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12 from tempfile import mktemp
13 import os
14 from MMTK import Units
15
16
17 template = {'REF' : {}, 'NEW' : {}}
18
19 template['REF']['title'] = 'Velocity Auto-Correlation Function'
20 template['REF']['trajectory'] = ['../TrajectoryTest1.nc']
21 template['REF']['log_file'] = 'logfile.log'
22 template['REF']['output_files'] = {'vacf': 'test.plot'}
23 template['REF']['projection_vector'] = None
24 template['REF']['units_length'] = Units.nm
25
26 template['NEW']['projection'] = None
27 template['NEW']['trajectory'] = os.path.join(nmoldyn_package_path, 'Tests', 'TrajectoryTest1.nc')
28 template['NEW']['vacf'] = mktemp(suffix = '_VACF.nc', prefix = 'nMOLDYN_')
29 template['NEW']['normalize'] = 'No'
30 template['NEW']['pyroserver'] = 'No'
31 template['NEW']['analysis'] = 'CartesianVelocityAutoCorrelationFunction_serial(self.testParameters)'
32
33 test = []
34
35
36 test.append({'REF' : {}, 'NEW' : {}})
37
38
39 test[-1]['REF']['time_info'] = (0, 49, 1)
40 test[-1]['REF']['weights'] = "mass"
41 test[-1]['REF']['atoms_pdb'] = '../TrajectoryTest1_2.pdb'
42 test[-1]['REF']['deuter'] = None
43
44
45 test[-1]['NEW']['timeinfo'] = '1:49:1'
46 test[-1]['NEW']['weights'] = 'mass'
47 test[-1]['NEW']['subset'] = 'filename %s' % os.path.join(nmoldyn_package_path,"Tests",'TrajectoryTest1_2.nms')
48 test[-1]['NEW']['deuteration'] = None
49 test[-1]['NEW']['differentiation'] = 0
50
51
52
53 test.append({'REF' : {}, 'NEW' : {}})
54
55 test[-1]['REF']['time_info'] = (0, 49, 4)
56 test[-1]['REF']['weights'] = "none"
57 test[-1]['REF']['atoms'] = {'Protein.0': ["BackBone"]}
58 test[-1]['REF']['deuter'] = None
59
60
61 test[-1]['NEW']['timeinfo'] = '1:49:4'
62 test[-1]['NEW']['weights'] = 'equal'
63 test[-1]['NEW']['subset'] = 'objectname P892 misc backbone'
64 test[-1]['NEW']['deuteration'] = None
65 test[-1]['NEW']['differentiation'] = 0
66
67
68
69 test.append({'REF' : {}, 'NEW' : {}})
70
71 test[-1]['REF']['time_info'] = (8, 29, 2)
72 test[-1]['REF']['weights'] = 'none'
73 test[-1]['REF']['atoms'] = {'Protein.0': ['Methyl']}
74 test[-1]['REF']['deuter'] = None
75
76
77 test[-1]['NEW']['timeinfo'] = '9:29:2'
78 test[-1]['NEW']['weights'] = 'equal'
79 test[-1]['NEW']['subset'] = 'objectname P892 chemfragment methyl'
80 test[-1]['NEW']['deuteration'] = None
81 test[-1]['NEW']['differentiation'] = 0
82
83
84
85 test.append({'REF' : {}, 'NEW' : {}})
86
87 test[-1]['REF']['time_info'] = (16, 39, 4)
88 test[-1]['REF']['weights'] = 'none'
89 test[-1]['REF']['atoms'] = {'Protein.0': ['*']}
90 test[-1]['REF']['deuter'] = {'Protein.0': ['Methyl']}
91
92
93 test[-1]['NEW']['timeinfo'] = '17:39:4'
94 test[-1]['NEW']['weights'] = 'equal'
95 test[-1]['NEW']['subset'] = 'objectname P892 chainname *'
96 test[-1]['NEW']['deuteration'] = 'objectname P892 chemfragment methyl'
97 test[-1]['NEW']['differentiation'] = 0
98
99
100
101 test.append({'REF' : {}, 'NEW' : {}})
102
103 test[-1]['REF']['time_info'] = (1, 20, 2)
104 test[-1]['REF']['weights'] = 'none'
105 test[-1]['REF']['atoms'] = {'Protein.0': ['Oxygen','Nitrogen']}
106 test[-1]['REF']['deuter'] = None
107
108
109 test[-1]['NEW']['timeinfo'] = '2:20:2'
110 test[-1]['NEW']['weights'] = 'equal'
111 test[-1]['NEW']['subset'] = 'objectname P892 atomelement oxygen,nitrogen'
112 test[-1]['NEW']['deuteration'] = None
113 test[-1]['NEW']['differentiation'] = 0
114
115
116
117 test.append({'REF' : {}, 'NEW' : {}})
118
119 test[-1]['REF']['time_info'] = (1, 20, 2)
120 test[-1]['REF']['weights'] = 'mass'
121 test[-1]['REF']['atoms'] = {'Protein.0': ['Nitrogen']}
122 test[-1]['REF']['deuter'] = None
123
124
125 test[-1]['NEW']['timeinfo'] = "2:20:2"
126 test[-1]['NEW']['weights'] = 'mass'
127 test[-1]['NEW']['subset'] = 'objectname P892 atomelement nitrogen'
128 test[-1]['NEW']['deuteration'] = None
129 test[-1]['NEW']['differentiation'] = 0
130
131
132
133 test.append({'REF' : {}, 'NEW' : {}})
134
135 test[-1]['REF']['time_info'] = (1, 20, 2)
136 test[-1]['REF']['weights'] = 'none'
137 test[-1]['REF']['atoms'] = {'Protein.0': ['Carbon']}
138 test[-1]['REF']['deuter'] = None
139
140
141 test[-1]['NEW']['timeinfo'] = "2:20:2"
142 test[-1]['NEW']['weights'] = 'equal'
143 test[-1]['NEW']['subset'] = 'objectname P892 atomelement carbon'
144 test[-1]['NEW']['deuteration'] = None
145 test[-1]['NEW']['differentiation'] = 0
146
147
148
149 test.append({'REF' : {}, 'NEW' : {}})
150
151 test[-1]['REF']['time_info'] = (1, 20, 2)
152 test[-1]['REF']['weights'] = 'mass'
153 test[-1]['REF']['atoms'] = {'Protein.0': ['Sulfur']}
154 test[-1]['REF']['deuter'] = None
155
156
157 test[-1]['NEW']['timeinfo'] = "2:20:2"
158 test[-1]['NEW']['weights'] = 'mass'
159 test[-1]['NEW']['subset'] = 'objectname P892 atomelement sulfur'
160 test[-1]['NEW']['deuteration'] = None
161 test[-1]['NEW']['differentiation'] = 1
162
163
164
165 test.append({'REF' : {}, 'NEW' : {}})
166
167 test[-1]['REF']['time_info'] = (1, 20, 2)
168 test[-1]['REF']['weights'] = 'none'
169 test[-1]['REF']['atoms'] = {'Protein.0': ['Hydrogen']}
170 test[-1]['REF']['deuter'] = None
171
172
173 test[-1]['NEW']['timeinfo'] = "2:20:2"
174 test[-1]['NEW']['weights'] = 'equal'
175 test[-1]['NEW']['subset'] = 'objectname P892 atomelement hydrogen'
176 test[-1]['NEW']['deuteration'] = None
177 test[-1]['NEW']['differentiation'] = 1
178
179
180
181 test.append({'REF' : {}, 'NEW' : {}})
182
183 test[-1]['REF']['time_info'] = (1, 20, 2)
184 test[-1]['REF']['weights'] = 'none'
185 test[-1]['REF']['atoms'] = {'Protein.0': ['SideChain']}
186 test[-1]['REF']['deuter'] = {'Protein.0': ['Hydrogen']}
187
188
189 test[-1]['NEW']['timeinfo'] = "2:20:2"
190 test[-1]['NEW']['weights'] = 'equal'
191 test[-1]['NEW']['subset'] = 'objectname P892 misc sidechains'
192 test[-1]['NEW']['deuteration'] = 'objectname P892 atomelement hydrogen'
193 test[-1]['NEW']['differentiation'] = 1
194
195
196
197 test.append({'REF' : {}, 'NEW' : {}})
198
199 test[-1]['REF']['time_info'] = (1, 20, 2)
200 test[-1]['REF']['weights'] = 'none'
201 test[-1]['REF']['atoms'] = {'Protein.0': ['SideChain']}
202 test[-1]['REF']['deuter'] = {'Protein.0': ['SideChain']}
203
204
205 test[-1]['NEW']['timeinfo'] = "2:20:2"
206 test[-1]['NEW']['weights'] = 'equal'
207 test[-1]['NEW']['subset'] = 'objectname P892 misc sidechains'
208 test[-1]['NEW']['deuteration'] = 'objectname P892 misc sidechains'
209 test[-1]['NEW']['differentiation'] = 1
210
211
212
213 test.append({'REF' : {}, 'NEW' : {}})
214
215 test[-1]['REF']['time_info'] = (1, 20, 2)
216 test[-1]['REF']['weights'] = 'none'
217 test[-1]['REF']['atoms'] = {'Protein.0': ['BackBone','SideChain']}
218 test[-1]['REF']['deuter'] = {'Protein.0': ['SideChain']}
219
220
221 test[-1]['NEW']['timeinfo'] = "2:20:2"
222 test[-1]['NEW']['weights'] = 'equal'
223 test[-1]['NEW']['subset'] = 'objectname P892 misc backbone,sidechains'
224 test[-1]['NEW']['deuteration'] = 'objectname P892 misc sidechains'
225 test[-1]['NEW']['differentiation'] = 1
226
227
228
229 test.append({'REF' : {}, 'NEW' : {}})
230
231 test[-1]['REF']['time_info'] = (1, 20, 2)
232 test[-1]['REF']['weights'] = 'none'
233 test[-1]['REF']['atoms'] = {'Protein.0': ['Oxygen', 'Nitrogen', 'Carbon', 'Sulfur', 'Hydrogen']}
234 test[-1]['REF']['deuter'] = {'Protein.0': ['BackBone']}
235
236
237 test[-1]['NEW']['timeinfo'] = "2:20:2"
238 test[-1]['NEW']['weights'] = 'equal'
239 test[-1]['NEW']['subset'] = 'objectname P892 atomelement carbon,nitrogen,oxygen,sulfur,hydrogen'
240 test[-1]['NEW']['deuteration'] = 'objectname P892 misc backbone'
241 test[-1]['NEW']['differentiation'] = 1
242
243
244
245 test.append({'REF' : {}, 'NEW' : {}})
246
247 test[-1]['REF']['time_info'] = (1, 40, 2)
248 test[-1]['REF']['weights'] = 'none'
249 test[-1]['REF']['atoms'] = {'Protein.0': ['C_alpha']}
250 test[-1]['REF']['deuter'] = None
251
252
253 test[-1]['NEW']['timeinfo'] = "2:40:2"
254 test[-1]['NEW']['weights'] = 'equal'
255 test[-1]['NEW']['subset'] = 'objectname P892 chemfragment c_alphas'
256 test[-1]['NEW']['deuteration'] = None
257 test[-1]['NEW']['differentiation'] = 1
258