreter.structure.read_pdb('Ap4Aase_res1-12.pdb', dir=path, set_model_num=3)
295 self.interpreter.structure.rotate(R, model=3)
296
297
298 models = [1, 2]
299 trans_vect = [
300 [[0.0, 0.0, 0.0],
301 [ 2.270857972754659, -1.811667138656451, 1.878400649688508]],
302 [[ -2.270857972754659, 1.811667138656451, -1.878400649688508],
303 [0.0, 0.0, 0.0]]
304 ]
305 dist = [
306 [0.0000000000000000, 3.4593818457148173],
307 [3.4593818457148173, 0.0000000000000000]
308 ]
309 rot_axis = [
310 [None,
311 [ 0.646165066909452, 0.018875759848125, -0.762964227206007]],
312 [[ -0.646165066909452, -0.018875759848125, 0.762964227206007],
313 None]
314 ]
315 angle = [
316 [0.0000000000000000, 0.6247677290742989],
317 [0.6247677290742989, 0.0000000000000000]
318 ]
319
320
321 self.assert_(hasattr(cdp.structure, 'displacements'))
322 for i in range(len(models)):
323 for j in range(len(models)):
324
325 self.assertAlmostEqual(cdp.structure.displacements._translation_distance[models[i]][models[j]], dist[i][j])
326 for k in range(3):
327 self.assertAlmostEqual(cdp.structure.displacements._translation_vector[models[i]][models[j]][k], trans_vect[i][j][k])
328
329
330 self.assertAlmostEqual(cdp.structure.displacements._rotation_angle[models[i]][models[j]], angle[i][j])
331 if rot_axis[i][j] != None:
332 for k in range(3):
333 self.assertAlmostEqual(cdp.structure.displacements._rotation_axis[models[i]][models[j]][k], rot_axis[i][j][k])
334
335
336 self.tmpfile = mktemp()
337 self.interpreter.state.save(self.tmpfile, dir=None, force=True)
338
339
340 self.interpreter.reset()
341
342
343 self.interpreter.state.load(self.tmpfile)
344
345
346 self.assert_(hasattr(cdp.structure, 'displacements'))
347 for i in range(len(models)):
348 for j in range(len(models)):
349
350 self.assertAlmostEqual(cdp.structure.displacements._translation_distance[models[i]][models[j]], dist[i][j])
351 for k in range(3):
352 self.assertAlmostEqual(cdp.structure.displacements._translation_vector[models[i]][models[j]][k], trans_vect[i][j][k])
353
354
355 self.assertAlmostEqual(cdp.structure.displacements._rotation_angle[models[i]][models[j]], angle[i][j])
356 if rot_axis[i][j] != None:
357 for k in range(3):
358 self.assertAlmostEqual(cdp.structure.displacements._rotation_axis[models[i]][models[j]][k], rot_axis[i][j][k])
359
360
362 """Test the loading of spins from different molecules into one molecule container."""
363
364
365 path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'structures'+sep+'lactose'
366
367
368 self.interpreter.structure.read_pdb(file='lactose_MCMM4_S1_1.pdb', dir=path, set_mol_name='L1')
369 self.interpreter.structure.read_pdb(file='lactose_MCMM4_S1_2.pdb', dir=path, set_mol_name='L2')
370
371
372 self.interpreter.structure.load_spins('#L1:900@C1', mol_name_target='Lactose')
373 self.interpreter.structure.load_spins('#L2:900@C2', mol_name_target='Lactose')
374
375
376 self.assertEqual(len(cdp.mol), 1)
377 self.assertEqual(cdp.mol[0].name, 'Lactose')
378 self.assertEqual(len(cdp.mol[0].res), 1)
379 self.assertEqual(cdp.mol[0].res[0].name, 'UNK')
380 self.assertEqual(cdp.mol[0].res[0].num, 900)
381 self.assertEqual(len(cdp.mol[0].res[0].spin), 2)
382 self.assertEqual(cdp.mol[0].res[0].spin[0].name, 'C1')
383 self.assertEqual(cdp.mol[0].res[0].spin[0].num, 1)
384 self.assertEqual(cdp.mol[0].res[0].spin[1].name, 'C2')
385 self.assertEqual(cdp.mol[0].res[0].spin[1].num, 2)
386
387
389 """Load the PDB file using the information in a results file (using the internal structural object)."""
390
391
392 path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'structures'
393
394
395 self.interpreter.results.read(file='str_internal', dir=path)
396
397
398 self.assert_(hasattr(cdp, 'structure'))
399 self.assert_(hasattr(cdp.structure, 'structural_data'))
400 self.assert_(len(cdp.structure.structural_data))
401 self.assert_(len(cdp.structure.structural_data[0].mol))
402
403 mol = cdp.structure.structural_data[0].mol[0]
404 self.assertEqual(mol.file_name, 'Ap4Aase_res1-12.pdb')
405 self.assertEqual(mol.file_path, '')
406 self.assertEqual(mol.file_model, 1)
407 self.assertEqual(mol.file_mol_num, 1)
408
409
410 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']
411 bonded = [[]]*174
412 chain_id = [None]*174
413 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']
414 pdb_record = ['ATOM']*174
415 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']
416 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]
417 seg_id = [None]*174
418 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]
419 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]
420 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]
421
422
423 mol = cdp.structure.structural_data[0].mol[0]
424 for i in range(len(mol.atom_name)):
425 self.assertEqual(mol.atom_name[i], atom_name[i])
426 self.assertEqual(mol.bonded[i], bonded[i])
427 self.assertEqual(mol.chain_id[i], chain_id[i])
428 self.assertEqual(mol.element[i], element[i])
429 self.assertEqual(mol.pdb_record[i], pdb_record[i])
430 self.assertEqual(mol.res_name[i], res_name[i])
431 self.assertEqual(mol.res_num[i], res_num[i])
432 self.assertEqual(mol.seg_id[i], seg_id[i])
433 self.assertEqual(mol.x[i], x[i])
434 self.assertEqual(mol.y[i], y[i])
435 self.assertEqual(mol.z[i], z[i])
436
437
439 """Load the PDB file using the information in a results file (using the internal structural object)."""
440
441
442 path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'structures'
443
444
445 self.interpreter.results.read(file=path+sep+'str_internal')
446
447
488
489
491 """Load the structure from the 'strychnine_opt_cdcl3_b3lyp_gaussian.log.bz2' compressed Gaussian log file."""
492
493
494 path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'structures'
495
496
497 self.interpreter.structure.read_gaussian(file='strychnine_opt_cdcl3_b3lyp_gaussian.log.bz2', dir=path, set_mol_name='strychnine')
498
499
500 self.assertEqual(len(cdp.structure.structural_data), 1)
501 self.assertEqual(len(cdp.structure.structural_data[0].mol), 1)
502
503
504 self.interpreter.structure.load_spins('@C')
505 self.assertEqual(count_spins(), 21)
506
507
508 self.interpreter.structure.load_spins('@H')
509 self.assertEqual(count_spins(), 43)
510
511
512 self.interpreter.structure.load_spins()
513
514
515 data = [
516 [ 5, 'C', -0.258837, -2.073956, -0.558021],
517 [ 6, 'C', -0.824223, -1.406962, -1.808433],
518 [ 7, 'C', -1.741283, -0.250780, -1.378644],
519 [ 8, 'C', -0.819735, 0.828965, -0.783392],
520 [ 9, 'C', 0.003153, 0.334416, 0.415455],
521 [10, 'C', 2.358372, 0.448322, 0.162421],
522 [11, 'C', 3.667689, 0.888405, -0.010558],
523 [12, 'C', 4.632616, -0.056196, -0.360560],
524 [13, 'C', 4.303015, -1.398582, -0.525823],
525 [14, 'C', 2.988069, -1.825141, -0.331972],
526 [15, 'C', 2.015427, -0.899636, 0.012625],
527 [16, 'C', 0.561728, -1.122705, 0.360284],
528 [17, 'C', 0.390886, -1.834862, 1.723978],
529 [18, 'C', -1.067936, -2.282629, 1.709808],
530 [19, 'C', -2.708975, -2.252045, -0.131301],
531 [20, 'C', -2.815469, -0.775379, -0.431910],
532 [21, 'C', -3.718174, 0.023460, 0.134879],
533 [22, 'C', -3.726395, 1.516213, -0.058936],
534 [23, 'C', -1.423939, 2.193179, -0.407936],
535 [24, 'C', -0.372897, 3.059448, 0.332496],
536 [25, 'C', 1.064718, 2.558120, 0.325331],
537 [26, 'H', 0.399932, -2.896344, -0.855386],
538 [27, 'H', -1.364146, -2.140645, -2.409934],
539 [28, 'H', -0.007016, -1.035292, -2.430851],
540 [29, 'H', -2.229948, 0.177326, -2.261725],
541 [30, 'H', -0.101863, 1.055799, -1.581061],
542 [31, 'H', -0.582210, 0.470722, 1.326014],
543 [32, 'H', 3.918694, 1.929549, 0.116264],
544 [33, 'H', 5.656588, 0.267474, -0.505165],
545 [34, 'H', 5.068478, -2.115052, -0.797816],
546 [35, 'H', 2.736463, -2.873299, -0.445917],
547 [36, 'H', 1.059165, -2.698455, 1.760657],
548 [37, 'H', 0.631843, -1.189746, 2.570301],
549 [38, 'H', -1.243126, -3.142405, 2.361743],
550 [39, 'H', -1.719677, -1.470258, 2.058429],
551 [40, 'H', -3.410692, -2.541912, 0.651788],
552 [41, 'H', -2.971493, -2.840572, -1.016009],
553 [42, 'H', -4.455619, -0.395106, 0.813636],
554 [43, 'H', -3.834304, 1.785629, -1.118252],
555 [44, 'H', -4.559845, 1.966160, 0.480526],
556 [45, 'H', -1.736135, 2.699031, -1.329897],
557 [46, 'H', -0.354638, 4.078330, -0.048526],
558 [47, 'H', -0.690723, 3.116119, 1.378208],
559 [ 1, 'O', -2.547545, 2.139059, 0.472310],
560 [ 2, 'O', 2.015408, 3.324289, 0.213156],
561 [ 3, 'N', 1.207610, 1.203922, 0.478894],
562 [ 4, 'N', -1.350394, -2.624460, 0.301178]
563 ]
564
565
566 i = 0
567 for spin in spin_loop():
568 self.assertEqual(spin.num, data[i][0])
569 self.assertEqual(spin.name, data[i][1])
570 self.assertEqual(spin.element, data[i][1])
571 self.assertEqual(spin.pos[0], data[i][2])
572 self.assertEqual(spin.pos[1], data[i][3])
573 self.assertEqual(spin.pos[2], data[i][4])
574
575
576 i += 1
577
578
580 """Test the merging of two molecules into one."""
581
582
583 path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'structures'
584
585
586 self.interpreter.structure.read_pdb(file='Ap4Aase_res1-6.pdb', dir=path, set_mol_name='Ap4Aase', set_model_num=1)
587 self.interpreter.structure.read_pdb(file='Ap4Aase_res7-12.pdb', dir=path, set_mol_name='Ap4Aase', set_model_num=1, merge=True)
588 self.interpreter.structure.read_pdb(file='Ap4Aase_res1-12.pdb', dir=path, set_mol_name='Ap4Aase', set_model_num=2)
589
590
591 cdp.structure.validate_models()
592
593
595 """Test the reading of a file by structure.read_pdb that is not a PDB."""
596
597
598 path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'saved_states'
599
600
601 self.interpreter.structure.read_pdb(file='basic_single_pipe.bz2', dir=path)
602
603
631
632
647
648
666
667
682
683
698
699
715
716
732
733
735 """Load a few 'lactose_MCMM4_S1_*.pdb' PDB files as models (using the internal structural object PDB reader)."""
736
737
738 path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'structures'+sep+'lactose'
739
740
741 files = ['lactose_MCMM4_S1_1.pdb',
742 'lactose_MCMM4_S1_2.pdb',
743 'lactose_MCMM4_S1_3.pdb']
744
745
746 self.interpreter.structure.read_pdb(file=files[0], dir=path, set_model_num=1)
747 self.interpreter.structure.read_pdb(file=files[1], dir=path, set_model_num=1)
748 self.interpreter.structure.read_pdb(file=files[2], dir=path, set_model_num=1)
749
750
751 self.interpreter.structure.load_spins('@*H*')
752
753
754 self.interpreter.structure.load_spins()
755
756
757 self.assert_(hasattr(cdp, 'structure'))
758 self.assert_(hasattr(cdp.structure, 'structural_data'))
759 self.assertEqual(len(cdp.structure.structural_data), 1)
760 self.assertEqual(len(cdp.structure.structural_data[0].mol), 3)
761
762 i = 0
763 for mol in cdp.structure.structural_data[0].mol:
764 self.assertEqual(mol.file_name, files[i])
765 self.assertEqual(mol.file_path, path)
766 self.assertEqual(mol.file_model, 1)
767 self.assertEqual(mol.file_mol_num, 1)
768 i = i + 1
769
770
772 """Load the 2 models of the 'gromacs.pdb' PDB file as separate molecules of the same model (using the internal structural object PDB reader)."""
773
774
775 path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'structures'+sep+'phthalic_acid'
776
777
778 self.interpreter.structure.read_pdb(file='gromacs.pdb', dir=path, read_model=1, set_model_num=1)
779 self.interpreter.structure.read_pdb(file='gromacs.pdb', dir=path, read_model=2, set_model_num=1)
780
781
782 self.interpreter.structure.load_spins('@*H*')
783
784
785 self.interpreter.structure.load_spins()
786
787
788 self.assert_(hasattr(cdp, 'structure'))
789 self.assert_(hasattr(cdp.structure, 'structural_data'))
790 self.assertEqual(len(cdp.structure.structural_data), 1)
791 self.assertEqual(len(cdp.structure.structural_data[0].mol), 2)
792
793 i = 0
794 for mol in cdp.structure.structural_data[0].mol:
795 self.assertEqual(mol.file_name, 'gromacs.pdb')
796 self.assertEqual(mol.file_path, path)
797 self.assertEqual(mol.file_model, i+1)
798 self.assertEqual(mol.file_mol_num, 1)
799 i = i + 1
800
801
803 """Test the packing of models and molecules using 'gromacs.pdb' and 'lactose_MCMM4_S1_*.pdb' (using the internal structural object PDB reader)."""
804
805
806 path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'structures'
807
808
809 self.interpreter.structure.read_pdb(file='gromacs.pdb', dir=path+sep+'phthalic_acid')
810 self.interpreter.structure.read_pdb(file='lactose'+sep+'lactose_MCMM4_S1_1.pdb', dir=path, set_model_num=1, set_mol_name='lactose_MCMM4_S1')
811 self.interpreter.structure.read_pdb(file='lactose'+sep+'lactose_MCMM4_S1_2.pdb', dir=path, set_model_num=2, set_mol_name='lactose_MCMM4_S1')
812 self.interpreter.structure.read_pdb(file='lactose'+sep+'lactose_MCMM4_S1_3.pdb', dir=path, set_model_num=1, set_mol_name='lactose_MCMM4_S1b')
813 self.interpreter.structure.read_pdb(file='lactose'+sep+'lactose_MCMM4_S1_4.pdb', dir=path, set_model_num=2, set_mol_name='lactose_MCMM4_S1b')
814
815
816 self.interpreter.structure.load_spins('@*H*')
817
818
819 self.interpreter.structure.load_spins()
820
821
822 self.assert_(hasattr(cdp, 'structure'))
823 self.assert_(hasattr(cdp.structure, 'structural_data'))
824 self.assertEqual(len(cdp.structure.structural_data), 2)
825 self.assertEqual(len(cdp.structure.structural_data[0].mol), 3)
826 self.assertEqual(len(cdp.structure.structural_data[1].mol), 3)
827
828 files = [['gromacs.pdb', 'lactose_MCMM4_S1_1.pdb', 'lactose_MCMM4_S1_3.pdb'],
829 ['gromacs.pdb', 'lactose_MCMM4_S1_2.pdb', 'lactose_MCMM4_S1_4.pdb']]
830 paths = [[path+sep+'phthalic_acid', path+sep+'lactose', path+sep+'lactose'],
831 [path+sep+'phthalic_acid', path+sep+'lactose', path+sep+'lactose']]
832 models = [[1, 1, 1], [2, 1, 1]]
833
834 for i in range(len(cdp.structure.structural_data)):
835 for j in range(len(cdp.structure.structural_data[i].mol)):
836 mol = cdp.structure.structural_data[i].mol[j]
837 self.assertEqual(mol.file_name, files[i][j])
838 self.assertEqual(mol.file_path, paths[i][j])
839 self.assertEqual(mol.file_model, models[i][j])
840 self.assertEqual(mol.file_mol_num, 1)
841
842
844 """Test the reading of the complete 1UBQ PDB file."""
845
846
847 path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'structures'
848 self.interpreter.structure.read_pdb('1UBQ.pdb', dir=path)
849
850
851 self.assert_(hasattr(cdp, 'structure'))
852 self.assert_(hasattr(cdp.structure, 'structural_data'))
853 self.assertEqual(len(cdp.structure.structural_data), 1)
854 self.assertEqual(len(cdp.structure.structural_data[0].mol), 1)
855
856
857 self.assertEqual(cdp.structure.structural_data[0].mol[0].atom_num[0], 1)
858 self.assertEqual(cdp.structure.structural_data[0].mol[0].atom_name[0], 'N')
859 self.assertEqual(cdp.structure.structural_data[0].mol[0].chain_id[0], 'A')
860 self.assertEqual(cdp.structure.structural_data[0].mol[0].res_name[0], 'MET')
861 self.assertEqual(cdp.structure.structural_data[0].mol[0].res_num[0], 1)
862 self.assertEqual(cdp.structure.structural_data[0].mol[0].x[0], 27.340)
863 self.assertEqual(cdp.structure.structural_data[0].mol[0].y[0], 24.430)
864 self.assertEqual(cdp.structure.structural_data[0].mol[0].z[0], 2.614)
865 self.assertEqual(cdp.structure.structural_data[0].mol[0].element[0], 'N')
866
867
868 self.assertEqual(cdp.structure.structural_data[0].mol[0].atom_num[-1], 661)
869 self.assertEqual(cdp.structure.structural_data[0].mol[0].atom_name[-1], 'O')
870 self.assertEqual(cdp.structure.structural_data[0].mol[0].chain_id[-1], None)
871 self.assertEqual(cdp.structure.structural_data[0].mol[0].res_name[-1], 'HOH')
872 self.assertEqual(cdp.structure.structural_data[0].mol[0].res_num[-1], 58)
873 self.assertEqual(cdp.structure.structural_data[0].mol[0].x[-1], 37.667)
874 self.assertEqual(cdp.structure.structural_data[0].mol[0].y[-1], 43.421)
875 self.assertEqual(cdp.structure.structural_data[0].mol[0].z[-1], 17.000)
876 self.assertEqual(cdp.structure.structural_data[0].mol[0].element[-1], 'O')
877
878
880 """Test the reading and writing of the 1UBQ PDB file."""
881
882
883 path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'structures'
884 self.interpreter.structure.read_pdb('1UBQ.pdb', dir=path)
885
886
887 self.interpreter.structure.delete(":35-76")
888
889
890 self.interpreter.structure.delete(":HOH")
891
892
893 self.tmpfile = mktemp() + '.pdb'
894 self.interpreter.structure.write_pdb(self.tmpfile)
895
896
897 file = open(self.tmpfile)
898 lines = file.readlines()
899 file.close()
900
901
902 real_data = [
903 "HELIX 1 H1 ILE A 23 GLU A 34 1 12 \n",
904 "SHEET 1 BET 5 GLY A 10 VAL A 17 0 \n",
905 "SHEET 2 BET 5 MET A 1 THR A 7 -1 \n",
906 "ATOM 1 N MET A 1 27.340 24.430 2.614 1.00 0.00 N \n",
907 "ATOM 2 CA MET A 1 26.266 25.413 2.842 1.00 0.00 C \n",
908 "ATOM 3 C MET A 1 26.913 26.639 3.531 1.00 0.00 C \n",
909 "ATOM 4 O MET A 1 27.886 26.463 4.263 1.00 0.00 O \n",
910 "ATOM 5 CB MET A 1 25.112 24.880 3.649 1.00 0.00 C \n",
911 "ATOM 6 CG MET A 1 25.353 24.860 5.134 1.00 0.00 C \n",
912 "ATOM 7 SD MET A 1 23.930 23.959 5.904 1.00 0.00 S \n",
913 "ATOM 8 CE MET A 1 24.447 23.984 7.620 1.00 0.00 C \n",
914 "ATOM 9 N GLN A 2 26.335 27.770 3.258 1.00 0.00 N \n",
915 "ATOM 10 CA GLN A 2 26.850 29.021 3.898 1.00 0.00 C \n",
916 "ATOM 11 C GLN A 2 26.100 29.253 5.202 1.00 0.00 C \n",
917 "ATOM 12 O GLN A 2 24.865 29.024 5.330 1.00 0.00 O \n",
918 "ATOM 13 CB GLN A 2 26.733 30.148 2.905 1.00 0.00 C \n",
919 "ATOM 14 CG GLN A 2 26.882 31.546 3.409 1.00 0.00 C \n",
920 "ATOM 15 CD GLN A 2 26.786 32.562 2.270 1.00 0.00 C \n",
921 "ATOM 16 OE1 GLN A 2 27.783 33.160 1.870 1.00 0.00 O \n",
922 "ATOM 17 NE2 GLN A 2 25.562 32.733 1.806 1.00 0.00 N \n",
923 "ATOM 18 N ILE A 3 26.849 29.656 6.217 1.00 0.00 N \n",
924 "ATOM 19 CA ILE A 3 26.235 30.058 7.497 1.00 0.00 C \n",
925 "ATOM 20 C ILE A 3 26.882 31.428 7.862 1.00 0.00 C \n",
926 "ATOM 21 O ILE A 3 27.906 31.711 7.264 1.00 0.00 O \n",
927 "ATOM 22 CB ILE A 3 26.344 29.050 8.645 1.00 0.00 C \n",
928 "ATOM 23 CG1 ILE A 3 27.810 28.748 8.999 1.00 0.00 C \n",
929 "ATOM 24 CG2 ILE A 3 25.491 27.771 8.287 1.00 0.00 C \n",
930 "ATOM 25 CD1 ILE A 3 27.967 28.087 10.417 1.00 0.00 C \n",
931 "ATOM 26 N PHE A 4 26.214 32.097 8.771 1.00 0.00 N \n",
932 "ATOM 27 CA PHE A 4 26.772 33.436 9.197 1.00 0.00 C \n",
933 "ATOM 28 C PHE A 4 27.151 33.362 10.650 1.00 0.00 C \n",
934 "ATOM 29 O PHE A 4 26.350 32.778 11.395 1.00 0.00 O \n",
935 "ATOM 30 CB PHE A 4 25.695 34.498 8.946 1.00 0.00 C \n",
936 "ATOM 31 CG PHE A 4 25.288 34.609 7.499 1.00 0.00 C \n",
937 "ATOM 32 CD1 PHE A 4 24.147 33.966 7.038 1.00 0.00 C \n",
938 "ATOM 33 CD2 PHE A 4 26.136 35.346 6.640 1.00 0.00 C \n",
939 "ATOM 34 CE1 PHE A 4 23.812 34.031 5.677 1.00 0.00 C \n",
940 "ATOM 35 CE2 PHE A 4 25.810 35.392 5.267 1.00 0.00 C \n",
941 "ATOM 36 CZ PHE A 4 24.620 34.778 4.853 1.00 0.00 C \n",
942 "ATOM 37 N VAL A 5 28.260 33.943 11.096 1.00 0.00 N \n",
943 "ATOM 38 CA VAL A 5 28.605 33.965 12.503 1.00 0.00 C \n",
944 "ATOM 39 C VAL A 5 28.638 35.461 12.900 1.00 0.00 C \n",
945 "ATOM 40 O VAL A 5 29.522 36.103 12.320 1.00 0.00 O \n",
946 "ATOM 41 CB VAL A 5 29.963 33.317 12.814 1.00 0.00 C \n",
947 "ATOM 42 CG1 VAL A 5 30.211 33.394 14.304 1.00 0.00 C \n",
948 "ATOM 43 CG2 VAL A 5 29.957 31.838 12.352 1.00 0.00 C \n",
949 "ATOM 44 N LYS A 6 27.751 35.867 13.740 1.00 0.00 N \n",
950 "ATOM 45 CA LYS A 6 27.691 37.315 14.143 1.00 0.00 C \n",
951 "ATOM 46 C LYS A 6 28.469 37.475 15.420 1.00 0.00 C \n",
952 "ATOM 47 O LYS A 6 28.213 36.753 16.411 1.00 0.00 O \n",
953 "ATOM 48 CB LYS A 6 26.219 37.684 14.307 1.00 0.00 C \n",
954 "ATOM 49 CG LYS A 6 25.884 39.139 14.615 1.00 0.00 C \n",
955 "ATOM 50 CD LYS A 6 24.348 39.296 14.642 1.00 0.00 C \n",
956 "ATOM 51 CE LYS A 6 23.865 40.723 14.749 1.00 0.00 C \n",
957 "ATOM 52 NZ LYS A 6 22.375 40.720 14.907 1.00 0.00 N \n",
958 "ATOM 53 N THR A 7 29.426 38.430 15.446 1.00 0.00 N \n",
959 "ATOM 54 CA THR A 7 30.225 38.643 16.662 1.00 0.00 C \n",
960 "ATOM 55 C THR A 7 29.664 39.839 17.434 1.00 0.00 C \n",
961 "ATOM 56 O THR A 7 28.850 40.565 16.859 1.00 0.00 O \n",
962 "ATOM 57 CB THR A 7 31.744 38.879 16.299 1.00 0.00 C \n",
963 "ATOM 58 OG1 THR A 7 31.737 40.257 15.824 1.00 0.00 O \n",
964 "ATOM 59 CG2 THR A 7 32.260 37.969 15.171 1.00 0.00 C \n",
965 "ATOM 60 N LEU A 8 30.132 40.069 18.642 1.00 0.00 N \n",
966 "ATOM 61 CA LEU A 8 29.607 41.180 19.467 1.00 0.00 C \n",
967 "ATOM 62 C LEU A 8 30.075 42.538 18.984 1.00 0.00 C \n",
968 "ATOM 63 O LEU A 8 29.586 43.570 19.483 1.00 0.00 O \n",
969 "ATOM 64 CB LEU A 8 29.919 40.890 20.938 1.00 0.00 C \n",
970 "ATOM 65 CG LEU A 8 29.183 39.722 21.581 1.00 0.00 C \n",
971 "ATOM 66 CD1 LEU A 8 29.308 39.750 23.095 1.00 0.00 C \n",
972 "ATOM 67 CD2 LEU A 8 27.700 39.721 21.228 1.00 0.00 C \n",
973 "ATOM 68 N THR A 9 30.991 42.571 17.998 1.00 0.00 N \n",
974 "ATOM 69 CA THR A 9 31.422 43.940 17.553 1.00 0.00 C \n",
975 "ATOM 70 C THR A 9 30.755 44.351 16.277 1.00 0.00 C \n",
976 "ATOM 71 O THR A 9 31.207 45.268 15.566 1.00 0.00 O \n",
977 "ATOM 72 CB THR A 9 32.979 43.918 17.445 1.00 0.00 C \n",
978 "ATOM 73 OG1 THR A 9 33.174 43.067 16.265 1.00 0.00 O \n",
979 "ATOM 74 CG2 THR A 9 33.657 43.319 18.672 1.00 0.00 C \n",
980 "ATOM 75 N GLY A 10 29.721 43.673 15.885 1.00 0.00 N \n",
981 "ATOM 76 CA GLY A 10 28.978 43.960 14.678 1.00 0.00 C \n",
982 "ATOM 77 C GLY A 10 29.604 43.507 13.393 1.00 0.00 C \n",
983 "ATOM 78 O GLY A 10 29.219 43.981 12.301 1.00 0.00 O \n",
984 "ATOM 79 N LYS A 11 30.563 42.623 13.495 1.00 0.00 N \n",
985 "ATOM 80 CA LYS A 11 31.191 42.012 12.331 1.00 0.00 C \n",
986 "ATOM 81 C LYS A 11 30.459 40.666 12.130 1.00 0.00 C \n",
987 "ATOM 82 O LYS A 11 30.253 39.991 13.133 1.00 0.00 O \n",
988 "ATOM 83 CB LYS A 11 32.672 41.717 12.505 1.00 0.00 C \n",
989 "ATOM 84 CG LYS A 11 33.280 41.086 11.227 1.00 0.00 C \n",
990 "ATOM 85 CD LYS A 11 34.762 40.799 11.470 1.00 0.00 C \n",
991 "ATOM 86 CE LYS A 11 35.614 40.847 10.240 1.00 0.00 C \n",
992 "ATOM 87 NZ LYS A 11 35.100 40.073 9.101 1.00 0.00 N \n",
993 "ATOM 88 N THR A 12 30.163 40.338 10.886 1.00 0.00 N \n",
994 "ATOM 89 CA THR A 12 29.542 39.020 10.653 1.00 0.00 C \n",
995 "ATOM 90 C THR A 12 30.494 38.261 9.729 1.00 0.00 C \n",
996 "ATOM 91 O THR A 12 30.849 38.850 8.706 1.00 0.00 O \n",
997 "ATOM 92 CB THR A 12 28.113 39.049 10.015 1.00 0.00 C \n",
998 "ATOM 93 OG1 THR A 12 27.280 39.722 10.996 1.00 0.00 O \n",
999 "ATOM 94 CG2 THR A 12 27.588 37.635 9.715 1.00 0.00 C \n",
1000 "ATOM 95 N ILE A 13 30.795 37.015 10.095 1.00 0.00 N \n",
1001 "ATOM 96 CA ILE A 13 31.720 36.289 9.176 1.00 0.00 C \n",
1002 "ATOM 97 C ILE A 13 30.955 35.211 8.459 1.00 0.00 C \n",
1003 "ATOM 98 O ILE A 13 30.025 34.618 9.040 1.00 0.00 O \n",
1004 "ATOM 99 CB ILE A 13 32.995 35.883 9.934 1.00 0.00 C \n",
1005 "ATOM 100 CG1 ILE A 13 33.306 34.381 9.840 1.00 0.00 C \n",
1006 "ATOM 101 CG2 ILE A 13 33.109 36.381 11.435 1.00 0.00 C \n",
1007 "ATOM 102 CD1 ILE A 13 34.535 34.028 10.720 1.00 0.00 C \n",
1008 "ATOM 103 N THR A 14 31.244 34.986 7.197 1.00 0.00 N \n",
1009 "ATOM 104 CA THR A 14 30.505 33.884 6.512 1.00 0.00 C \n",
1010 "ATOM 105 C THR A 14 31.409 32.680 6.446 1.00 0.00 C \n",
1011 "ATOM 106 O THR A 14 32.619 32.812 6.125 1.00 0.00 O \n",
1012 "ATOM 107 CB THR A 14 30.091 34.393 5.078 1.00 0.00 C \n",
1013 "ATOM 108 OG1 THR A 14 31.440 34.513 4.487 1.00 0.00 O \n",
1014 "ATOM 109 CG2 THR A 14 29.420 35.756 5.119 1.00 0.00 C \n",
1015 "ATOM 110 N LEU A 15 30.884 31.485 6.666 1.00 0.00 N \n",
1016 "ATOM 111 CA LEU A 15 31.677 30.275 6.639 1.00 0.00 C \n",
1017 "ATOM 112 C LEU A 15 31.022 29.288 5.665 1.00 0.00 C \n",
1018 "ATOM 113 O LEU A 15 29.809 29.395 5.545 1.00 0.00 O \n",
1019 "ATOM 114 CB LEU A 15 31.562 29.686 8.045 1.00 0.00 C \n",
1020 "ATOM 115 CG LEU A 15 32.631 29.444 9.060 1.00 0.00 C \n",
1021 "ATOM 116 CD1 LEU A 15 33.814 30.390 9.030 1.00 0.00 C \n",
1022 "ATOM 117 CD2 LEU A 15 31.945 29.449 10.436 1.00 0.00 C \n",
1023 "ATOM 118 N GLU A 16 31.834 28.412 5.125 1.00 0.00 N \n",
1024 "ATOM 119 CA GLU A 16 31.220 27.341 4.275 1.00 0.00 C \n",
1025 "ATOM 120 C GLU A 16 31.440 26.079 5.080 1.00 0.00 C \n",
1026 "ATOM 121 O GLU A 16 32.576 25.802 5.461 1.00 0.00 O \n",
1027 "ATOM 122 CB GLU A 16 31.827 27.262 2.894 1.00 0.00 C \n",
1028 "ATOM 123 CG GLU A 16 31.363 28.410 1.962 1.00 0.00 C \n",
1029 "ATOM 124 CD GLU A 16 31.671 28.291 0.498 1.00 0.00 C \n",
1030 "ATOM 125 OE1 GLU A 16 30.869 28.621 -0.366 1.00 0.00 O \n",
1031 "ATOM 126 OE2 GLU A 16 32.835 27.861 0.278 1.00 0.00 O \n",
1032 "ATOM 127 N VAL A 17 30.310 25.458 5.384 1.00 0.00 N \n",
1033 "ATOM 128 CA VAL A 17 30.288 24.245 6.193 1.00 0.00 C \n",
1034 "ATOM 129 C VAL A 17 29.279 23.227 5.641 1.00 0.00 C \n",
1035 "ATOM 130 O VAL A 17 28.478 23.522 4.725 1.00 0.00 O \n",
1036 "ATOM 131 CB VAL A 17 29.903 24.590 7.665 1.00 0.00 C \n",
1037 "ATOM 132 CG1 VAL A 17 30.862 25.496 8.389 1.00 0.00 C \n",
1038 "ATOM 133 CG2 VAL A 17 28.476 25.135 7.705 1.00 0.00 C \n",
1039 "ATOM 134 N GLU A 18 29.380 22.057 6.232 1.00 0.00 N \n",
1040 "ATOM 135 CA GLU A 18 28.468 20.940 5.980 1.00 0.00 C \n",
1041 "ATOM 136 C GLU A 18 27.819 20.609 7.316 1.00 0.00 C \n",
1042 "ATOM 137 O GLU A 18 28.449 20.674 8.360 1.00 0.00 O \n",
1043 "ATOM 138 CB GLU A 18 29.213 19.697 5.506 1.00 0.00 C \n",
1044 "ATOM 139 CG GLU A 18 29.728 19.755 4.060 1.00 0.00 C \n",
1045 "ATOM 140 CD GLU A 18 28.754 20.061 2.978 1.00 0.00 C \n",
1046 "ATOM 141 OE1 GLU A 18 27.546 19.992 2.985 1.00 0.00 O \n",
1047 "ATOM 142 OE2 GLU A 18 29.336 20.423 1.904 1.00 0.00 O \n",
1048 "ATOM 143 N PRO A 19 26.559 20.220 7.288 1.00 0.00 N \n",
1049 "ATOM 144 CA PRO A 19 25.829 19.825 8.494 1.00 0.00 C \n",
1050 "ATOM 145 C PRO A 19 26.541 18.732 9.251 1.00 0.00 C \n",
1051 "ATOM 146 O PRO A 19 26.333 18.536 10.457 1.00 0.00 O \n",
1052 "ATOM 147 CB PRO A 19 24.469 19.332 7.952 1.00 0.00 C \n",
1053 "ATOM 148 CG PRO A 19 24.299 20.134 6.704 1.00 0.00 C \n",
1054 "ATOM 149 CD PRO A 19 25.714 20.108 6.073 1.00 0.00 C \n",
1055 "ATOM 150 N SER A 20 27.361 17.959 8.559 1.00 0.00 N \n",
1056 "ATOM 151 CA SER A 20 28.054 16.835 9.210 1.00 0.00 C \n",
1057 "ATOM 152 C SER A 20 29.258 17.318 9.984 1.00 0.00 C \n",
1058 "ATOM 153 O SER A 20 29.930 16.477 10.606 1.00 0.00 O \n",
1059 "ATOM 154 CB SER A 20 28.523 15.820 8.182 1.00 0.00 C \n",
1060 "ATOM 155 OG SER A 20 28.946 16.445 6.967 1.00 0.00 O \n",
1061 "ATOM 156 N ASP A 21 29.599 18.599 9.828 1.00 0.00 N \n",
1062 "ATOM 157 CA ASP A 21 30.796 19.083 10.566 1.00 0.00 C \n",
1063 "ATOM 158 C ASP A 21 30.491 19.162 12.040 1.00 0.00 C \n",
1064 "ATOM 159 O ASP A 21 29.367 19.523 12.441 1.00 0.00 O \n",
1065 "ATOM 160 CB ASP A 21 31.155 20.515 10.048 1.00 0.00 C \n",
1066 "ATOM 161 CG ASP A 21 31.923 20.436 8.755 1.00 0.00 C \n",
1067 "ATOM 162 OD1 ASP A 21 32.493 19.374 8.456 1.00 0.00 O \n",
1068 "ATOM 163 OD2 ASP A 21 31.838 21.402 7.968 1.00 0.00 O \n",
1069 "ATOM 164 N THR A 22 31.510 18.936 12.852 1.00 0.00 N \n",
1070 "ATOM 165 CA THR A 22 31.398 19.064 14.286 1.00 0.00 C \n",
1071 "ATOM 166 C THR A 22 31.593 20.553 14.655 1.00 0.00 C \n",
1072 "ATOM 167 O THR A 22 32.159 21.311 13.861 1.00 0.00 O \n",
1073 "ATOM 168 CB THR A 22 32.492 18.193 14.995 1.00 0.00 C \n",
1074 "ATOM 169 OG1 THR A 22 33.778 18.739 14.516 1.00 0.00 O \n",
1075 "ATOM 170 CG2 THR A 22 32.352 16.700 14.630 1.00 0.00 C \n",
1076 "ATOM 171 N ILE A 23 31.113 20.863 15.860 1.00 0.00 N \n",
1077 "ATOM 172 CA ILE A 23 31.288 22.201 16.417 1.00 0.00 C \n",
1078 "ATOM 173 C ILE A 23 32.776 22.519 16.577 1.00 0.00 C \n",
1079 "ATOM 174 O ILE A 23 33.233 23.659 16.384 1.00 0.00 O \n",
1080 "ATOM 175 CB ILE A 23 30.520 22.300 17.764 1.00 0.00 C \n",
1081 "ATOM 176 CG1 ILE A 23 29.006 22.043 17.442 1.00 0.00 C \n",
1082 "ATOM 177 CG2 ILE A 23 30.832 23.699 18.358 1.00 0.00 C \n",
1083 "ATOM 178 CD1 ILE A 23 28.407 22.948 16.366 1.00 0.00 C \n",
1084 "ATOM 179 N GLU A 24 33.548 21.526 16.950 1.00 0.00 N \n",
1085 "ATOM 180 CA GLU A 24 35.031 21.722 17.069 1.00 0.00 C \n",
1086 "ATOM 181 C GLU A 24 35.615 22.190 15.759 1.00 0.00 C \n",
1087 "ATOM 182 O GLU A 24 36.532 23.046 15.724 1.00 0.00 O \n",
1088 "ATOM 183 CB GLU A 24 35.667 20.383 17.447 1.00 0.00 C \n",
1089 "ATOM 184 CG GLU A 24 37.128 20.293 17.872 1.00 0.00 C \n",
1090 "ATOM 185 CD GLU A 24 37.561 18.851 18.082 1.00 0.00 C \n",
1091 "ATOM 186 OE1 GLU A 24 37.758 18.024 17.195 1.00 0.00 O \n",
1092 "ATOM 187 OE2 GLU A 24 37.628 18.599 19.313 1.00 0.00 O \n",
1093 "ATOM 188 N ASN A 25 35.139 21.624 14.662 1.00 0.00 N \n",
1094 "ATOM 189 CA ASN A 25 35.590 21.945 13.302 1.00 0.00 C \n",
1095 "ATOM 190 C ASN A 25 35.238 23.382 12.920 1.00 0.00 C \n",
1096 "ATOM 191 O ASN A 25 36.066 24.109 12.333 1.00 0.00 O \n",
1097 "ATOM 192 CB ASN A 25 35.064 20.957 12.255 1.00 0.00 C \n",
1098 "ATOM 193 CG ASN A 25 35.541 21.418 10.871 1.00 0.00 C \n",
1099 "ATOM 194 OD1 ASN A 25 36.772 21.623 10.676 1.00 0.00 O \n",
1100 "ATOM 195 ND2 ASN A 25 34.628 21.595 9.920 1.00 0.00 N \n",
1101 "ATOM 196 N VAL A 26 34.007 23.745 13.250 1.00 0.00 N \n",
1102 "ATOM 197 CA VAL A 26 33.533 25.097 12.978 1.00 0.00 C \n",
1103 "ATOM 198 C VAL A 26 34.441 26.099 13.684 1.00 0.00 C \n",
1104 "ATOM 199 O VAL A 26 34.883 27.090 13.093 1.00 0.00 O \n",
1105 "ATOM 200 CB VAL A 26 32.060 25.257 13.364 1.00 0.00 C \n",
1106 "ATOM 201 CG1 VAL A 26 31.684 26.749 13.342 1.00 0.00 C \n",
1107 "ATOM 202 CG2 VAL A 26 31.152 24.421 12.477 1.00 0.00 C \n",
1108 "ATOM 203 N LYS A 27 34.734 25.822 14.949 1.00 0.00 N \n",
1109 "ATOM 204 CA LYS A 27 35.596 26.715 15.736 1.00 0.00 C \n",
1110 "ATOM 205 C LYS A 27 36.975 26.826 15.107 1.00 0.00 C \n",
1111 "ATOM 206 O LYS A 27 37.579 27.926 15.159 1.00 0.00 O \n",
1112 "ATOM 207 CB LYS A 27 35.715 26.203 17.172 1.00 0.00 C \n",
1113 "ATOM 208 CG LYS A 27 34.343 26.445 17.898 1.00 0.00 C \n",
1114 "ATOM 209 CD LYS A 27 34.509 26.077 19.360 1.00 0.00 C \n",
1115 "ATOM 210 CE LYS A 27 33.206 26.311 20.122 1.00 0.00 C \n",
1116 "ATOM 211 NZ LYS A 27 33.455 25.910 21.546 1.00 0.00 N \n",
1117 "ATOM 212 N ALA A 28 37.499 25.743 14.571 1.00 0.00 N \n",
1118 "ATOM 213 CA ALA A 28 38.794 25.761 13.880 1.00 0.00 C \n",
1119 "ATOM 214 C ALA A 28 38.728 26.591 12.611 1.00 0.00 C \n",
1120 "ATOM 215 O ALA A 28 39.704 27.346 12.277 1.00 0.00 O \n",
1121 "ATOM 216 CB ALA A 28 39.285 24.336 13.566 1.00 0.00 C \n",
1122 "ATOM 217 N LYS A 29 37.633 26.543 11.867 1.00 0.00 N \n",
1123 "ATOM 218 CA LYS A 29 37.471 27.391 10.668 1.00 0.00 C \n",
1124 "ATOM 219 C LYS A 29 37.441 28.882 11.052 1.00 0.00 C \n",
1125 "ATOM 220 O LYS A 29 38.020 29.772 10.382 1.00 0.00 O \n",
1126 "ATOM 221 CB LYS A 29 36.193 27.058 9.911 1.00 0.00 C \n",
1127 "ATOM 222 CG LYS A 29 36.153 25.620 9.409 1.00 0.00 C \n",
1128 "ATOM 223 CD LYS A 29 34.758 25.280 8.900 1.00 0.00 C \n",
1129 "ATOM 224 CE LYS A 29 34.793 24.264 7.767 1.00 0.00 C \n",
1130 "ATOM 225 NZ LYS A 29 34.914 24.944 6.441 1.00 0.00 N \n",
1131 "ATOM 226 N ILE A 30 36.811 29.170 12.192 1.00 0.00 N \n",
1132 "ATOM 227 CA ILE A 30 36.731 30.570 12.645 1.00 0.00 C \n",
1133 "ATOM 228 C ILE A 30 38.148 30.981 13.069 1.00 0.00 C \n",
1134 "ATOM 229 O ILE A 30 38.544 32.150 12.856 1.00 0.00 O \n",
1135 "ATOM 230 CB ILE A 30 35.708 30.776 13.806 1.00 0.00 C \n",
1136 "ATOM 231 CG1 ILE A 30 34.228 30.630 13.319 1.00 0.00 C \n",
1137 "ATOM 232 CG2 ILE A 30 35.874 32.138 14.512 1.00 0.00 C \n",
1138 "ATOM 233 CD1 ILE A 30 33.284 30.504 14.552 1.00 0.00 C \n",
1139 "ATOM 234 N GLN A 31 38.883 30.110 13.713 1.00 0.00 N \n",
1140 "ATOM 235 CA GLN A 31 40.269 30.508 14.115 1.00 0.00 C \n",
1141 "ATOM 236 C GLN A 31 41.092 30.808 12.851 1.00 0.00 C \n",
1142 "ATOM 237 O GLN A 31 41.828 31.808 12.681 1.00 0.00 O \n",
1143 "ATOM 238 CB GLN A 31 40.996 29.399 14.865 1.00 0.00 C \n",
1144 "ATOM 239 CG GLN A 31 42.445 29.848 15.182 1.00 0.00 C \n",
1145 "ATOM 240 CD GLN A 31 43.090 28.828 16.095 1.00 0.00 C \n",
1146 "ATOM 241 OE1 GLN A 31 42.770 27.655 15.906 1.00 0.00 O \n",
1147 "ATOM 242 NE2 GLN A 31 43.898 29.252 17.050 1.00 0.00 N \n",
1148 "ATOM 243 N ASP A 32 41.001 29.878 11.931 1.00 0.00 N \n",
1149 "ATOM 244 CA ASP A 32 41.718 30.022 10.643 1.00 0.00 C \n",
1150 "ATOM 245 C ASP A 32 41.399 31.338 9.967 1.00 0.00 C \n",
1151 "ATOM 246 O ASP A 32 42.260 32.036 9.381 1.00 0.00 O \n",
1152 "ATOM 247 CB ASP A 32 41.398 28.780 9.810 1.00 0.00 C \n",
1153 "ATOM 248 CG ASP A 32 42.626 28.557 8.928 1.00 0.00 C \n",
1154 "ATOM 249 OD1 ASP A 32 43.666 28.262 9.539 1.00 0.00 O \n",
1155 "ATOM 250 OD2 ASP A 32 42.430 28.812 7.728 1.00 0.00 O \n",
1156 "ATOM 251 N LYS A 33 40.117 31.750 9.988 1.00 0.00 N \n",
1157 "ATOM 252 CA LYS A 33 39.808 32.994 9.233 1.00 0.00 C \n",
1158 "ATOM 253 C LYS A 33 39.837 34.271 9.995 1.00 0.00 C \n",
1159 "ATOM 254 O LYS A 33 40.164 35.323 9.345 1.00 0.00 O \n",
1160 "ATOM 255 CB LYS A 33 38.615 32.801 8.320 1.00 0.00 C \n",
1161 "ATOM 256 CG LYS A 33 37.220 32.822 8.827 1.00 0.00 C \n",
1162 "ATOM 257 CD LYS A 33 36.351 33.613 7.838 1.00 0.00 C \n",
1163 "ATOM 258 CE LYS A 33 36.322 32.944 6.477 1.00 0.00 C \n",
1164 "ATOM 259 NZ LYS A 33 35.768 33.945 5.489 1.00 0.00 N \n",
1165 "ATOM 260 N GLU A 34 39.655 34.335 11.285 1.00 0.00 N \n",
1166 "ATOM 261 CA GLU A 34 39.676 35.547 12.072 1.00 0.00 C \n",
1167 "ATOM 262 C GLU A 34 40.675 35.527 13.200 1.00 0.00 C \n",
1168 "ATOM 263 O GLU A 34 40.814 36.528 13.911 1.00 0.00 O \n",
1169 "ATOM 264 CB GLU A 34 38.290 35.814 12.698 1.00 0.00 C \n",
1170 "ATOM 265 CG GLU A 34 37.156 35.985 11.688 1.00 0.00 C \n",
1171 "ATOM 266 CD GLU A 34 37.192 37.361 11.033 1.00 0.00 C \n",
1172 "ATOM 267 OE1 GLU A 34 37.519 38.360 11.645 1.00 0.00 O \n",
1173 "ATOM 268 OE2 GLU A 34 36.861 37.320 9.822 1.00 0.00 O \n",
1174 "TER 269 GLU A 34 \n",
1175 "MASTER 0 0 0 0 0 0 0 0 268 1 0 0 \n",
1176 "END \n"
1177 ]
1178
1179
1180 self.strip_remarks(lines)
1181 for i in range(len(real_data)):
1182 self.assertEqual(real_data[i], lines[i])
1183
1184
1206
1207
1209 """Load the 'SSS-cluster4-new-test.xyz' XYZ file (using the internal structural object XYZ reader)."""
1210
1211
1212 path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'structures'
1213
1214
1215 self.interpreter.structure.read_xyz(file='SSS-cluster4-new-test.xyz', dir=path, read_model=[1])
1216
1217
1218 self.assertEqual(cdp.structure.structural_data[0].mol[0].mol_name, 'SSS-cluster4-new-test_mol1')
1219
1220
1221 self.interpreter.structure.load_spins('#SSS-cluster4-new-test_mol1@2')
1222 self.assertEqual(count_spins(), 1)
1223
1224
1225 a=return_spin('#SSS-cluster4-new-test_mol1@2')
1226 self.assertAlmostEqual(a.pos[0], -12.398)
1227 self.assertAlmostEqual(a.pos[1], -15.992)
1228 self.assertAlmostEqual(a.pos[2], 11.448)
1229
1230
1231
1232
1233
1234 self.interpreter.structure.load_spins()
1235
1236
1237 self.interpreter.interatom.define(spin_id1='@2', spin_id2='@10')
1238 self.interpreter.interatom.unit_vectors()
1239 self.assertAlmostEqual(cdp.interatomic[0].vector[0], -0.4102707)
1240 self.assertAlmostEqual(cdp.interatomic[0].vector[1], 0.62128879)
1241 self.assertAlmostEqual(cdp.interatomic[0].vector[2], -0.6675913)
1242
1243
1267
1268
1270 """Test the structure.rmsd user function."""
1271
1272
1273 self.interpreter.structure.add_model(model_num=1)
1274 self.interpreter.structure.add_model(model_num=2)
1275 self.interpreter.structure.add_model(model_num=4)
1276
1277
1278 self.assert_(hasattr(cdp, 'structure'))
1279 self.assert_(hasattr(cdp.structure, 'structural_data'))
1280 self.assertEqual(len(cdp.structure.structural_data), 3)
1281
1282
1283 self.interpreter.structure.add_atom(atom_name='A', res_name='UNK', res_num=1, pos=[[1., 0., -1.], [0., 0., 0.], [-1., 0., 1.]], element='S')
1284 self.interpreter.structure.add_atom(atom_name='A', res_name='UNK', res_num=2, pos=[[1., 2., -1.], [0., 2., 0.], [-1., 2., 1.]], element='S')
1285 self.interpreter.structure.add_atom(atom_name='A', res_name='UNK', res_num=3, pos=[[1., 20., -1.], [0., 20., 0.], [-1., 20., 1.]], element='S')
1286
1287
1288 self.assertEqual(cdp.structure.structural_data[0].mol[0].x, [1., 1., 1.])
1289 self.assertEqual(cdp.structure.structural_data[0].mol[0].y, [0., 2., 20.])
1290 self.assertEqual(cdp.structure.structural_data[0].mol[0].z, [-1., -1., -1.])
1291 self.assertEqual(cdp.structure.structural_data[1].mol[0].x, [0., 0., 0.])
1292 self.assertEqual(cdp.structure.structural_data[1].mol[0].y, [0., 2., 20.])
1293 self.assertEqual(cdp.structure.structural_data[1].mol[0].z, [0., 0., 0.])
1294 self.assertEqual(cdp.structure.structural_data[2].mol[0].x, [-1., -1., -1.])
1295 self.assertEqual(cdp.structure.structural_data[2].mol[0].y, [0., 2., 20.])
1296 self.assertEqual(cdp.structure.structural_data[2].mol[0].z, [1., 1., 1.])
1297
1298
1299 self.interpreter.structure.rmsd()
1300
1301
1302 self.assert_(hasattr(cdp.structure, 'rmsd'))
1303 self.assertAlmostEqual(cdp.structure.rmsd, 2./3*sqrt(2))
1304
1305
1307 """Test the structure.rmsd user function on the truncated ubiquitin ensemble."""
1308
1309
1310 path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'structures'
1311 self.interpreter.structure.read_pdb('trunc_ubi_pcs.pdb', dir=path)
1312
1313
1314 self.interpreter.structure.rmsd()
1315
1316
1317 self.assert_(hasattr(cdp.structure, 'rmsd'))
1318 self.assertAlmostEqual(cdp.structure.rmsd, 0.77282758781333061)
1319
1320
1322 """Test of the structure.superimpose user function, fitting to the first structure."""
1323
1324
1325 path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'frame_order'+sep+'cam'
1326
1327
1328 self.interpreter.structure.read_pdb('1J7P_1st_NH.pdb', dir=path, set_model_num=1, set_mol_name='CaM')
1329 self.interpreter.structure.read_pdb('1J7P_1st_NH_rot.pdb', dir=path, set_model_num=2, set_mol_name='CaM')
1330 self.interpreter.structure.read_pdb('1J7P_1st_NH.pdb', dir=path, set_model_num=3, set_mol_name='CaM')
1331
1332
1333 self.interpreter.structure.superimpose(method='fit to first', atom_id='@N,C,CA,O')
1334
1335
1336 model1 = cdp.structure.structural_data[0].mol[0]
1337 model2 = cdp.structure.structural_data[1].mol[0]
1338 model3 = cdp.structure.structural_data[2].mol[0]
1339 for i in range(len(model1.atom_name)):
1340
1341 self.assertAlmostEqual(model1.x[i], model2.x[i], 2)
1342 self.assertAlmostEqual(model1.y[i], model2.y[i], 2)
1343 self.assertAlmostEqual(model1.z[i], model2.z[i], 2)
1344
1345
1346 self.assertAlmostEqual(model1.x[i], model3.x[i], 2)
1347 self.assertAlmostEqual(model1.y[i], model3.y[i], 2)
1348 self.assertAlmostEqual(model1.z[i], model3.z[i], 2)
1349
1350
1352 """Test of the structure.superimpose user function, fitting to the mean structure."""
1353
1354
1355 path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'frame_order'+sep+'cam'
1356
1357
1358 self.interpreter.structure.read_pdb('1J7P_1st_NH.pdb', dir=path, set_model_num=1, set_mol_name='CaM')
1359 self.interpreter.structure.read_pdb('1J7P_1st_NH_rot.pdb', dir=path, set_model_num=2, set_mol_name='CaM')
1360
1361
1362 self.interpreter.structure.superimpose(method='fit to mean', atom_id='@N,C,CA,O')
1363
1364
1365 model1 = cdp.structure.structural_data[0].mol[0]
1366 model2 = cdp.structure.structural_data[1].mol[0]
1367 for i in range(len(model1.atom_name)):
1368 self.assertAlmostEqual(model1.x[i], model2.x[i], 2)
1369 self.assertAlmostEqual(model1.y[i], model2.y[i], 2)
1370 self.assertAlmostEqual(model1.z[i], model2.z[i], 2)
1371
1372
1374 """Second test of the structure.superimpose user function, fitting to the mean structure."""
1375
1376
1377 path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'frame_order'+sep+'cam'
1378
1379
1380 self.interpreter.structure.read_pdb('1J7P_1st_NH.pdb', dir=path, set_model_num=1, set_mol_name='CaM')
1381 self.interpreter.structure.read_pdb('1J7P_1st_NH.pdb', dir=path, set_model_num=2, set_mol_name='CaM')
1382 self.interpreter.structure.read_pdb('1J7P_1st_NH.pdb', dir=path, set_model_num=3, set_mol_name='CaM')
1383
1384
1385 self.interpreter.structure.translate([20.0, 0.0, 0.0], model=3)
1386
1387
1388 self.interpreter.structure.superimpose(models=[2, 3], method='fit to mean', atom_id='@N,C,CA,O')
1389
1390
1391 model1 = cdp.structure.structural_data[0].mol[0]
1392 model2 = cdp.structure.structural_data[1].mol[0]
1393 model3 = cdp.structure.structural_data[2].mol[0]
1394 for i in range(len(model1.atom_name)):
1395
1396 self.assertAlmostEqual(model1.x[i] + 10, model2.x[i], 2)
1397 self.assertAlmostEqual(model1.y[i], model2.y[i], 2)
1398 self.assertAlmostEqual(model1.z[i], model2.z[i], 2)
1399
1400
1401 self.assertAlmostEqual(model2.x[i], model3.x[i], 2)
1402 self.assertAlmostEqual(model2.y[i], model3.y[i], 2)
1403 self.assertAlmostEqual(model2.z[i], model3.z[i], 2)
1404
1405
1407 """Check the operation of the structure.web_of_motion user function using structural models 1 and 2 (of 3)."""
1408
1409
1410 path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'structures'
1411 self.interpreter.structure.read_pdb('web_of_motion.pdb', dir=path)
1412
1413
1414 file = DummyFileObject()
1415 self.interpreter.structure.web_of_motion(file=file, models=[1, 2])
1416
1417
1418 result = [
1419 "ATOM 1 N LEU A 4 9.464 -9.232 27.573 1.00 0.00 N ",
1420 "ATOM 2 N LEU A 4 9.211 -9.425 26.970 1.00 0.00 N ",
1421 "ATOM 3 H LEU A 4 8.575 -8.953 27.963 1.00 0.00 H ",
1422 "ATOM 4 H LEU A 4 9.085 -9.743 27.919 1.00 0.00 H ",
1423 "ATOM 5 CA LEU A 4 10.302 -8.195 26.930 1.00 0.00 C ",
1424 "ATOM 6 CA LEU A 4 10.077 -8.221 26.720 1.00 0.00 C ",
1425 "ATOM 7 CB LEU A 4 9.494 -7.221 26.051 1.00 0.00 C ",
1426 "ATOM 8 CB LEU A 4 9.297 -7.096 26.024 1.00 0.00 C ",
1427 "ATOM 9 CG LEU A 4 10.107 -5.862 25.665 1.00 0.00 C ",
1428 "ATOM 10 CG LEU A 4 10.061 -5.803 25.679 1.00 0.00 C ",
1429 "ATOM 11 CD1 LEU A 4 11.182 -6.007 24.608 1.00 0.00 C ",
1430 "ATOM 12 CD1 LEU A 4 11.029 -6.002 24.507 1.00 0.00 C ",
1431 "ATOM 13 CD2 LEU A 4 9.036 -4.875 25.171 1.00 0.00 C ",
1432 "ATOM 14 CD2 LEU A 4 9.120 -4.618 25.384 1.00 0.00 C ",
1433 "ATOM 15 C LEU A 4 10.999 -7.436 28.046 1.00 0.00 C ",
1434 "ATOM 16 C LEU A 4 10.625 -7.721 28.047 1.00 0.00 C ",
1435 "TER 17 LEU A 4 ",
1436 "CONECT 1 2 ",
1437 "CONECT 2 1 ",
1438 "CONECT 3 4 ",
1439 "CONECT 4 3 ",
1440 "CONECT 5 6 ",
1441 "CONECT 6 5 ",
1442 "CONECT 7 8 ",
1443 "CONECT 8 7 ",
1444 "CONECT 9 10 ",
1445 "CONECT 10 9 ",
1446 "CONECT 11 12 ",
1447 "CONECT 12 11 ",
1448 "CONECT 13 14 ",
1449 "CONECT 14 13 ",
1450 "CONECT 15 16 ",
1451 "CONECT 16 15 ",
1452 "MASTER 0 0 0 0 0 0 0 0 16 1 16 0 ",
1453 "END "
1454 ]
1455
1456
1457 lines = file.readlines()
1458 self.strip_remarks(lines)
1459 for i in range(len(lines)):
1460 self.assertEqual(result[i]+'\n', lines[i])
1461
1462
1464 """Check the operation of the structure.web_of_motion user function using structural models 1 and 3 (of 3)."""
1465
1466
1467 path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'structures'
1468 self.interpreter.structure.read_pdb('web_of_motion.pdb', dir=path)
1469
1470
1471 file = DummyFileObject()
1472 self.interpreter.structure.web_of_motion(file=file, models=[1, 3])
1473
1474
1475 result = [
1476 "ATOM 1 N LEU A 4 9.464 -9.232 27.573 1.00 0.00 N ",
1477 "ATOM 2 N LEU A 4 7.761 -6.392 27.161 1.00 0.00 N ",
1478 "ATOM 3 H LEU A 4 8.575 -8.953 27.963 1.00 0.00 H ",
1479 "ATOM 4 H LEU A 4 7.278 -6.195 28.026 1.00 0.00 H ",
1480 "ATOM 5 CA LEU A 4 10.302 -8.195 26.930 1.00 0.00 C ",
1481 "ATOM 6 CA LEU A 4 9.256 -6.332 27.183 1.00 0.00 C ",
1482 "ATOM 7 CB LEU A 4 9.494 -7.221 26.051 1.00 0.00 C ",
1483 "ATOM 8 CB LEU A 4 9.799 -5.331 26.144 1.00 0.00 C ",
1484 "ATOM 9 CG LEU A 4 10.107 -5.862 25.665 1.00 0.00 C ",
1485 "ATOM 10 CG LEU A 4 10.293 -5.882 24.803 1.00 0.00 C ",
1486 "ATOM 11 CD1 LEU A 4 11.182 -6.007 24.608 1.00 0.00 C ",
1487 "ATOM 12 CD1 LEU A 4 9.404 -6.984 24.274 1.00 0.00 C ",
1488 "ATOM 13 CD2 LEU A 4 9.036 -4.875 25.171 1.00 0.00 C ",
1489 "ATOM 14 CD2 LEU A 4 10.355 -4.772 23.792 1.00 0.00 C ",
1490 "ATOM 15 C LEU A 4 10.999 -7.436 28.046 1.00 0.00 C ",
1491 "ATOM 16 C LEU A 4 9.816 -6.033 28.572 1.00 0.00 C ",
1492 "TER 17 LEU A 4 ",
1493 "CONECT 1 2 ",
1494 "CONECT 2 1 ",
1495 "CONECT 3 4 ",
1496 "CONECT 4 3 ",
1497 "CONECT 5 6 ",
1498 "CONECT 6 5 ",
1499 "CONECT 7 8 ",
1500 "CONECT 8 7 ",
1501 "CONECT 9 10 ",
1502 "CONECT 10 9 ",
1503 "CONECT 11 12 ",
1504 "CONECT 12 11 ",
1505 "CONECT 13 14 ",
1506 "CONECT 14 13 ",
1507 "CONECT 15 16 ",
1508 "CONECT 16 15 ",
1509 "MASTER 0 0 0 0 0 0 0 0 16 1 16 0 ",
1510 "END "
1511 ]
1512
1513
1514 lines = file.readlines()
1515 self.strip_remarks(lines)
1516 for i in range(len(lines)):
1517 self.assertEqual(result[i]+'\n', lines[i])
1518
1519
1521 """Check the operation of the structure.web_of_motion user function using all structural models."""
1522
1523
1524 path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'structures'
1525 self.interpreter.structure.read_pdb('web_of_motion.pdb', dir=path)
1526
1527
1528 file = DummyFileObject()
1529 self.interpreter.structure.web_of_motion(file=file)
1530
1531
1532 result = [
1533 "ATOM 1 N LEU A 4 9.464 -9.232 27.573 1.00 0.00 N ",
1534 "ATOM 2 N LEU A 4 9.211 -9.425 26.970 1.00 0.00 N ",
1535 "ATOM 3 N LEU A 4 7.761 -6.392 27.161 1.00 0.00 N ",
1536 "ATOM 4 H LEU A 4 8.575 -8.953 27.963 1.00 0.00 H ",
1537 "ATOM 5 H LEU A 4 9.085 -9.743 27.919 1.00 0.00 H ",
1538 "ATOM 6 H LEU A 4 7.278 -6.195 28.026 1.00 0.00 H ",
1539 "ATOM 7 CA LEU A 4 10.302 -8.195 26.930 1.00 0.00 C ",
1540 "ATOM 8 CA LEU A 4 10.077 -8.221 26.720 1.00 0.00 C ",
1541 "ATOM 9 CA LEU A 4 9.256 -6.332 27.183 1.00 0.00 C ",
1542 "ATOM 10 CB LEU A 4 9.494 -7.221 26.051 1.00 0.00 C ",
1543 "ATOM 11 CB LEU A 4 9.297 -7.096 26.024 1.00 0.00 C ",
1544 "ATOM 12 CB LEU A 4 9.799 -5.331 26.144 1.00 0.00 C ",
1545 "ATOM 13 CG LEU A 4 10.107 -5.862 25.665 1.00 0.00 C ",
1546 "ATOM 14 CG LEU A 4 10.061 -5.803 25.679 1.00 0.00 C ",
1547 "ATOM 15 CG LEU A 4 10.293 -5.882 24.803 1.00 0.00 C ",
1548 "ATOM 16 CD1 LEU A 4 11.182 -6.007 24.608 1.00 0.00 C ",
1549 "ATOM 17 CD1 LEU A 4 11.029 -6.002 24.507 1.00 0.00 C ",
1550 "ATOM 18 CD1 LEU A 4 9.404 -6.984 24.274 1.00 0.00 C ",
1551 "ATOM 19 CD2 LEU A 4 9.036 -4.875 25.171 1.00 0.00 C ",
1552 "ATOM 20 CD2 LEU A 4 9.120 -4.618 25.384 1.00 0.00 C ",
1553 "ATOM 21 CD2 LEU A 4 10.355 -4.772 23.792 1.00 0.00 C ",
1554 "ATOM 22 C LEU A 4 10.999 -7.436 28.046 1.00 0.00 C ",
1555 "ATOM 23 C LEU A 4 10.625 -7.721 28.047 1.00 0.00 C ",
1556 "ATOM 24 C LEU A 4 9.816 -6.033 28.572 1.00 0.00 C ",
1557 "TER 25 LEU A 4 ",
1558 "CONECT 1 2 3 ",
1559 "CONECT 2 1 3 ",
1560 "CONECT 3 1 2 ",
1561 "CONECT 4 5 6 ",
1562 "CONECT 5 4 6 ",
1563 "CONECT 6 4 5 ",
1564 "CONECT 7 8 9 ",
1565 "CONECT 8 7 9 ",
1566 "CONECT 9 7 8 ",
1567 "CONECT 10 11 12 ",
1568 "CONECT 11 10 12 ",
1569 "CONECT 12 10 11 ",
1570 "CONECT 13 14 15 ",
1571 "CONECT 14 13 15 ",
1572 "CONECT 15 13 14 ",
1573 "CONECT 16 17 18 ",
1574 "CONECT 17 16 18 ",
1575 "CONECT 18 16 17 ",
1576 "CONECT 19 20 21 ",
1577 "CONECT 20 19 21 ",
1578 "CONECT 21 19 20 ",
1579 "CONECT 22 23 24 ",
1580 "CONECT 23 22 24 ",
1581 "CONECT 24 22 23 ",
1582 "MASTER 0 0 0 0 0 0 0 0 24 1 24 0 ",
1583 "END "
1584 ]
1585
1586
1587 lines = file.readlines()
1588 self.strip_remarks(lines)
1589 for i in range(len(lines)):
1590 self.assertEqual(result[i]+'\n', lines[i])
1591