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24 from os import sep
25
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27 from base_classes import SystemTestCase
28 from data import Relax_data_store; ds = Relax_data_store()
29 from status import Status; status = Status()
30
31
33 """Class for testing the sequence functions."""
34
36 """Set up for all the functional tests."""
37
38
39 self.interpreter.pipe.create('mf', 'mf')
40
41
43 """Load all aspartic acid atoms from the single residue in a loaded protein PDB file."""
44
45
46 self.interpreter.structure.read_pdb(file='Ap4Aase_res1-12.pdb', dir=status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'structures', read_model=1)
47
48
49 self.interpreter.structure.load_spins(spin_id=':ASP')
50
51
52 self.assertEqual(len(cdp.mol), 1)
53 self.assertEqual(cdp.mol[0].name, 'Ap4Aase_res1-12_mol1')
54 self.assertEqual(len(cdp.mol[0].res), 1)
55
56
57 self.assertEqual(cdp.mol[0].res[0].num, 7)
58 self.assertEqual(cdp.mol[0].res[0].name, 'ASP')
59 self.assertEqual(len(cdp.mol[0].res[0].spin), 12)
60 self.assertEqual(cdp.mol[0].res[0].spin[0].num, 91)
61 self.assertEqual(cdp.mol[0].res[0].spin[0].name, 'N')
62 self.assertEqual(cdp.mol[0].res[0].spin[1].num, 92)
63 self.assertEqual(cdp.mol[0].res[0].spin[1].name, 'H')
64 self.assertEqual(cdp.mol[0].res[0].spin[2].num, 93)
65 self.assertEqual(cdp.mol[0].res[0].spin[2].name, 'CA')
66 self.assertEqual(cdp.mol[0].res[0].spin[3].num, 94)
67 self.assertEqual(cdp.mol[0].res[0].spin[3].name, 'HA')
68 self.assertEqual(cdp.mol[0].res[0].spin[4].num, 95)
69 self.assertEqual(cdp.mol[0].res[0].spin[4].name, 'CB')
70 self.assertEqual(cdp.mol[0].res[0].spin[5].num, 96)
71 self.assertEqual(cdp.mol[0].res[0].spin[5].name, '1HB')
72 self.assertEqual(cdp.mol[0].res[0].spin[6].num, 97)
73 self.assertEqual(cdp.mol[0].res[0].spin[6].name, '2HB')
74 self.assertEqual(cdp.mol[0].res[0].spin[7].num, 99)
75 self.assertEqual(cdp.mol[0].res[0].spin[7].name, 'CG')
76 self.assertEqual(cdp.mol[0].res[0].spin[8].num, 100)
77 self.assertEqual(cdp.mol[0].res[0].spin[8].name, 'OD1')
78 self.assertEqual(cdp.mol[0].res[0].spin[9].num, 101)
79 self.assertEqual(cdp.mol[0].res[0].spin[9].name, 'OD2')
80 self.assertEqual(cdp.mol[0].res[0].spin[10].num, 102)
81 self.assertEqual(cdp.mol[0].res[0].spin[10].name, 'C')
82 self.assertEqual(cdp.mol[0].res[0].spin[11].num, 103)
83 self.assertEqual(cdp.mol[0].res[0].spin[11].name, 'O')
84
85
87 """Load the glycine backbone amide N and Ca spins from a loaded protein PDB file."""
88
89
90 self.interpreter.structure.read_pdb(file='Ap4Aase_res1-12.pdb', dir=status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'structures', read_model=1)
91
92
93 self.interpreter.structure.load_spins(spin_id=':GLY@N')
94
95
96 self.interpreter.structure.load_spins(spin_id=':GLY@CA')
97
98
99 self.assertEqual(len(cdp.mol), 1)
100 self.assertEqual(cdp.mol[0].name, 'Ap4Aase_res1-12_mol1')
101 self.assertEqual(len(cdp.mol[0].res), 3)
102
103
104 self.assertEqual(cdp.mol[0].res[0].num, 1)
105 self.assertEqual(cdp.mol[0].res[0].name, 'GLY')
106 self.assertEqual(len(cdp.mol[0].res[0].spin), 2)
107 self.assertEqual(cdp.mol[0].res[0].spin[0].num, 1)
108 self.assertEqual(cdp.mol[0].res[0].spin[0].name, 'N')
109 self.assertEqual(cdp.mol[0].res[0].spin[1].num, 2)
110 self.assertEqual(cdp.mol[0].res[0].spin[1].name, 'CA')
111
112
113 self.assertEqual(cdp.mol[0].res[1].num, 4)
114 self.assertEqual(cdp.mol[0].res[1].name, 'GLY')
115 self.assertEqual(len(cdp.mol[0].res[1].spin), 2)
116 self.assertEqual(cdp.mol[0].res[1].spin[0].num, 51)
117 self.assertEqual(cdp.mol[0].res[1].spin[0].name, 'N')
118 self.assertEqual(cdp.mol[0].res[1].spin[1].num, 53)
119 self.assertEqual(cdp.mol[0].res[1].spin[1].name, 'CA')
120
121
122 self.assertEqual(cdp.mol[0].res[2].num, 12)
123 self.assertEqual(cdp.mol[0].res[2].name, 'GLY')
124 self.assertEqual(len(cdp.mol[0].res[2].spin), 2)
125 self.assertEqual(cdp.mol[0].res[2].spin[0].num, 167)
126 self.assertEqual(cdp.mol[0].res[2].spin[0].name, 'N')
127 self.assertEqual(cdp.mol[0].res[2].spin[1].num, 169)
128 self.assertEqual(cdp.mol[0].res[2].spin[1].name, 'CA')
129
130
132 """Load the glycine backbone amide N spins from a loaded protein PDB file."""
133
134
135 self.interpreter.structure.read_pdb(file='Ap4Aase_res1-12.pdb', dir=status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'structures', read_model=1)
136
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138 self.interpreter.structure.load_spins(spin_id=':GLY@N')
139
140
141 self.assertEqual(len(cdp.mol), 1)
142 self.assertEqual(cdp.mol[0].name, 'Ap4Aase_res1-12_mol1')
143 self.assertEqual(len(cdp.mol[0].res), 3)
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145
146 self.assertEqual(cdp.mol[0].res[0].num, 1)
147 self.assertEqual(cdp.mol[0].res[0].name, 'GLY')
148 self.assertEqual(len(cdp.mol[0].res[0].spin), 1)
149 self.assertEqual(cdp.mol[0].res[0].spin[0].num, 1)
150 self.assertEqual(cdp.mol[0].res[0].spin[0].name, 'N')
151
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153 self.assertEqual(cdp.mol[0].res[1].num, 4)
154 self.assertEqual(cdp.mol[0].res[1].name, 'GLY')
155 self.assertEqual(len(cdp.mol[0].res[1].spin), 1)
156 self.assertEqual(cdp.mol[0].res[1].spin[0].num, 51)
157 self.assertEqual(cdp.mol[0].res[1].spin[0].name, 'N')
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160 self.assertEqual(cdp.mol[0].res[2].num, 12)
161 self.assertEqual(cdp.mol[0].res[2].name, 'GLY')
162 self.assertEqual(len(cdp.mol[0].res[2].spin), 1)
163 self.assertEqual(cdp.mol[0].res[2].spin[0].num, 167)
164 self.assertEqual(cdp.mol[0].res[2].spin[0].name, 'N')
165
166
168 """Load the protein backbone amide N spins from a loaded PDB file."""
169
170
171 self.interpreter.structure.read_pdb(file='Ap4Aase_res1-12.pdb', dir=status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'structures', read_model=1)
172
173
174 self.interpreter.structure.load_spins(spin_id='@N')
175
176
177 self.assertEqual(len(cdp.mol), 1)
178 self.assertEqual(cdp.mol[0].name, 'Ap4Aase_res1-12_mol1')
179 self.assertEqual(len(cdp.mol[0].res), 12)
180
181
182 self.assertEqual(cdp.mol[0].res[0].num, 1)
183 self.assertEqual(cdp.mol[0].res[0].name, 'GLY')
184 self.assertEqual(len(cdp.mol[0].res[0].spin), 1)
185 self.assertEqual(cdp.mol[0].res[0].spin[0].num, 1)
186 self.assertEqual(cdp.mol[0].res[0].spin[0].name, 'N')
187
188
189 self.assertEqual(cdp.mol[0].res[1].num, 2)
190 self.assertEqual(cdp.mol[0].res[1].name, 'PRO')
191 self.assertEqual(len(cdp.mol[0].res[1].spin), 1)
192 self.assertEqual(cdp.mol[0].res[1].spin[0].num, 11)
193 self.assertEqual(cdp.mol[0].res[1].spin[0].name, 'N')
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195
196 self.assertEqual(cdp.mol[0].res[2].num, 3)
197 self.assertEqual(cdp.mol[0].res[2].name, 'LEU')
198 self.assertEqual(len(cdp.mol[0].res[2].spin), 1)
199 self.assertEqual(cdp.mol[0].res[2].spin[0].num, 28)
200 self.assertEqual(cdp.mol[0].res[2].spin[0].name, 'N')
201
202
203 self.assertEqual(cdp.mol[0].res[3].num, 4)
204 self.assertEqual(cdp.mol[0].res[3].name, 'GLY')
205 self.assertEqual(len(cdp.mol[0].res[3].spin), 1)
206 self.assertEqual(cdp.mol[0].res[3].spin[0].num, 51)
207 self.assertEqual(cdp.mol[0].res[3].spin[0].name, 'N')
208
209
210 self.assertEqual(cdp.mol[0].res[4].num, 5)
211 self.assertEqual(cdp.mol[0].res[4].name, 'SER')
212 self.assertEqual(len(cdp.mol[0].res[4].spin), 1)
213 self.assertEqual(cdp.mol[0].res[4].spin[0].num, 59)
214 self.assertEqual(cdp.mol[0].res[4].spin[0].name, 'N')
215
216
217 self.assertEqual(cdp.mol[0].res[5].num, 6)
218 self.assertEqual(cdp.mol[0].res[5].name, 'MET')
219 self.assertEqual(len(cdp.mol[0].res[5].spin), 1)
220 self.assertEqual(cdp.mol[0].res[5].spin[0].num, 71)
221 self.assertEqual(cdp.mol[0].res[5].spin[0].name, 'N')
222
223
224 self.assertEqual(cdp.mol[0].res[6].num, 7)
225 self.assertEqual(cdp.mol[0].res[6].name, 'ASP')
226 self.assertEqual(len(cdp.mol[0].res[6].spin), 1)
227 self.assertEqual(cdp.mol[0].res[6].spin[0].num, 91)
228 self.assertEqual(cdp.mol[0].res[6].spin[0].name, 'N')
229
230
231 self.assertEqual(cdp.mol[0].res[7].num, 8)
232 self.assertEqual(cdp.mol[0].res[7].name, 'SER')
233 self.assertEqual(len(cdp.mol[0].res[7].spin), 1)
234 self.assertEqual(cdp.mol[0].res[7].spin[0].num, 104)
235 self.assertEqual(cdp.mol[0].res[7].spin[0].name, 'N')
236
237
238 self.assertEqual(cdp.mol[0].res[8].num, 9)
239 self.assertEqual(cdp.mol[0].res[8].name, 'PRO')
240 self.assertEqual(len(cdp.mol[0].res[8].spin), 1)
241 self.assertEqual(cdp.mol[0].res[8].spin[0].num, 116)
242 self.assertEqual(cdp.mol[0].res[8].spin[0].name, 'N')
243
244
245 self.assertEqual(cdp.mol[0].res[9].num, 10)
246 self.assertEqual(cdp.mol[0].res[9].name, 'PRO')
247 self.assertEqual(len(cdp.mol[0].res[9].spin), 1)
248 self.assertEqual(cdp.mol[0].res[9].spin[0].num, 133)
249 self.assertEqual(cdp.mol[0].res[9].spin[0].name, 'N')
250
251
252 self.assertEqual(cdp.mol[0].res[10].num, 11)
253 self.assertEqual(cdp.mol[0].res[10].name, 'GLU')
254 self.assertEqual(len(cdp.mol[0].res[10].spin), 1)
255 self.assertEqual(cdp.mol[0].res[10].spin[0].num, 150)
256 self.assertEqual(cdp.mol[0].res[10].spin[0].name, 'N')
257
258
259 self.assertEqual(cdp.mol[0].res[11].num, 12)
260 self.assertEqual(cdp.mol[0].res[11].name, 'GLY')
261 self.assertEqual(len(cdp.mol[0].res[11].spin), 1)
262 self.assertEqual(cdp.mol[0].res[11].spin[0].num, 167)
263 self.assertEqual(cdp.mol[0].res[11].spin[0].name, 'N')
264
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271