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9
10 from tempfile import mktemp
11 import os
12 from MMTK import Units
13
14
15 template = {'REF' : {}, 'NEW' : {}}
16
17 template['REF']['title'] = 'Mean-Square Displacement'
18 template['REF']['trajectory'] = ['../TrajectoryTest1.nc']
19 template['REF']['log_file'] = 'logfile.log'
20 template['REF']['output_files'] = {'msd': 'test.plot'}
21 template['REF']['projection_vector'] = None
22 template['REF']['units_length'] = Units.nm
23
24 template['NEW']['pyroserver'] = 'monoprocessor'
25 template['NEW']['projection'] = None
26 template['NEW']['trajectory'] = os.path.join(nmoldyn_package_path, 'Tests', 'TrajectoryTest1.nc')
27 template['NEW']['msd'] = mktemp(suffix = '_MSD.nc', prefix = 'nMOLDYN_')
28 template['NEW']['analysis'] = 'MeanSquareDisplacement_serial(self.testParameters)'
29
30 test = []
31
32
33 test.append({'REF' : {}, 'NEW' : {}})
34
35
36 test[-1]['REF']['time_info'] = (0, 49, 1)
37 test[-1]['REF']['weights'] = "mass"
38 test[-1]['REF']['atoms_pdb'] = '../TrajectoryTest1_1.pdb'
39 test[-1]['REF']['deuter'] = None
40
41
42 test[-1]['NEW']['timeinfo'] = '1:49:1'
43 test[-1]['NEW']['weights'] = 'mass'
44 test[-1]['NEW']['subset'] = 'filename %s' % os.path.join(nmoldyn_package_path,"Tests",'TrajectoryTest1_1.nms')
45 test[-1]['NEW']['deuteration'] = None
46
47
48
49 test.append({'REF' : {}, 'NEW' : {}})
50
51
52 test[-1]['REF']['time_info'] = (0, 49, 4)
53 test[-1]['REF']['weights'] = "none"
54 test[-1]['REF']['atoms'] = {'Protein.0': ["BackBone"]}
55 test[-1]['REF']['deuter'] = None
56
57
58 test[-1]['NEW']['timeinfo'] = '1:49:4'
59 test[-1]['NEW']['weights'] = 'equal'
60 test[-1]['NEW']['subset'] = 'objectname P892 misc backbone'
61 test[-1]['NEW']['deuteration'] = None
62
63
64
65 test.append({'REF' : {}, 'NEW' : {}})
66
67
68 test[-1]['REF']['time_info'] = (8, 29, 2)
69 test[-1]['REF']['weights'] = 'none'
70 test[-1]['REF']['atoms'] = {'Protein.0': ['Methyl']}
71 test[-1]['REF']['deuter'] = None
72
73
74 test[-1]['NEW']['timeinfo'] = '9:29:2'
75 test[-1]['NEW']['weights'] = 'equal'
76 test[-1]['NEW']['subset'] = 'objectname P892 chemfragment methyl'
77 test[-1]['NEW']['deuteration'] = None
78
79
80
81 test.append({'REF' : {}, 'NEW' : {}})
82
83
84 test[-1]['REF']['time_info'] = (16, 39, 4)
85 test[-1]['REF']['weights'] = 'none'
86 test[-1]['REF']['atoms'] = {'Protein.0': ['*']}
87 test[-1]['REF']['deuter'] = {'Protein.0': ['Methyl']}
88
89
90 test[-1]['NEW']['timeinfo'] = '17:39:4'
91 test[-1]['NEW']['weights'] = 'equal'
92 test[-1]['NEW']['subset'] = 'objectname P892 chainname *'
93 test[-1]['NEW']['deuteration'] = 'objectname P892 chemfragment methyl'
94
95
96
97 test.append({'REF' : {}, 'NEW' : {}})
98
99
100 test[-1]['REF']['time_info'] = (1, 20, 2)
101 test[-1]['REF']['weights'] = 'none'
102 test[-1]['REF']['atoms'] = {'Protein.0': ['Oxygen','Nitrogen']}
103 test[-1]['REF']['deuter'] = None
104
105
106 test[-1]['NEW']['timeinfo'] = '2:20:2'
107 test[-1]['NEW']['weights'] = 'equal'
108 test[-1]['NEW']['subset'] = 'objectname P892 atomelement oxygen,nitrogen'
109 test[-1]['NEW']['deuteration'] = None
110
111
112
113 test.append({'REF' : {}, 'NEW' : {}})
114
115 test[-1]['REF']['time_info'] = (1, 20, 2)
116 test[-1]['REF']['weights'] = 'mass'
117 test[-1]['REF']['atoms'] = {'Protein.0': ['Nitrogen']}
118 test[-1]['REF']['deuter'] = None
119
120
121 test[-1]['NEW']['timeinfo'] = "2:20:2"
122 test[-1]['NEW']['weights'] = 'mass'
123 test[-1]['NEW']['subset'] = 'objectname P892 atomelement nitrogen'
124 test[-1]['NEW']['deuteration'] = None
125
126
127
128 test.append({'REF' : {}, 'NEW' : {}})
129
130 test[-1]['REF']['time_info'] = (1, 20, 2)
131 test[-1]['REF']['weights'] = 'none'
132 test[-1]['REF']['atoms'] = {'Protein.0': ['Carbon']}
133 test[-1]['REF']['deuter'] = None
134
135
136 test[-1]['NEW']['timeinfo'] = "2:20:2"
137 test[-1]['NEW']['weights'] = 'equal'
138 test[-1]['NEW']['subset'] = 'objectname P892 atomelement carbon'
139 test[-1]['NEW']['deuteration'] = None
140
141
142
143 test.append({'REF' : {}, 'NEW' : {}})
144
145 test[-1]['REF']['time_info'] = (1, 20, 2)
146 test[-1]['REF']['weights'] = 'mass'
147 test[-1]['REF']['atoms'] = {'Protein.0': ['Sulfur']}
148 test[-1]['REF']['deuter'] = None
149
150
151 test[-1]['NEW']['timeinfo'] = "2:20:2"
152 test[-1]['NEW']['weights'] = 'mass'
153 test[-1]['NEW']['subset'] = 'objectname P892 atomelement sulfur'
154 test[-1]['NEW']['deuteration'] = None
155
156
157
158 test.append({'REF' : {}, 'NEW' : {}})
159
160 test[-1]['REF']['time_info'] = (1, 20, 2)
161 test[-1]['REF']['weights'] = 'none'
162 test[-1]['REF']['atoms'] = {'Protein.0': ['Hydrogen']}
163 test[-1]['REF']['deuter'] = None
164
165
166 test[-1]['NEW']['timeinfo'] = "2:20:2"
167 test[-1]['NEW']['weights'] = 'equal'
168 test[-1]['NEW']['subset'] = 'objectname P892 atomelement hydrogen'
169 test[-1]['NEW']['deuteration'] = None
170
171
172
173 test.append({'REF' : {}, 'NEW' : {}})
174
175 test[-1]['REF']['time_info'] = (1, 20, 2)
176 test[-1]['REF']['weights'] = 'incoherent'
177 test[-1]['REF']['atoms'] = {'Protein.0': ['SideChain']}
178 test[-1]['REF']['deuter'] = {'Protein.0': ['Hydrogen']}
179
180
181 test[-1]['NEW']['timeinfo'] = "2:20:2"
182 test[-1]['NEW']['weights'] = 'incoherent'
183 test[-1]['NEW']['subset'] = 'objectname P892 misc sidechains'
184 test[-1]['NEW']['deuteration'] = 'objectname P892 atomelement hydrogen'
185
186
187
188 test.append({'REF' : {}, 'NEW' : {}})
189
190 test[-1]['REF']['time_info'] = (1, 20, 2)
191 test[-1]['REF']['weights'] = 'none'
192 test[-1]['REF']['atoms'] = {'Protein.0': ['SideChain']}
193 test[-1]['REF']['deuter'] = {'Protein.0': ['SideChain']}
194
195
196 test[-1]['NEW']['timeinfo'] = "2:20:2"
197 test[-1]['NEW']['weights'] = 'equal'
198 test[-1]['NEW']['subset'] = 'objectname P892 misc sidechains'
199 test[-1]['NEW']['deuteration'] = 'objectname P892 misc sidechains'
200
201
202
203 test.append({'REF' : {}, 'NEW' : {}})
204
205 test[-1]['REF']['time_info'] = (1, 20, 2)
206 test[-1]['REF']['weights'] = 'none'
207 test[-1]['REF']['atoms'] = {'Protein.0': ['BackBone','SideChain']}
208 test[-1]['REF']['deuter'] = {'Protein.0': ['SideChain']}
209
210
211 test[-1]['NEW']['timeinfo'] = "2:20:2"
212 test[-1]['NEW']['weights'] = 'equal'
213 test[-1]['NEW']['subset'] = 'objectname P892 misc backbone,sidechains'
214 test[-1]['NEW']['deuteration'] = 'objectname P892 misc sidechains'
215
216
217
218 test.append({'REF' : {}, 'NEW' : {}})
219
220 test[-1]['REF']['time_info'] = (1, 20, 2)
221 test[-1]['REF']['weights'] = 'incoherent'
222 test[-1]['REF']['atoms'] = {'Protein.0': ['Oxygen', 'Nitrogen', 'Carbon', 'Sulfur', 'Hydrogen']}
223 test[-1]['REF']['deuter'] = {'Protein.0': ['BackBone']}
224
225
226 test[-1]['NEW']['timeinfo'] = "2:20:2"
227 test[-1]['NEW']['weights'] = 'incoherent'
228 test[-1]['NEW']['subset'] = 'objectname P892 atomelement carbon,nitrogen,oxygen,sulfur,hydrogen'
229 test[-1]['NEW']['deuteration'] = 'objectname P892 misc backbone'
230
231
232
233 test.append({'REF' : {}, 'NEW' : {}})
234
235 test[-1]['REF']['time_info'] = (1, 40, 2)
236 test[-1]['REF']['weights'] = 'none'
237 test[-1]['REF']['atoms'] = {'Protein.0': ['C_alpha']}
238 test[-1]['REF']['deuter'] = None
239
240
241 test[-1]['NEW']['timeinfo'] = "2:40:2"
242 test[-1]['NEW']['weights'] = 'equal'
243 test[-1]['NEW']['subset'] = 'objectname P892 chemfragment c_alphas'
244 test[-1]['NEW']['deuteration'] = None
245