@datagrok/bio 1.7.7 → 1.7.8
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/detectors.js +5 -5
- package/dist/package-test.js +57 -13
- package/dist/package.js +35 -11
- package/files/tests/testActivityCliffs.csv +311 -0
- package/package.json +1 -1
- package/src/tests/detectors-test.ts +8 -2
- package/src/tests/splitters-test.ts +19 -0
- package/src/utils/convert.ts +15 -3
- package/src/utils/multiple-sequence-alignment.ts +2 -1
- package/src/utils/utils.ts +10 -8
- package/{test-Bio-34f75e5127b8-7c42ea4b.html → test-Bio-34f75e5127b8-cdc230d8.html} +6 -2
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chembl_tid,smiles,Activity
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214
|
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CHEMBL4128,COC(=O)NC1=NC2=CC=C(OC3=CC=C(NC(=S)NC4=CC=CC(C(F)(F)F)=C4)C=C3)C=C2[NH]1,5.83117
|
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215
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CHEMBL3438,CN1CCN(C2=CC=CC3=C2N=C(C2=N[NH]C4=CC(C5=CC=C(CO)C=C5)=CC=C24)[NH]3)CC1,6.53760
|
|
216
|
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CHEMBL5251,CN1N=CC2=C(NC3=CC=C(C(=O)N4CCOCC4)C=C3)N=C(C3=CC=CC(NC(=O)C4=CC=C(C(C)(C)C)C=C4)=C3)N=C21,4.89620
|
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217
|
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CHEMBL5251,C=CC(=O)NC1=CC=CC(OC2=NC(NC3=CC=C(N4CCN(C)CC4)C=C3)=NC3=C2SC=C3)=C1,9.00000
|
|
218
|
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CHEMBL5251,CN1C=C(C2=CC=CC(N3CCC4=C(N=C5CCCCN54)C3=O)=C2CO)C=C(NC2=CC=NC=N2)C1=O,4.77728
|
|
219
|
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CHEMBL5251,CN1C=C(C2=CC=CC(N3CCN4C(=NC5=C4CCCC5)C3=O)=C2CO)C=C(NC2=CC=NC=N2)C1=O,5.58503
|
|
220
|
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CHEMBL5251,CC(C)(C)C1=CC=C(C(=O)NC2=CC=CC(C3=CC=NC(NC4=CC=C5C=N[NH]C5=C4)=N3)=C2)C=C1,5.13668
|
|
221
|
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CHEMBL5251,C=CC(=O)N[C@H]1CCN(C2=CC=C(C(N)=O)C(OC3=CC=C(C(=O)N4CCOCC4)C=C3)=N2)C1,5.00000
|
|
222
|
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CHEMBL4599,NC1=NC=CN2C(C3CCC3)=NC(C3=CC=C(OC4=CC=CC=C4)C(O)=C3)=C12,7.22988
|
|
223
|
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CHEMBL5331,CCCCNC1=NC=C(C2=CC=C(F)C=N2)C(N[C@H]2CC[C@H](O)CC2)=N1,8.20066
|
|
224
|
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CHEMBL5464,CN1C(=O)[C@@H](NC(=O)C2=N[NH]C(CC3=CC=CC=C3)=C2)COC2=CC=CC=C21,9.39794
|
|
225
|
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CHEMBL5464,CN1C(=O)[C@@H](NC(=O)C2=NOC(CC3=CC=CC=C3)=C2)COC2=CC=CC=C21,8.44957
|
|
226
|
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CHEMBL2292,C1=CN=CC(CNC2=NC=CC(C3=CC=C4OCOC4=C3)=N2)=C1,7.77642
|
|
227
|
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CHEMBL2292,ClC1=CC=C(CNC2=NC=CC(C3=CC=C4OCOC4=C3)=N2)C=C1Cl,7.19045
|
|
228
|
+
CHEMBL2292,N#C/C(=C\C1=CC=CN=C1)C1=C[NH]C2=NC=CC=C12,7.67778
|
|
229
|
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CHEMBL2292,N#CC1=CC2=NC=CC=C2C2=C1C1=CC=CC=C1[NH]2,5.00000
|
|
230
|
+
CHEMBL2292,NC1=CC(C2=C[NH]C3=CN=CC=C23)=CC=N1,5.69379
|
|
231
|
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CHEMBL2292,NC1=NC=CC(C2=C[NH]C3=CN=CC=C23)=N1,9.00000
|
|
232
|
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CHEMBL2292,NC1=NC=CC(C2=C[NH]C3=CN=CC=C23)=N1,9.00000
|
|
233
|
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CHEMBL2292,C1=CN=CC(C2=C[NH]C3=CN=CC=C23)=C1,5.09925
|
|
234
|
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CHEMBL3529,N#CC1=CC(C2=CC=NC(NC3=NC=CC(C4CCNCC4)=N3)=C2)=CC=C1OC1CCOCC1,6.92082
|
|
235
|
+
CHEMBL4766,CC1=NC=C(C)C(C2=CC=C(N(CC3=CC=CN=C3)C(=O)C3=CC=C(O)C=C3O)C=C2)=N1,8.00000
|
|
236
|
+
CHEMBL4766,CC1=CC=C(C)C(C2=CC=C(N(CC3=CC=CN=C3)C(=O)C3=CC=C(O)C=C3O)C=C2)=N1,6.00000
|
|
237
|
+
CHEMBL4766,CNC1=NC=CC(C2=CC=C(N(CC3=CC=CN=C3)C(=O)C3=CC=C(O)C=C3O)C=C2)=N1,7.00000
|
|
238
|
+
CHEMBL4766,O=C(C1=CC=C(O)C=C1O)N(CC1=CC=CN=C1)C1=CC=C(C2=NC3=CC=C(Cl)C=C3C=C2CO)C=C1,8.00000
|
|
239
|
+
CHEMBL4766,CN(C)C(=O)C1=CC=C(N(CC2=CC=NC=C2)C(=O)C2=CC(Cl)=C(O)C=C2O)C=C1,6.00000
|
|
240
|
+
CHEMBL4766,CN(C)C(=O)C1=CC=C(N(CC2=CC=NC=C2)C(=O)C2=CC(Cl)=C(O)C=C2O)C=C1,6.00000
|
|
241
|
+
CHEMBL4766,CCOC(=O)C1=NC(C)=NC(C2=CC=C(N(CC3=CC=CN=C3)C(=O)C3=CC=C(O)C=C3O)C=C2)=C1C,7.00000
|
|
242
|
+
CHEMBL4766,CC1=CC=CN=C1C1=CC=C(N(CC2=CC=CN=C2)C(=O)C2=CC(Cl)=C(O)C=C2O)C=C1,8.00000
|
|
243
|
+
CHEMBL4766,O=C(C1=CC=C(O)C=C1O)N(CC1=CC=CN=C1)C1=CC=C(C2=NC=NC3=CC=CC(F)=C23)C=C1,8.00000
|
|
244
|
+
CHEMBL4766,CCOC(=O)C1=NC(C2=CC=C(N(CC3=CC=CN=C3)C(=O)C3=CC=C(O)C=C3O)C=C2)=C2C=CC=CC2=N1,7.00000
|
|
245
|
+
CHEMBL4766,CN(CC1=CC=C2N=CC=CC2=C1)C(=O)C1=CC=C(N(CC2=CC=CC=C2)C(=O)C2=CC=C(O)C=C2O)C=C1,7.00000
|
|
246
|
+
CHEMBL4766,NC(=O)C1=NC(C2=CC=C(N(CC3=CC=CN=C3)C(=O)C3=CC=C(O)C=C3O)C=C2)=C2C=CC=CC2=N1,7.00000
|
|
247
|
+
CHEMBL4766,O=C(C1=CC=C(O)C=C1O)N(CC1=CC=CN=C1)C1=CC=C(C2=NC3=CC=CC=C3C=C2CO)C=C1,7.00000
|
|
248
|
+
CHEMBL4766,O=C(C1=CC=C(O)C=C1O)N(CC1=CC=CN=C1)C1=CC=C(C2=CC=CC=C2Cl)C=C1,6.00000
|
|
249
|
+
CHEMBL4766,O=C(C1=CC=C(O)C=C1O)N(CC1=CC=CN=C1)C1=CC=C(C2=NC(Cl)=C3CSCCC3=N2)C=C1,6.00000
|
|
250
|
+
CHEMBL4766,O=C(C1=CC=C(O)C=C1O)N(CC1=CC=CN=C1)C1=CC=C(C2=CC=NC3=C2SC=C3)C=C1,7.00000
|
|
251
|
+
CHEMBL4766,CN(CC1=CC=CC2=CN=CC=C12)C(=O)C1=CC=C(N(CC2=CSC=C2)C(=O)C2=CC=C(O)C=C2O)C=C1,8.00000
|
|
252
|
+
CHEMBL4766,CN(CC1=CC=C2C=CC=CC2=N1)C(=O)C1=CC=C(N(CC2=CC=CC=C2)C(=O)C2=CC=C(O)C=C2O)C=C1,7.00000
|
|
253
|
+
CHEMBL4766,O=C(C1=CC=C(O)C=C1O)N(CC1=CC=CN=C1)C1=CC=C(C2=NC(Cl)=NC3=C2SC=C3)C=C1,7.00000
|
|
254
|
+
CHEMBL4766,CC1=CC(S(=O)(=O)N2CCC(F)(F)CC2)=CN=C1C1=CC=C(N(CC2=CC=CN=C2)C(=O)C2=CC=C(O)C=C2O)C=C1,8.00000
|
|
255
|
+
CHEMBL4766,CN(CC1=CC=CC2=CC=CC=C12)C(=O)C1=CC=C(N(CC2=CC=CN=C2)C(=O)C2=CC=C(O)C=C2O)C=C1,8.00000
|
|
256
|
+
CHEMBL4766,CC1=C(Cl)N=C(Cl)N=C1C1=CC=C(N(CC2=CC=CN=C2)C(=O)C2=CC=C(O)C=C2O)C=C1,8.00000
|
|
257
|
+
CHEMBL4766,CN(CC1=CC=C2C=CC=CC2=C1)C(=O)C1=CC=C(N(CC2=CC=CN=C2)C(=O)C2=CC=C(O)C=C2O)C=C1,8.00000
|
|
258
|
+
CHEMBL4766,CC1=NC(C(F)(F)F)=NC(C2=CC=C(N(CC3=CC=CN=C3)C(=O)C3=CC=C(O)C=C3O)C=C2)=C1C,8.00000
|
|
259
|
+
CHEMBL260,CC1=NN=C(C2=CC=C(C)C(C3=CC=C4C(=C3)NC(=O)C43CCOCC3)=C2)[NH]1,8.05959
|
|
260
|
+
CHEMBL260,O=C1C2=CC=C(OC3=CC=C(F)C=C3F)C=C2CCC2=CC=C(OC[C@@H](O)CO)C=C12,5.17393
|
|
261
|
+
CHEMBL260,O=C1C2=CC=C(NC3=CC=C(F)C=C3F)C=C2OCC2=C(OC[C@H](O)CO)C=CC=C12,7.37675
|
|
262
|
+
CHEMBL260,O=C1C2=CC(OCCC3CCOCC3)=CC=C2COC2=CC(NC3=CC=C(F)C=C3F)=CC=C12,6.77064
|
|
263
|
+
CHEMBL260,COC1=CC=CC2=C1COC1=CC(NC3=CC=C(F)C=C3F)=CC=C1C2=O,7.20066
|
|
264
|
+
CHEMBL260,COC1=CC=CC2=C1COC1=CC(NC3=CC=CC=C3N)=CC=C1C2=O,7.02687
|
|
265
|
+
CHEMBL260,O=C1C2=CC=C(NC3=CC=C(F)C=C3F)C=C2OCC2=C(OCCN3CCOCC3)C=CC=C12,7.46852
|
|
266
|
+
CHEMBL5260,CNS(=O)(=O)C1=CC=CC(NC2=NC=NC3=C2C=C[NH]3)=C1,7.09691
|
|
267
|
+
CHEMBL5260,CNS(=O)(=O)C1=CC=CC(OC2=NC=NC3=C2C=C[NH]3)=C1,4.79588
|
|
268
|
+
CHEMBL5260,CNS(=O)(=O)C1=CC=CC(NC2=CC=NC(NC3=CC=CC(C)=C3)=C2)=C1,5.30103
|
|
269
|
+
CHEMBL1075104,FC(F)(F)C1=CC=CC(SC2=NN3C(C4=CC=CS4)=NC=C3C=C2)=C1,5.05535
|
|
270
|
+
CHEMBL1075104,N#CC1=CC=CC(C2=C[NH]C3=NC=NC(N4CCOCC4)=C23)=C1,7.97686
|
|
271
|
+
CHEMBL1075104,N#CC1=CN=CC(C2=C[NH]C3=NC=NC(N4CCOCC4)=C23)=C1,5.41485
|
|
272
|
+
CHEMBL1075104,O=C(NC1=CN=CC=N1)C1=CC(Br)=CC=C1OCC1=CC=CC=C1,5.70000
|
|
273
|
+
CHEMBL1075104,O=C(NC1=CN=CC=N1)C1=CC(Br)=CC=C1OCC1=CC=CC=C1,5.70000
|
|
274
|
+
CHEMBL5407,COC1=CC=C2C(=O)/C(=C/C3=C[NH]C4=NC=CC=C34)OC2=C1CN1CCNCC1,8.88606
|
|
275
|
+
CHEMBL5407,N[C@H]1CCCN(C2=NC=NC=C2NC2=CC=CC3=CN=C(C4=C(F)C=CC=C4F)N=C23)C1,5.40894
|
|
276
|
+
CHEMBL2185,CC1=CC(NC2=NC(SC3=CC=C(NC(=O)CN4C[C@H](SC(C)(C)C)C[C@H]4CO)C=C3)=NN3C=CC=C23)=N[NH]1,5.74715
|
|
277
|
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CHEMBL2185,CCOC(=O)C1=C2NC3=C(C(=O)CCC3)C(C3=CC=NC(SC4=NC5=CC=CC=C5[NH]4)=C3)C2=C[NH]1,5.95861
|
|
278
|
+
CHEMBL2185,CCOC(=O)C1=C2NC3=C(C(=O)CCC3)C(C3=CC=NC(SC4=NC5=CC=CC=C5[NH]4)=C3)C2=C[NH]1,5.95861
|
|
279
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+
CHEMBL4896,O=C(NCC1CCCNC1)C1=CC=NC2=C1N=C(C1=CC=CS1)[NH]2,7.13077
|
|
280
|
+
CHEMBL4896,O=C(N[C@H]1CCCNC1)C1=CC=NC2=C1[NH]C(C1=CC(N3CCOCC3)=CS1)=N2,4.65758
|
|
281
|
+
CHEMBL4896,NC1CCCC(NC(=O)C2=CC=NC3=C2[NH]C(C2=CC=CS2)=N3)C1,7.45593
|
|
282
|
+
CHEMBL5284,COC1=CC=CC=C1NC1=NC=CC(C2=CC=C(C(N)=O)C(C(C)C)=C2)=N1,5.80000
|
|
283
|
+
CHEMBL4203,C1=CN=CC(CNC2=CC=NC(C3=CC=C4OCOC4=C3)=N2)=C1,7.20066
|
|
284
|
+
CHEMBL4203,C1=CN=CC(CNC2=CC=NC(C3=CC=C4OCOC4=C3)=N2)=C1,7.20066
|
|
285
|
+
CHEMBL4203,C1=CN=CC(CNC2=CC=NC(C3=CC=C4OCOC4=C3)=N2)=C1,7.20066
|
|
286
|
+
CHEMBL4203,C1=CN=CC(CNC2=CC=NC(C3=CC=C4OCOC4=C3)=N2)=C1,7.20066
|
|
287
|
+
CHEMBL4203,C1=CN=CC(CNC2=NC=CC(C3=CC=C4OCOC4=C3)=N2)=C1,7.74743
|
|
288
|
+
CHEMBL4203,ClC1=CC=C(CNC2=NC=CC(C3=CC=C4OCOC4=C3)=N2)C=C1Cl,7.62591
|
|
289
|
+
CHEMBL4203,ClC1=CC=C(CNC2=NC=CC(C3=CC=C4OCOC4=C3)=N2)C=C1Cl,7.62591
|
|
290
|
+
CHEMBL4203,BrC1=CC=C(CNC2=NC=CC(C3=CC=C4OCOC4=C3)=N2)C=C1Br,7.42082
|
|
291
|
+
CHEMBL4203,C1=NC=C(CNC2=CC=NC(C3=CC=C4OCOC4=C3)=N2)C=N1,4.58503
|
|
292
|
+
CHEMBL4203,ClC1=CC=C(CNC2=NC=CC(C3=CC=C4OCOC4=C3)=N2)C=C1,7.30103
|
|
293
|
+
CHEMBL4203,BrC1=CC(Br)=CC(CNC2=NC=CC(C3=CC=C4OCOC4=C3)=N2)=C1,7.72185
|
|
294
|
+
CHEMBL4203,COC1=CC=C(C2=NC=CC(NCC3=CC=C(Cl)C(Cl)=C3)=N2)C=C1,4.83565
|
|
295
|
+
CHEMBL4204,CCN1CCN(CC2=CC=C(NC(=O)COC3=CC=C(C4=CC=NC=C4)C=C3)C=C2C(F)(F)F)CC1,5.71897
|
|
296
|
+
CHEMBL3778,OC[C@H]1C[C@@H](NC2=NC(NC3CCC3)=NC=C2C2=NC3=CC=CC=C3S2)[C@H](O)[C@@H]1O,3.39470
|
|
297
|
+
CHEMBL3778,OC[C@H]1C[C@@H](NC2=NC(NC3=CN=CN=C3)=NC=C2C2=NC3=CC=CC=C3S2)[C@H](O)[C@@H]1O,5.22185
|
|
298
|
+
CHEMBL3778,OC[C@H]1C[C@@H](NC2=NC(NC3=CN=CN=C3)=NC=C2C2=NC3=CC=CC=C3S2)[C@H](O)[C@@H]1O,5.22185
|
|
299
|
+
CHEMBL3778,CN1C=C(NC(=O)C2=C3N=C(OCCN)C=CN3N=C2)C(C(N)=O)=N1,5.03621
|
|
300
|
+
CHEMBL3778,CC1=CC(NC2=NC=C(C3=NC4=CN=CC=C4S3)C(N[C@@H]3C[C@H](CO)[C@@H](O)[C@H]3O)=N2)=CC=N1,8.52288
|
|
301
|
+
CHEMBL3778,OC[C@H]1C[C@@H](NC2=NC(NC3=CN=CN=C3)=NC=C2C2=NC3=CN=CC=C3S2)[C@H](O)[C@@H]1O,7.92082
|
|
302
|
+
CHEMBL3778,OC[C@H]1C[C@@H](NC2=NC(NC3=CN=CN=C3)=NC=C2C2=NC3=CC=NC=C3S2)[C@H](O)[C@@H]1O,8.22185
|
|
303
|
+
CHEMBL3886,O=S(=O)(NC1=CC=C(F)C(C#CC2=CN=C3[NH]N=CC3=C2)=C1F)C1=CC=CC(Cl)=C1,8.29243
|
|
304
|
+
CHEMBL4523,O=C(O)C1=CC2=CC(Br)=CC(N[C@H]3CC[C@@H](O)CC3)=C2O1,5.16749
|
|
305
|
+
CHEMBL4523,FC1=CC=CC(F)=C1C1=CC=C2[NH]N=C(C3=CN=CC(N4CCNCC4)=N3)C2=C1,7.53760
|
|
306
|
+
CHEMBL4523,N[C@H]1CCCN(C2=NC=NC=C2NC2=NC=C3C=CC(C4=C(F)C=CC=C4F)=NN23)C1,6.95861
|
|
307
|
+
CHEMBL4247,COC1=CC(C2CCN(CC(N)=O)CC2)=CC=C1NC1=NN2C(C3=NC=CC=C3OC)=CC=C2C=N1,5.97428
|
|
308
|
+
CHEMBL4247,COC1=CC(C2CCN(CC(N)=O)CC2)=CC=C1NC1=NN2C(C3=NC=CC=C3OC)=CC=C2C=N1,5.97428
|
|
309
|
+
CHEMBL4247,CC1=CC(NC2=NC=C(Cl)C(NC3=CC=CC=C3S(=O)(=O)C(C)C)=N2)=C(OC(C)C)C=C1C1CCN(C)CC1,7.93930
|
|
310
|
+
CHEMBL4247,CC1=CC(NC2=NC=C(Cl)C(NC3=CN(C)N=C3S(=O)(=O)N(C)C)=N2)=C(OC(C)C)C=C1C1CCNCC1,5.17503
|
|
311
|
+
CHEMBL4816,CNC1=NC=CC(C2=CC=C(C(=O)N[C@H](CO)CC3=CC=C(Cl)C=C3Cl)S2)=N1,6.55284
|
package/package.json
CHANGED
|
@@ -2,7 +2,7 @@
|
|
|
2
2
|
"name": "@datagrok/bio",
|
|
3
3
|
"beta": false,
|
|
4
4
|
"friendlyName": "Bio",
|
|
5
|
-
"version": "1.7.
|
|
5
|
+
"version": "1.7.8",
|
|
6
6
|
"description": "Bio is a [package](https://datagrok.ai/help/develop/develop#packages) for the [Datagrok](https://datagrok.ai) platform",
|
|
7
7
|
"repository": {
|
|
8
8
|
"type": "git",
|
|
@@ -114,6 +114,7 @@ MWRSWY-CKHP
|
|
|
114
114
|
testSmilesCsv = 'testSmilesCsv',
|
|
115
115
|
testSmiles2Csv = 'testSmiles2Csv',
|
|
116
116
|
testCerealCsv = 'testCerealCsv',
|
|
117
|
+
testActivityCliffsCsv = 'testActivityCliffsCsv',
|
|
117
118
|
}
|
|
118
119
|
|
|
119
120
|
const samples: { [key: string]: string } = {
|
|
@@ -129,6 +130,7 @@ MWRSWY-CKHP
|
|
|
129
130
|
'testIdCsv': 'System:AppData/Bio/tests/testId.csv',
|
|
130
131
|
'testSmilesCsv': 'System:AppData/Bio/tests/testSmiles.csv',
|
|
131
132
|
'testSmiles2Csv': 'System:AppData/Bio/tests/testSmiles2.csv',
|
|
133
|
+
'testActivityCliffsCsv': 'System:AppData/Bio/tests/testActivityCliffs.csv', // smiles
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'testCerealCsv': 'System:AppData/Bio/tests/testCereal.csv',
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};
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@@ -305,12 +307,16 @@ MWRSWY-CKHP
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await _testNeg(readSamples(Samples.testSmiles2Csv), 'SMILES');
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});
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+
test('samplesTestActivityCliffsNegativeSmiles', async () => {
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+
await _testNeg(readSamples(Samples.testActivityCliffsCsv), 'smiles');
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+
});
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+
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test('samplesFastaPtPosSequence', async () => {
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-
await
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+
await _testPos(readSamples(Samples.fastaPtCsv), 'sequence', 'fasta:SEQ:PT');
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});
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test('samplesTestCerealNegativeCerealName', async () => {
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-
await
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+
await _testNeg(readSamples(Samples.testCerealCsv), 'cereal_name');
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});
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});
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@@ -27,11 +27,30 @@ category('splitters', () => {
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['meI', 'hHis', 'Aca', 'N', 'T', 'dK', 'Thr_PO3H2', 'Aca',
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'D-Tyr_Et', 'D-Dap', 'dV', 'E', 'N', 'pnG', 'Phe_4Me']
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],
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+
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+
testHelm1: [
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+
'RNA1{R(U)P.R(T)P.R(G)P.R(C)P.R(A)}$$$$',
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+
['R(U)P', 'R(T)P', 'R(G)P', 'R(C)P', 'R(A)']
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+
],
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35
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+
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+
testHelm2: [
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+
'RNA1{P.R(U)P.R(T)}$$$$',
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+
['P', 'R(U)P', 'R(T)']
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+
],
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40
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+
testHelm3: [
|
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+
'RNA1{P.R(U).P.R(T)}$$$$',
|
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+
['P', 'R(U)', 'P', 'R(T)']
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+
],
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};
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31
45
|
|
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test('helm1', async () => { await _testHelmSplitter(data.helm1[0], data.helm1[1]); });
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test('helm2', async () => { await _testHelmSplitter(data.helm2[0], data.helm2[1]); });
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test('helm3-multichar', async () => { await _testHelmSplitter(data.helm3[0], data.helm3[1]); });
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49
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+
|
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50
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+
// examples from Helm/tests/test.csv file
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51
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+
test('testHelm1', async () => { await _testHelmSplitter(data.testHelm1[0], data.testHelm1[1]); });
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52
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+
test('testHelm2', async () => { await _testHelmSplitter(data.testHelm2[0], data.testHelm2[1]); });
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53
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+
test('testHelm3', async () => { await _testHelmSplitter(data.testHelm3[0], data.testHelm3[1]); });
|
|
35
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|
});
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36
55
|
|
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37
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|
export async function _testHelmSplitter(src: string, tgt: string[]) {
|
package/src/utils/convert.ts
CHANGED
|
@@ -1,6 +1,7 @@
|
|
|
1
1
|
import * as DG from 'datagrok-api/dg';
|
|
2
2
|
import * as ui from 'datagrok-api/ui';
|
|
3
3
|
import * as grok from 'datagrok-api/grok';
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4
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+
import $ from 'cash-dom';
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4
5
|
|
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5
6
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import {Subscription} from 'rxjs';
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6
7
|
import {NotationConverter, NOTATION} from '@datagrok-libraries/bio/src/utils/notation-converter';
|
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@@ -27,14 +28,26 @@ export function convert(col: DG.Column): void {
|
|
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27
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|
const filteredNotations = notations.filter((e) => e !== current);
|
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28
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const targetNotationInput = ui.choiceInput('Convert to', filteredNotations[0], filteredNotations);
|
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29
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|
|
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30
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-
const separatorInput = ui.choiceInput('
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+
const separatorInput = ui.choiceInput('Separator', separatorArray[0], separatorArray);
|
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|
+
|
|
33
|
+
// hide the separator input for non-SEPARATOR target notations
|
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|
+
if (targetNotationInput.value !== NOTATION.SEPARATOR)
|
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+
$(separatorInput.root).hide();
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+
else
|
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+
$(separatorInput.root).show();
|
|
38
|
+
|
|
39
|
+
targetNotationInput.onChanged(async () => {
|
|
40
|
+
if (targetNotationInput.value !== NOTATION.SEPARATOR)
|
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|
+
$(separatorInput.root).hide();
|
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|
+
else
|
|
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|
+
$(separatorInput.root).show();
|
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+
});
|
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45
|
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|
if (convertDialog == null) {
|
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|
convertDialog = ui.dialog('Convert sequence notation')
|
|
34
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|
.add(ui.div([
|
|
35
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|
ui.h1('Current notation: ' + current),
|
|
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|
targetNotationInput.root,
|
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|
-
// TODO: conditional separator input
|
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|
separatorInput.root
|
|
39
52
|
]))
|
|
40
53
|
.onOK(async () => {
|
|
@@ -62,4 +75,3 @@ export async function convertDo(
|
|
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75
|
await grok.data.detectSemanticTypes(srcCol.dataFrame);
|
|
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|
return newColumn;
|
|
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77
|
}
|
|
65
|
-
|
|
@@ -30,9 +30,10 @@ function _fastaToStrings(fasta: string): string[] {
|
|
|
30
30
|
*
|
|
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|
* @param {DG.Column} srcCol Column with sequences.
|
|
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|
* @param {boolean} isAligned Whether the column is aligned.
|
|
33
|
+
* @param {string} unUsedName
|
|
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|
* @return {Promise<DG.Column>} Aligned sequences.
|
|
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|
*/
|
|
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|
-
export async function runKalign(srcCol: DG.Column, isAligned = false, unUsedName:string = ''): Promise<DG.Column> {
|
|
36
|
+
export async function runKalign(srcCol: DG.Column, isAligned = false, unUsedName: string = ''): Promise<DG.Column> {
|
|
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|
let sequences = srcCol.toList();
|
|
37
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|
|
|
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|
if (isAligned)
|
package/src/utils/utils.ts
CHANGED
|
@@ -1,7 +1,10 @@
|
|
|
1
1
|
import * as DG from 'datagrok-api/dg';
|
|
2
2
|
import {WebLogo, SplitterFunc} from '@datagrok-libraries/bio/src/viewers/web-logo';
|
|
3
3
|
import * as grok from 'datagrok-api/grok';
|
|
4
|
-
import {
|
|
4
|
+
import {
|
|
5
|
+
CAP_GROUP_NAME, CAP_GROUP_SMILES, jsonSdfMonomerLibDict, MONOMER_SYMBOL,
|
|
6
|
+
RGROUP_ALTER_ID, RGROUP_FIELD, RGROUP_LABEL, SDF_MONOMER_NAME
|
|
7
|
+
} from '../const';
|
|
5
8
|
|
|
6
9
|
export const HELM_CORE_LIB_FILENAME = '/samples/HELMCoreLibrary.json';
|
|
7
10
|
export const HELM_CORE_LIB_MONOMER_SYMBOL = 'symbol';
|
|
@@ -50,7 +53,7 @@ export function createJsonMonomerLibFromSdf(table: DG.DataFrame): any {
|
|
|
50
53
|
const resultLib = [];
|
|
51
54
|
for (let i = 0; i < table.rowCount; i++) {
|
|
52
55
|
const monomer: { [key: string]: string | any } = {};
|
|
53
|
-
Object.keys(jsonSdfMonomerLibDict).forEach(key => {
|
|
56
|
+
Object.keys(jsonSdfMonomerLibDict).forEach((key) => {
|
|
54
57
|
if (key === MONOMER_SYMBOL) {
|
|
55
58
|
const monomerSymbol = table.get(jsonSdfMonomerLibDict[key], i);
|
|
56
59
|
monomer[key] = monomerSymbol === '.' ? table.get(SDF_MONOMER_NAME, i) : monomerSymbol;
|
|
@@ -59,21 +62,20 @@ export function createJsonMonomerLibFromSdf(table: DG.DataFrame): any {
|
|
|
59
62
|
const jsonRgroups: any[] = [];
|
|
60
63
|
rgroups.forEach((g: string) => {
|
|
61
64
|
const rgroup: { [key: string]: string | any } = {};
|
|
62
|
-
const altAtom = g.substring(g.lastIndexOf(
|
|
63
|
-
|
|
65
|
+
const altAtom = g.substring(g.lastIndexOf(']') + 1);
|
|
66
|
+
const radicalNum = g.match(/\[R(\d+)\]/)![1];
|
|
64
67
|
rgroup[CAP_GROUP_SMILES] = altAtom === 'H' ? `[*:${radicalNum}][H]` : `O[*:${radicalNum}]`;
|
|
65
68
|
rgroup[RGROUP_ALTER_ID] = altAtom === 'H' ? `R${radicalNum}-H` : `R${radicalNum}-OH`;
|
|
66
69
|
rgroup[CAP_GROUP_NAME] = altAtom === 'H' ? `H` : `OH`;
|
|
67
70
|
rgroup[RGROUP_LABEL] = `R${radicalNum}`;
|
|
68
71
|
jsonRgroups.push(rgroup);
|
|
69
|
-
})
|
|
72
|
+
});
|
|
70
73
|
monomer[key] = jsonRgroups;
|
|
71
74
|
} else {
|
|
72
|
-
if((jsonSdfMonomerLibDict as { [key: string]: string | any })[key])
|
|
75
|
+
if ((jsonSdfMonomerLibDict as { [key: string]: string | any })[key])
|
|
73
76
|
monomer[key] = table.get((jsonSdfMonomerLibDict as { [key: string]: string | any })[key], i);
|
|
74
|
-
}
|
|
75
77
|
}
|
|
76
|
-
})
|
|
78
|
+
});
|
|
77
79
|
resultLib.push(monomer);
|
|
78
80
|
}
|
|
79
81
|
return resultLib;
|
|
@@ -1,4 +1,4 @@
|
|
|
1
|
-
<html><head><meta charset="utf-8"/><title>Bio Test Report. Datagrok version datagrok/datagrok:latest SHA=34f75e5127b8. Commit
|
|
1
|
+
<html><head><meta charset="utf-8"/><title>Bio Test Report. Datagrok version datagrok/datagrok:latest SHA=34f75e5127b8. Commit cdc230d8.</title><style type="text/css">html,
|
|
2
2
|
body {
|
|
3
3
|
font-family: Arial, Helvetica, sans-serif;
|
|
4
4
|
font-size: 1rem;
|
|
@@ -229,7 +229,10 @@ header {
|
|
|
229
229
|
font-size: 1rem;
|
|
230
230
|
padding: 0 0.5rem;
|
|
231
231
|
}
|
|
232
|
-
</style></head><body><div id="jesthtml-content"><header><h1 id="title">Bio Test Report. Datagrok version datagrok/datagrok:latest SHA=34f75e5127b8. Commit
|
|
232
|
+
</style></head><body><div id="jesthtml-content"><header><h1 id="title">Bio Test Report. Datagrok version datagrok/datagrok:latest SHA=34f75e5127b8. Commit cdc230d8.</h1></header><div id="metadata-container"><div id="timestamp">Started: 2022-07-19 10:23:49</div><div id="summary"><div id="suite-summary"><div class="summary-total">Suites (1)</div><div class="summary-passed summary-empty">0 passed</div><div class="summary-failed">1 failed</div><div class="summary-pending summary-empty">0 pending</div></div><div id="test-summary"><div class="summary-total">Tests (1)</div><div class="summary-passed summary-empty">0 passed</div><div class="summary-failed">1 failed</div><div class="summary-pending summary-empty">0 pending</div></div></div></div><div id="suite-1" class="suite-container"><div class="suite-info"><div class="suite-path">/home/runner/work/public/public/packages/Bio/src/__jest__/remote.test.ts</div><div class="suite-time warn">179.806s</div></div><div class="suite-tests"><div class="test-result failed"><div class="test-info"><div class="test-suitename"> </div><div class="test-title">TEST</div><div class="test-status">failed</div><div class="test-duration">168.85s</div></div><div class="failureMessages"> <pre class="failureMsg">Error: Test result : Bio.MSA.is_correct : TypeError: Cannot read properties of undefined (reading 'split')
|
|
233
|
+
Test result : Bio.splitters.testHelm1 : Error: Expected R(U)P at position 0, got U
|
|
234
|
+
Test result : Bio.splitters.testHelm2 : Error: Expected R(U)P at position 1, got U
|
|
235
|
+
Test result : Bio.splitters.testHelm3 : Error: Expected R(U) at position 1, got U)
|
|
233
236
|
Test result : Bio.converters.testFastaGapsToSeparator : Error: Units are not specified in column
|
|
234
237
|
Test result : Bio.converters.testFastaGapsToHelm : Error: Units are not specified in column
|
|
235
238
|
Test result : Bio.converters.HelmDnaToFasta : Error: Units are not specified in column
|
|
@@ -304,6 +307,7 @@ Test result : Bio.detectors.samplesTestHelmNegativeMolFormula : OK
|
|
|
304
307
|
Test result : Bio.detectors.samplesTestHelmNegativeSmiles : OK
|
|
305
308
|
Test result : Bio.detectors.samplesTestDemogNegativeAll : OK
|
|
306
309
|
Test result : Bio.detectors.samplesTestSmiles2NegativeSmiles : OK
|
|
310
|
+
Test result : Bio.detectors.samplesTestActivityCliffsNegativeSmiles : OK
|
|
307
311
|
Test result : Bio.detectors.samplesFastaPtPosSequence : OK
|
|
308
312
|
Test result : Bio.detectors.samplesTestCerealNegativeCerealName : OK
|
|
309
313
|
Test result : Bio.MSA.test_table.is_not_empty : OK
|