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Update Python wf
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‎biobb_wf_flexdyn/python/workflow.py

Lines changed: 9 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -3,6 +3,7 @@
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import time
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import argparse
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import zipfile
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import os
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from pathlib import Path, PurePath
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from biobb_common.configuration import settings
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from biobb_common.tools import file_utils as fu
@@ -52,11 +53,17 @@ def main(config, system=None):
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global_log.info("step3_cpptraj_mask: Generating the reduced (coarse-grained) structure (alpha carbons)")
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cpptraj_mask(**global_paths["step3_cpptraj_mask"], properties=global_prop["step3_cpptraj_mask"])
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56+
props = global_prop["step4_concoord_dist"]
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props["env_vars_dict"]["CONCOORDLIB"] = os.getenv('CONDA_PREFIX') + '/share/concoord/lib'
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5559
global_log.info("step4_concoord_dist: CONCOORD dist")
56-
concoord_dist(**global_paths["step4_concoord_dist"], properties=global_prop["step4_concoord_dist"])
60+
concoord_dist(**global_paths["step4_concoord_dist"], properties=props)
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props = global_prop["step5_concoord_disco"]
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props["env_vars_dict"]["CONCOORDLIB"] = os.getenv('CONDA_PREFIX') + '/share/concoord/lib'
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5865
global_log.info("step5_concoord_disco: CONCOORD disco")
59-
concoord_disco(**global_paths["step5_concoord_disco"], properties=global_prop["step5_concoord_disco"])
66+
concoord_disco(**global_paths["step5_concoord_disco"], properties=props)
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global_log.info("step6_cpptraj_rms: RMSd distribution of the generated ensemble (CONCOORD)")
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cpptraj_rms(**global_paths["step6_cpptraj_rms"], properties=global_prop["step6_cpptraj_rms"])

‎biobb_wf_flexdyn/tests/python/reference/step0_extract_model/structure_model.pdb

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‎biobb_wf_flexdyn/tests/python/reference/step10_cpptraj_convert/structure_prody_anm_traj.trr

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‎biobb_wf_flexdyn/tests/python/reference/step11_bd_run/structure_flexserv_bd_ensemble.log

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@@ -0,0 +1,2 @@
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Applied 12.0000000 A cutoff, 2919 pairs
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Beginning trajectory for 214 atoms

‎biobb_wf_flexdyn/tests/python/reference/step11_bd_run/structure_flexserv_bd_ensemble.mdcrd

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‎biobb_wf_flexdyn/tests/python/reference/step12_cpptraj_rms/structure_flexserv_bd_rmsd.dat

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#Frame RMSD_00004
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1 0.1050
3+
2 0.2308
4+
3 0.3452
5+
4 0.4421
6+
5 0.5211
7+
6 0.5725
8+
7 0.6057
9+
8 0.6472
10+
9 0.7035
11+
10 0.7458
12+
11 0.7740
13+
12 0.8024
14+
13 0.8214
15+
14 0.8362
16+
15 0.8521
17+
16 0.8651
18+
17 0.8648
19+
18 0.8701
20+
19 0.8724
21+
20 0.8858
22+
21 0.9055
23+
22 0.9236
24+
23 0.9345
25+
24 0.9429
26+
25 0.9582
27+
26 0.9658
28+
27 0.9697
29+
28 0.9729
30+
29 0.9797
31+
30 0.9900
32+
31 1.0087
33+
32 1.0343
34+
33 1.0561
35+
34 1.0766
36+
35 1.0951
37+
36 1.1040
38+
37 1.1115
39+
38 1.1187
40+
39 1.1191
41+
40 1.1188
42+
41 1.1316
43+
42 1.1407
44+
43 1.1435
45+
44 1.1633
46+
45 1.1794
47+
46 1.1787
48+
47 1.1779
49+
48 1.1708
50+
49 1.1596
51+
50 1.1395
52+
51 1.1117
53+
52 1.0858
54+
53 1.0722
55+
54 1.0633
56+
55 1.0538
57+
56 1.0493
58+
57 1.0463
59+
58 1.0412
60+
59 1.0249
61+
60 1.0128
62+
61 1.0073
63+
62 1.0053
64+
63 1.0086
65+
64 1.0073
66+
65 1.0060
67+
66 1.0088
68+
67 1.0078
69+
68 1.0099
70+
69 1.0060
71+
70 0.9934
72+
71 0.9926
73+
72 0.9955
74+
73 1.0073
75+
74 1.0092
76+
75 0.9957
77+
76 0.9882
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77 0.9755
79+
78 0.9681
80+
79 0.9633
81+
80 0.9631
82+
81 0.9570
83+
82 0.9474
84+
83 0.9408
85+
84 0.9398
86+
85 0.9370
87+
86 0.9310
88+
87 0.9339
89+
88 0.9363
90+
89 0.9275
91+
90 0.9190
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91 0.9137
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92 0.9144
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93 0.9200
95+
94 0.9409
96+
95 0.9702
97+
96 0.9873
98+
97 0.9999
99+
98 1.0180
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99 1.0431
101+
100 1.0575
102+
101 1.0656
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102 1.0679
104+
103 1.0638
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104 1.0534
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105 1.0419
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106 1.0268
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107 1.0102
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108 0.9858
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109 0.9665
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110 0.9492
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111 0.9405
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112 0.9374
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113 0.9342
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114 0.9351
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115 0.9474
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116 0.9565
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117 0.9684
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118 0.9733
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119 0.9761
121+
120 0.9705
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121 0.9687
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122 0.9790
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123 0.9844
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124 1.0011
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125 1.0185
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126 1.0248
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127 1.0239
129+
128 1.0381
130+
129 1.0565
131+
130 1.0632
132+
131 1.0557
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132 1.0473
134+
133 1.0366
135+
134 1.0138
136+
135 1.0037
137+
136 1.0007
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137 0.9953
139+
138 0.9948
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139 0.9911
141+
140 0.9877
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141 0.9950
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142 1.0044
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143 1.0174
145+
144 1.0285
146+
145 1.0262
147+
146 1.0315
148+
147 1.0366
149+
148 1.0384
150+
149 1.0473
151+
150 1.0648
152+
151 1.0660
153+
152 1.0591
154+
153 1.0345
155+
154 1.0142
156+
155 0.9922
157+
156 0.9936
158+
157 1.0088
159+
158 1.0323
160+
159 1.0414
161+
160 1.0444
162+
161 1.0472
163+
162 1.0445
164+
163 1.0370
165+
164 1.0318
166+
165 1.0346
167+
166 1.0365
168+
167 1.0486
169+
168 1.0589
170+
169 1.0687
171+
170 1.0831
172+
171 1.1072
173+
172 1.1155
174+
173 1.1144
175+
174 1.1099
176+
175 1.1091
177+
176 1.1149
178+
177 1.1241
179+
178 1.1297
180+
179 1.1198
181+
180 1.1027
182+
181 1.0893
183+
182 1.0769
184+
183 1.0705
185+
184 1.0621
186+
185 1.0616
187+
186 1.0635
188+
187 1.0489
189+
188 1.0408
190+
189 1.0353
191+
190 1.0411
192+
191 1.0357
193+
192 1.0331
194+
193 1.0192
195+
194 1.0091
196+
195 1.0033
197+
196 1.0137
198+
197 1.0377
199+
198 1.0571
200+
199 1.0697
201+
200 1.0826
202+
201 1.0912
203+
202 1.0936
204+
203 1.0988
205+
204 1.1080
206+
205 1.1118
207+
206 1.1203
208+
207 1.1295
209+
208 1.1222
210+
209 1.1134
211+
210 1.1094
212+
211 1.1009
213+
212 1.0924
214+
213 1.0775
215+
214 1.0718
216+
215 1.0640
217+
216 1.0630
218+
217 1.0642
219+
218 1.0674
220+
219 1.0626
221+
220 1.0647
222+
221 1.0700
223+
222 1.0831
224+
223 1.0929
225+
224 1.1108
226+
225 1.1240
227+
226 1.1203
228+
227 1.1189
229+
228 1.1199
230+
229 1.1162
231+
230 1.1128
232+
231 1.1108
233+
232 1.1135
234+
233 1.1199
235+
234 1.1270
236+
235 1.1310
237+
236 1.1534
238+
237 1.1791
239+
238 1.1821
240+
239 1.1816
241+
240 1.1822
242+
241 1.1779
243+
242 1.1736
244+
243 1.1701
245+
244 1.1585
246+
245 1.1544
247+
246 1.1492
248+
247 1.1487
249+
248 1.1515
250+
249 1.1504
251+
250 1.1474
252+
251 1.1555
253+
252 1.1655
254+
253 1.1662
255+
254 1.1631
256+
255 1.1559
257+
256 1.1404
258+
257 1.1333
259+
258 1.1311
260+
259 1.1235
261+
260 1.1229
262+
261 1.1316
263+
262 1.1392
264+
263 1.1507
265+
264 1.1467
266+
265 1.1442
267+
266 1.1544
268+
267 1.1733
269+
268 1.1884
270+
269 1.1974
271+
270 1.1998
272+
271 1.1927
273+
272 1.1795
274+
273 1.1729
275+
274 1.1605
276+
275 1.1474
277+
276 1.1407
278+
277 1.1411
279+
278 1.1375
280+
279 1.1274
281+
280 1.1021
282+
281 1.0848
283+
282 1.0700
284+
283 1.0484
285+
284 1.0282
286+
285 1.0134
287+
286 1.0098
288+
287 1.0069
289+
288 1.0026
290+
289 1.0165
291+
290 1.0345
292+
291 1.0621
293+
292 1.0895
294+
293 1.1031
295+
294 1.1185
296+
295 1.1292
297+
296 1.1259
298+
297 1.1184
299+
298 1.1219
300+
299 1.1451
301+
300 1.1744

‎biobb_wf_flexdyn/tests/python/reference/step12_cpptraj_rms/structure_flexserv_bd_traj_fitted.trr

777 KB
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