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14 from tempfile import mktemp
15 import os
16 from MMTK import Units
17
18
19 template = {'REF' : {}, 'NEW' : {}}
20
21 template['REF']['title'] = 'Angular Velocity Autocorrelation Function'
22 template['REF']['trajectory'] = ['../TrajectoryTest1.nc']
23 template['REF']['log_file'] = 'logfile.log'
24 template['REF']['output_files'] = {'avacf' : 'test.plot'}
25 template['REF']['projection_vector'] = None
26 template['REF']['differentiation'] = 'fast'
27 template['REF']['time_steps'] = None
28
29 template['NEW']['projection'] = None
30 template['NEW']['trajectory'] = os.path.join(nmoldyn_package_path, 'Tests', 'TrajectoryTest1.nc')
31 template['NEW']['avacf'] = mktemp(suffix = '_AVACF.nc', prefix = 'nMOLDYN_')
32 template['NEW']['differentiation'] = 1
33 template['NEW']['stepwiserbt'] = 'No'
34 template['NEW']['pyroserver'] = 'No'
35 template['NEW']['analysis'] = 'AngularVelocityAutoCorrelationFunction_serial(self.testParameters)'
36
37 test = []
38
39
40 test.append({'REF' : {}, 'NEW' : {}})
41
42 test[-1]['REF']['time_info'] = (0, 19, 1)
43 test[-1]['REF']['groups'] = [{'Protein.0 BackBone': ['*']}]
44 test[-1]['REF']['reference'] = [{'Protein.0 BackBone': {'*': None}}]
45
46
47
48 test[-1]['NEW']['timeinfo'] = '1:19:1'
49 test[-1]['NEW']['group'] = 'group1 groupinglevel residue objectname P892 misc backbone'
50 test[-1]['NEW']['referenceframe'] = 1
51
52
53
54 test.append({'REF' : {}, 'NEW' : {}})
55
56 test[-1]['REF']['time_info'] = (0, 49, 4)
57 test[-1]['REF']['groups'] = [{'Protein.0 Methyl': ['*']}]
58 test[-1]['REF']['reference'] = [{'Protein.0 Methyl': {'*': None}}]
59
60
61 test[-1]['NEW']['timeinfo'] = '1:49:4'
62 test[-1]['NEW']['group'] = 'group1 groupinglevel methyl objectname P892 chemfragment methyl'
63 test[-1]['NEW']['referenceframe'] = 1
64
65
66
67 test.append({'REF' : {}, 'NEW' : {}})
68
69 test[-1]['REF']['time_info'] = (8, 29, 2)
70 test[-1]['REF']['groups'] = [{'Protein.0 Methyl': ['*']}]
71 test[-1]['REF']['reference'] = [{'Protein.0 Methyl': {'*': None}}]
72
73
74 test[-1]['NEW']['timeinfo'] = '9:29:2'
75 test[-1]['NEW']['group'] = 'group1 groupinglevel methyl objectname P892 chemfragment methyl'
76 test[-1]['NEW']['referenceframe'] = 9
77
78
79
80 test.append({'REF' : {}, 'NEW' : {}})
81
82 test[-1]['REF']['time_info'] = (16, 39, 4)
83 test[-1]['REF']['groups'] = [{'Protein.0 SideChain': ['alanine',\
84 'glycine',\
85 'proline',\
86 'glutamine',\
87 'arginine',\
88 'glutamic_acid',\
89 'leucine',\
90 'serine',\
91 'valine',\
92 'methionine',\
93 'isoleucine',\
94 'asparagine',\
95 'phenylalanine',\
96 'threonine',\
97 'tyrosine']}]
98 test[-1]['REF']['reference'] = [{'Protein.0 SideChain': {'alanine': None, 'glycine': None, 'proline': None, 'glutamine': None, 'arginine': None, 'glutamic_acid': None, 'leucine': None, 'serine': None, 'valine': None, 'methionine': None, 'isoleucine': None, 'asparagine': None, 'phenylalanine': None, 'threonine': None, 'tyrosine': None}}]
99
100
101 test[-1]['NEW']['timeinfo'] = '17:39:4'
102 test[-1]['NEW']['group'] = 'group1 groupinglevel residue objectname P892 restype Ala,Gly,Pro,Gln,Arg,Glu,Leu,Ser,Val,Met,Ile,Asn,Phe,Thr,Tyr'
103 test[-1]['NEW']['referenceframe'] = 17
104
105
106 test.append({'REF' : {}, 'NEW' : {}})
107
108 test[-1]['REF']['time_info'] = (1, 20, 2)
109 test[-1]['REF']['groups'] = [{'Protein.0 SideChain': ['aspartic_acid']}]
110 test[-1]['REF']['reference'] = [{'Protein.0 SideChain': {'aspartic_acid': None}}]
111
112
113 test[-1]['NEW']['timeinfo'] = '2:20:2'
114 test[-1]['NEW']['group'] = 'group1 groupinglevel residue objectname P892 restype Asp'
115 test[-1]['NEW']['referenceframe'] = 2
116
117
118 test.append({'REF' : {}, 'NEW' : {}})
119
120 test[-1]['REF']['time_info'] = (1, 20, 2)
121 test[-1]['REF']['groups'] = [{'Protein.0 SideChain': ['aspartic_acid']}]
122 test[-1]['REF']['reference'] = [{'Protein.0 SideChain': {'aspartic_acid': None}}]
123
124
125 test[-1]['NEW']['timeinfo'] = "2:20:2"
126 test[-1]['NEW']['group'] = 'group1 groupinglevel residue objectname P892 restype Asp'
127 test[-1]['NEW']['referenceframe'] = 2
128
129
130 test.append({'REF' : {}, 'NEW' : {}})
131
132 test[-1]['REF']['time_info'] = (1, 20, 2)
133 test[-1]['REF']['groups'] = [{'Protein.0 SideChain': ['valine']}]
134 test[-1]['REF']['reference'] = [{'Protein.0 SideChain': {'valine': None}}]
135
136
137 test[-1]['NEW']['timeinfo'] = "2:20:2"
138 test[-1]['NEW']['group'] = 'group1 groupinglevel residue objectname P892 restype Val'
139 test[-1]['NEW']['referenceframe'] = 2
140
141
142
143 test.append({'REF' : {}, 'NEW' : {}})
144
145 test[-1]['REF']['time_info'] = (1, 20, 2)
146 test[-1]['REF']['groups'] = [{'Protein.0 SideChain': ['valine']}]
147 test[-1]['REF']['reference'] = [{'Protein.0 SideChain': {'valine': None}}]
148
149
150 test[-1]['NEW']['timeinfo'] = "2:20:2"
151 test[-1]['NEW']['group'] = 'group1 groupinglevel residue objectname P892 restype Val'
152 test[-1]['NEW']['referenceframe'] = 2
153
154
155
156 test.append({'REF' : {}, 'NEW' : {}})
157
158 test[-1]['REF']['time_info'] = (1, 28, 2)
159 test[-1]['REF']['groups'] = [{'Protein.0 SideChain': ['alanine']}]
160 test[-1]['REF']['reference'] = [{'Protein.0 SideChain': {'alanine': None}}]
161
162
163 test[-1]['NEW']['timeinfo'] = "2:28:2"
164 test[-1]['NEW']['group'] = 'group1 groupinglevel residue objectname P892 restype Ala'
165 test[-1]['NEW']['referenceframe'] = 2
166
167
168
169 test.append({'REF' : {}, 'NEW' : {}})
170
171 test[-1]['REF']['time_info'] = (1, 33, 2)
172 test[-1]['REF']['groups'] = [{'Protein.0 SideChain': ['proline','glutamine','glutamic_acid']}]
173 test[-1]['REF']['reference'] = [{'Protein.0 SideChain': {'proline': None,'glutamine': None,'glutamic_acid': None}}]
174
175
176 test[-1]['NEW']['timeinfo'] = "2:33:2"
177 test[-1]['NEW']['group'] = 'group1 groupinglevel residue objectname P892 restype Pro,Gln,Glu'
178 test[-1]['NEW']['referenceframe'] = 2
179
180
181
182 test.append({'REF' : {}, 'NEW' : {}})
183
184 test[-1]['REF']['time_info'] = (1, 20, 2)
185 test[-1]['REF']['groups'] = [{'Protein.0 SideChain': ['lysine','glycine','arginine']}]
186 test[-1]['REF']['reference'] = [{'Protein.0 SideChain': {'lysine': None,'glycine': None,'arginine': None}}]
187
188
189 test[-1]['NEW']['timeinfo'] = "2:20:2"
190 test[-1]['NEW']['group'] = 'group1 groupinglevel residue objectname P892 restype Lys,Gly,Arg'
191 test[-1]['NEW']['referenceframe'] = 2
192
193
194
195 test.append({'REF' : {}, 'NEW' : {}})
196
197 test[-1]['REF']['time_info'] = (1, 40, 2)
198 test[-1]['REF']['groups'] = [{'Protein.0 SideChain': ['leucine','methionine']}]
199 test[-1]['REF']['reference'] = [{'Protein.0 SideChain': {'leucine': None,'methionine': None}}]
200
201
202 test[-1]['NEW']['timeinfo'] = "2:40:2"
203 test[-1]['NEW']['group'] = 'group1 groupinglevel residue objectname P892 restype Leu,Met'
204 test[-1]['NEW']['referenceframe'] = 2
205
206
207
208 test.append({'REF' : {}, 'NEW' : {}})
209
210 test[-1]['REF']['trajectory'] = ['../TrajectoryTest3.nc']
211 test[-1]['REF']['time_info'] = (3, 20, 2)
212 test[-1]['REF']['groups'] = [{'Water': ['*']}]
213 test[-1]['REF']['reference'] = [{'Water': {'*': None}}]
214
215
216 test[-1]['NEW']['trajectory'] = os.path.join(nmoldyn_package_path, 'Tests', 'TrajectoryTest3.nc')
217 test[-1]['NEW']['timeinfo'] = "4:20:2"
218 test[-1]['NEW']['group'] = 'group1 groupinglevel cluster objectname AC3 atomelement *'
219 test[-1]['NEW']['referenceframe'] = 4
220
221
222
223 test.append({'REF' : {}, 'NEW' : {}})
224
225 test[-1]['REF']['trajectory'] = ['../TrajectoryTest3.nc']
226 test[-1]['REF']['time_info'] = (1, 45, 3)
227 test[-1]['REF']['groups'] = [{'Water': ['*']}]
228 test[-1]['REF']['reference'] = [{'Water': {'*': None}}]
229
230
231 test[-1]['NEW']['trajectory'] = os.path.join(nmoldyn_package_path, 'Tests', 'TrajectoryTest3.nc')
232 test[-1]['NEW']['timeinfo'] = "2:45:3"
233 test[-1]['NEW']['group'] = 'group1 groupinglevel cluster objectname AC3 atomelement *'
234 test[-1]['NEW']['referenceframe'] = 2
235