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Merge pull request #406 from carlocamilloni/new_distances
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regtest reset and removed indexing from generate_LJ
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@carlocamilloni
carlocamilloni authored Apr 12, 2024
2 parents fd3698b + 59f711c commit af0a919
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Showing 13 changed files with 15,116 additions and 15,165 deletions.
5 changes: 1 addition & 4 deletions src/multiego/ensemble.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1556,10 +1556,6 @@ def generate_LJ(meGO_ensemble, train_dataset, check_dataset, parameters):
# will be the repulsive strength
meGO_LJ.loc[(meGO_LJ["epsilon"] < 0.0), "sigma"] = (-meGO_LJ["epsilon"]) ** (1.0 / 12.0)

# Here we are reindexing like before
meGO_LJ[["idx_ai", "idx_aj"]] = meGO_LJ[["ai", "aj"]]
meGO_LJ.set_index(["idx_ai", "idx_aj"], inplace=True)

# add a flag to identify learned contacts
meGO_LJ["learned"] = 1

Expand All @@ -1568,6 +1564,7 @@ def generate_LJ(meGO_ensemble, train_dataset, check_dataset, parameters):
if parameters.symmetry:
meGO_LJ_sym = apply_symmetries(meGO_ensemble, meGO_LJ, symmetries, parameters)
meGO_LJ = pd.concat([meGO_LJ, meGO_LJ_sym])
meGO_LJ.reset_index(inplace=True)

# meGO consistency checks
consistency_checks(meGO_LJ)
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6 changes: 0 additions & 6 deletions test/test_inputs/abetaref/ref/topol.top
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Expand Up @@ -1698,7 +1698,6 @@ ABeta 3
63 64 67 69 1 gd_45
64 67 69 70 1 gd_14
67 69 70 71 1 gd_49
67 69 70 71 1 gd_50
69 70 71 73 1 gd_48
69 70 71 73 1 gd_51
70 71 73 74 1 gd_14
Expand Down Expand Up @@ -1808,7 +1807,6 @@ ABeta 3
198 199 203 205 1 gd_45b
199 203 205 206 1 gd_14
203 205 206 207 1 gd_49
203 205 206 207 1 gd_50
205 206 207 209 1 gd_48
205 206 207 209 1 gd_51
206 207 209 210 1 gd_14
Expand All @@ -1835,7 +1833,6 @@ ABeta 3
226 227 228 229 1 gd_34
224 230 232 233 1 gd_14
230 232 233 234 1 gd_49
230 232 233 234 1 gd_50
232 233 234 236 1 gd_48
232 233 234 236 1 gd_51
233 234 236 237 1 gd_14
Expand All @@ -1859,7 +1856,6 @@ ABeta 3
250 251 252 254 1 gd_34
250 255 257 258 1 gd_14
255 257 258 259 1 gd_49
255 257 258 259 1 gd_50
257 258 259 261 1 gd_48
257 258 259 261 1 gd_51
258 259 261 262 1 gd_14
Expand All @@ -1885,12 +1881,10 @@ ABeta 3
277 278 282 284 1 gd_45b
278 282 284 285 1 gd_14
282 284 285 286 1 gd_49
282 284 285 286 1 gd_50
284 285 286 288 1 gd_48
284 285 286 288 1 gd_51
285 286 288 289 1 gd_14
286 288 289 290 1 gd_49
286 288 289 290 1 gd_50
288 289 290 292 1 gd_48
288 289 290 292 1 gd_51
289 290 292 293 1 gd_14
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4 changes: 0 additions & 4 deletions test/test_inputs/gpref/reference/topol.top
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Expand Up @@ -2302,7 +2302,6 @@ GB_1_Protein 3
62 63 64 66 1 gd_40
62 67 69 70 1 gd_14
67 69 70 71 1 gd_49
67 69 70 71 1 gd_50
69 70 71 73 1 gd_48
69 70 71 73 1 gd_51
70 71 73 74 1 gd_14
Expand Down Expand Up @@ -2338,7 +2337,6 @@ GB_1_Protein 3
100 101 102 103 1 gd_34
98 104 106 107 1 gd_14
104 106 107 108 1 gd_49
104 106 107 108 1 gd_50
106 107 108 110 1 gd_48
106 107 108 110 1 gd_51
107 108 110 111 1 gd_14
Expand Down Expand Up @@ -2496,7 +2494,6 @@ GB_1_Protein 3
279 280 281 283 1 gd_40
279 284 286 287 1 gd_14
284 286 287 288 1 gd_49
284 286 287 288 1 gd_50
286 287 288 290 1 gd_48
286 287 288 290 1 gd_51
287 288 290 291 1 gd_14
Expand All @@ -2514,7 +2511,6 @@ GB_1_Protein 3
298 299 300 301 1 gd_40
298 303 305 306 1 gd_14
303 305 306 307 1 gd_49
303 305 306 307 1 gd_50
305 306 307 309 1 gd_48
305 306 307 309 1 gd_51
306 307 309 310 1 gd_14
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11 changes: 0 additions & 11 deletions test/test_inputs/lyso-bnz_ref/reference/topol_Lyso.itp
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Expand Up @@ -6590,7 +6590,6 @@ Lyso 3
90 91 92 94 1 gd_40
89 95 97 98 1 gd_14
95 97 98 99 1 gd_49
95 97 98 99 1 gd_50
97 98 99 101 1 gd_48
97 98 99 101 1 gd_51
98 99 101 102 1 gd_14
Expand Down Expand Up @@ -6672,7 +6671,6 @@ Lyso 3
183 184 185 187 1 gd_40
182 188 190 191 1 gd_14
188 190 191 192 1 gd_49
188 190 191 192 1 gd_50
190 191 192 194 1 gd_48
190 191 192 194 1 gd_51
191 192 194 195 1 gd_14
Expand Down Expand Up @@ -6704,7 +6702,6 @@ Lyso 3
226 227 228 230 1 gd_34
226 231 233 234 1 gd_14
231 233 234 235 1 gd_49
231 233 234 235 1 gd_50
233 234 235 237 1 gd_48
233 234 235 237 1 gd_51
234 235 237 238 1 gd_14
Expand All @@ -6716,7 +6713,6 @@ Lyso 3
238 239 240 242 1 gd_34
238 243 245 246 1 gd_14
243 245 246 247 1 gd_49
243 245 246 247 1 gd_50
245 246 247 249 1 gd_48
245 246 247 249 1 gd_51
246 247 249 250 1 gd_14
Expand Down Expand Up @@ -6859,7 +6855,6 @@ Lyso 3
391 392 393 395 1 gd_34
391 396 398 399 1 gd_14
396 398 399 400 1 gd_49
396 398 399 400 1 gd_50
398 399 400 402 1 gd_48
398 399 400 402 1 gd_51
399 400 402 403 1 gd_14
Expand Down Expand Up @@ -6894,7 +6889,6 @@ Lyso 3
429 430 431 433 1 gd_40
429 434 436 437 1 gd_14
434 436 437 438 1 gd_49
434 436 437 438 1 gd_50
436 437 438 440 1 gd_48
436 437 438 440 1 gd_51
437 438 440 441 1 gd_14
Expand Down Expand Up @@ -7039,7 +7033,6 @@ Lyso 3
591 592 593 594 1 gd_14
588 596 598 599 1 gd_14
596 598 599 600 1 gd_49
596 598 599 600 1 gd_50
598 599 600 602 1 gd_48
598 599 600 602 1 gd_51
599 600 602 603 1 gd_14
Expand Down Expand Up @@ -7250,7 +7243,6 @@ Lyso 3
826 827 828 829 1 gd_26
825 830 832 833 1 gd_14
830 832 833 834 1 gd_49
830 832 833 834 1 gd_50
832 833 834 836 1 gd_48
832 833 834 836 1 gd_51
833 834 836 837 1 gd_14
Expand All @@ -7269,7 +7261,6 @@ Lyso 3
845 846 850 852 1 gd_45
846 850 852 853 1 gd_14
850 852 853 854 1 gd_49
850 852 853 854 1 gd_50
852 853 854 856 1 gd_48
852 853 854 856 1 gd_51
853 854 856 857 1 gd_14
Expand All @@ -7285,7 +7276,6 @@ Lyso 3
863 864 866 868 1 gd_45
864 866 868 869 1 gd_14
866 868 869 870 1 gd_49
866 868 869 870 1 gd_50
868 869 870 872 1 gd_48
868 869 870 872 1 gd_51
869 870 872 873 1 gd_14
Expand Down Expand Up @@ -7595,7 +7585,6 @@ Lyso 3
1218 1219 1223 1225 1 gd_45
1219 1223 1225 1226 1 gd_14
1223 1225 1226 1227 1 gd_49
1223 1225 1226 1227 1 gd_50
1225 1226 1227 1229 1 gd_48
1225 1226 1227 1229 1 gd_51
1226 1227 1229 1230 1 gd_14
Expand Down
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