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24 from os import sep
25 import sys
26 from tempfile import mktemp
27 try:
28 from hashlib import md5
29 except ImportError:
30 from md5 import new as md5
31
32
33 from data import Relax_data_store; ds = Relax_data_store()
34 from generic_fns import pipes
35 from relax_io import delete
36 from status import Status; status = Status()
37 from test_suite.unit_tests.base_classes import UnitTestCase
38
39
41 """Base class for the tests of both the 'prompt.sequence' and 'generic_fns.sequence' modules.
42
43 This base class also contains many shared unit tests.
44 """
45
47 """Set up for all the molecule unit tests."""
48
49
50 ds.add(pipe_name='orig', pipe_type='mf')
51
52
53 ds.tmpfile = mktemp()
54
55
56 self.Ap4Aase_res_num = [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, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165]
57 self.Ap4Aase_res_name = ['GLY', 'PRO', 'LEU', 'GLY', 'SER', 'MET', 'ASP', 'SER', 'PRO', 'PRO', 'GLU', 'GLY', 'TYR', 'ARG', 'ARG', 'ASN', 'VAL', 'GLY', 'ILE', 'CYS', 'LEU', 'MET', 'ASN', 'ASN', 'ASP', 'LYS', 'LYS', 'ILE', 'PHE', 'ALA', 'ALA', 'SER', 'ARG', 'LEU', 'ASP', 'ILE', 'PRO', 'ASP', 'ALA', 'TRP', 'GLN', 'MET', 'PRO', 'GLN', 'GLY', 'GLY', 'ILE', 'ASP', 'GLU', 'GLY', 'GLU', 'ASP', 'PRO', 'ARG', 'ASN', 'ALA', 'ALA', 'ILE', 'ARG', 'GLU', 'LEU', 'ARG', 'GLU', 'GLU', 'THR', 'GLY', 'VAL', 'THR', 'SER', 'ALA', 'GLU', 'VAL', 'ILE', 'ALA', 'GLU', 'VAL', 'PRO', 'TYR', 'TRP', 'LEU', 'THR', 'TYR', 'ASP', 'PHE', 'PRO', 'PRO', 'LYS', 'VAL', 'ARG', 'GLU', 'LYS', 'LEU', 'ASN', 'ILE', 'GLN', 'TRP', 'GLY', 'SER', 'ASP', 'TRP', 'LYS', 'GLY', 'GLN', 'ALA', 'GLN', 'LYS', 'TRP', 'PHE', 'LEU', 'PHE', 'LYS', 'PHE', 'THR', 'GLY', 'GLN', 'ASP', 'GLN', 'GLU', 'ILE', 'ASN', 'LEU', 'LEU', 'GLY', 'ASP', 'GLY', 'SER', 'GLU', 'LYS', 'PRO', 'GLU', 'PHE', 'GLY', 'GLU', 'TRP', 'SER', 'TRP', 'VAL', 'THR', 'PRO', 'GLU', 'GLN', 'LEU', 'ILE', 'ASP', 'LEU', 'THR', 'VAL', 'GLU', 'PHE', 'LYS', 'LYS', 'PRO', 'VAL', 'TYR', 'LYS', 'GLU', 'VAL', 'LEU', 'SER', 'VAL', 'PHE', 'ALA', 'PRO', 'HIS', 'LEU']
58
59
61 """Test the copying of an amino acid sequence.
62
63 The functions tested are generic_fns.sequence.copy() and prompt.sequence.copy().
64 """
65
66
67 dp_orig = pipes.get_pipe('orig')
68
69
70 dp_orig.mol[0].res[0].num = 1
71 dp_orig.mol[0].res[0].name = 'GLY'
72 dp_orig.mol[0].res.add_item('PRO', 2)
73 dp_orig.mol[0].res.add_item('LEU', 3)
74 dp_orig.mol[0].res.add_item('GLY', 4)
75 dp_orig.mol[0].res.add_item('SER', 5)
76
77
78 dp_orig.mol[0].res[2].spin[0].test = True
79
80
81 ds.add(pipe_name='new', pipe_type='mf')
82 dp_new = pipes.get_pipe('new')
83
84
85 self.sequence_fns.copy('orig')
86
87
88 self.assertEqual(dp_new.mol[0].res[0].num, 1)
89 self.assertEqual(dp_new.mol[0].res[0].name, 'GLY')
90 self.assertEqual(dp_new.mol[0].res[1].num, 2)
91 self.assertEqual(dp_new.mol[0].res[1].name, 'PRO')
92 self.assertEqual(dp_new.mol[0].res[2].num, 3)
93 self.assertEqual(dp_new.mol[0].res[2].name, 'LEU')
94 self.assertEqual(dp_new.mol[0].res[3].num, 4)
95 self.assertEqual(dp_new.mol[0].res[3].name, 'GLY')
96 self.assertEqual(dp_new.mol[0].res[4].num, 5)
97 self.assertEqual(dp_new.mol[0].res[4].name, 'SER')
98
99
100 self.assert_(not hasattr(dp_new.mol[0].res[2].spin[0], 'test'))
101
102
104 """Test the display of an amino acid sequence.
105
106 The functions tested are generic_fns.sequence.display() and prompt.sequence.display().
107 """
108
109
110 dp_orig = pipes.get_pipe('orig')
111
112
113 dp_orig.mol[0].res[0].num = 1
114 dp_orig.mol[0].res[0].name = 'GLY'
115 dp_orig.mol[0].res.add_item('PRO', 2)
116 dp_orig.mol[0].res.add_item('LEU', 3)
117 dp_orig.mol[0].res.add_item('GLY', 4)
118 dp_orig.mol[0].res.add_item('SER', 5)
119
120
121 self.sequence_fns.display(res_num_flag=True, res_name_flag=True)
122
123
125 """Test the reading of the amino acid sequence out of a protein NOE data file.
126
127 The functions tested are generic_fns.sequence.read() and prompt.sequence.read().
128 """
129
130
131 self.sequence_fns.read(file='Ap4Aase.Noe.600.bz2', dir=status.install_path+sep+'test_suite'+sep+'shared_data'+sep+'relaxation_data', res_num_col=1, res_name_col=2)
132
133
134 dp = pipes.get_pipe('orig')
135
136
137 for i in xrange(len(self.Ap4Aase_res_num)):
138 self.assertEqual(dp.mol[0].res[i].num, self.Ap4Aase_res_num[i])
139 self.assertEqual(dp.mol[0].res[i].name, self.Ap4Aase_res_name[i])
140
141
143 """Test the writing of an amino acid sequence.
144
145 The functions tested are generic_fns.sequence.write() and prompt.sequence.write().
146 """
147
148
149 dp_orig = pipes.get_pipe('orig')
150
151
152 dp_orig.mol[0].res[0].num = 1
153 dp_orig.mol[0].res[0].name = 'GLY'
154 dp_orig.mol[0].res.add_item('PRO', 2)
155 dp_orig.mol[0].res.add_item('LEU', 3)
156 dp_orig.mol[0].res.add_item('GLY', 4)
157 dp_orig.mol[0].res.add_item('SER', 5)
158
159
160 self.sequence_fns.write(file=ds.tmpfile, res_num_flag=True, res_name_flag=True)
161
162
163 file = open(ds.tmpfile)
164
165
166 file_md5 = md5()
167 file_md5.update(file.read())
168
169
170 self.assertEqual(file_md5.digest(), '\xc7\xa0\xd0i\xa54|f\xcc1\xd6|\xe7\x82#:')
171
172
173 file.close()
174