@datagrok/bio 2.0.27 → 2.0.29

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.
Files changed (15) hide show
  1. package/dist/package-test.js +181 -98
  2. package/dist/package.js +166 -82
  3. package/files/tests/sample_MSA_data.csv +1 -67
  4. package/files/tests/sample_MSA_data_empty_vals.csv +1 -67
  5. package/package.json +3 -3
  6. package/scripts/admet-run.py +27 -0
  7. package/src/analysis/sequence-activity-cliffs.ts +16 -1
  8. package/src/analysis/sequence-similarity-viewer.ts +2 -3
  9. package/src/package.ts +2 -1
  10. package/src/substructure-search/substructure-search.ts +4 -5
  11. package/src/tests/activity-cliffs-tests.ts +2 -2
  12. package/src/tests/checkInputColumn-tests.ts +2 -4
  13. package/src/tests/sequence-space-test.ts +4 -4
  14. package/src/tests/similarity-diversity-tests.ts +6 -7
  15. package/src/tests/substructure-filter-tests.ts +1 -1
package/files/tests/sample_MSA_data.csv CHANGED
@@ -27,70 +27,4 @@ meI//Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/dV/D-Thz/N/D-Orn/D-aThr/
27
27
  meI////T/dK/Thr_PO3H2/D-Thz/D-Tyr_Et/Tyr_ab-dehydroMe/dV/D-Thz/N/D-Orn/D-Nle//Phe_4Me,6.93933,-1.21695876121521,0.9705945253372192,104.92483520507812,true
28
28
  meI/////dK/Thr_PO3H2/D-Thz/D-Tyr_Et/Tyr_ab-dehydroMe/dV/D-Thz/N/D-Orn/D-Nle//Phe_4Me,5.14340,-1.609805703163147,1.0245943069458008,0,true
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29
  meI//Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/Phe_4NO2/Thr_PO3H2/N/D-Orn/D-aThr//Phe_4Me,5.90818,0.06358370929956436,0.709276020526886,0,true
30
- meI//Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/dV/Trp_Me/N/D-Orn/D-aThr//Phe_4Me,5.15504,0.007045681122690439,0.28774088621139526,7.176403522491455,true
31
- meI/hHis/Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/dV/Thr_PO3H2/N/D-Orn/D-Nle//Phe_4Me,5.33149,0.7007661461830139,0.25986868143081665,0,false
32
- dD/hHis/Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/dV/Trp_Me/N/D-Orn/D-aThr//Phe_4Me,6.14884,0.6452232599258423,0.39612022042274475,0,false
33
- hPhe/hHis/Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/dV/Phe_ab-dehydro/N/D-Orn/D-aThr//Phe_4Me,6.40426,0.7010866403579712,0.3945997357368469,0,true
34
- dI/hHis/Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/dV/Thz/N/D-Orn/D-aThr//Phe_4Me,4.57459,0.2392749786376953,-0.23711872100830078,0,false
35
- /D-Tic/Hcy/N/T/dK/Thr_PO3H2/Phe_4NH2/D-Tyr_Et/Tyr_ab-dehydroMe/dV/Cys_SEt/N/D-2Pal/D-aThr//Phe_4Me,5.75670,0.2600181996822357,1.9668617248535156,0,false
36
- meI//Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/dV/Tyr_Bn/N/D-Orn/D-aThr//Phe_4Me,5.29810,-0.04338091239333153,0.13291242718696594,17.476734161376953,true
37
- meI//Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/dV/D-hArg/N/D-Orn/D-aThr//Phe_4Me,5.94887,-0.013414794579148293,0.18237340450286865,97.71964263916016,true
38
- meI//Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/4Abz/Thr_PO3H2/N/D-Orn/D-aThr//Phe_4Me,6.05301,0.1423971801996231,0.6929029226303101,2.6069343090057373,true
39
- /Thr_PO3H2/Aca/Tyr_ab-dehydroMe/dV/D-Pip/N/D-Orn/D-aThr//Phe_4Me,5.58673,-1.874976396560669,-1.1251744031906128,0,false
40
- meI//Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/dV/dK/N/D-Orn/D-aThr//Phe_4Me,6.60328,0.022662760689854622,0.2533372938632965,214.72315979003906,true
41
- meI//Aca/N/T/dK/Tyr_ab-dehydroMe/dV/D-Phg/N/D-Orn/D-aThr//Phe_4Me,6.21215,-0.944249153137207,-0.5838506817817688,0,false
42
- meI//Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/dV/Gly_allyl/N/D-Orn/D-aThr//Phe_4Me,5.73739,-0.024882297962903976,0.2659182548522949,67.26651763916016,true
43
- meI////T/dK/Thr_PO3H2/D-Thz/D-Tyr_Et/Tyr_ab-dehydroMe/dV/D-Thz/N/D-Orn/Oic_3aR-7aS//Phe_4Me,3.52183,-1.289717674255371,0.796217679977417,0,true
44
- Oic_3axi-7axi//Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/dV/Cys_SEt/N/D-2Pal/D-aThr//Phe_4Me,4.94922,0.6311581134796143,1.0401051044464111,0,false
45
- meI/hHis/Trp_Ome/N/T/dK/Thr_PO3H2/D-Hyp/D-Tyr_Et/Tyr_ab-dehydroMe/dV/E/N/D-Orn/D-aThr//Phe_4Me,5.58059,-0.0681256651878357,-0.6029895544052124,0,false
46
- /Aca/D-Tyr_Et/Tyr_ab-dehydroMe/dV/Thz/N/D-Orn/D-aThr//Phe_4Me,6.14975,-1.911975622177124,-0.9528587460517883,0,true
47
- meI/hHis/Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/dV/Phe_ab-dehydro/N/D-Orn/D-aThr//Phe_4Me,6.93447,0.4047900140285492,0.0385725237429142,9.54377555847168,true
48
- meI/hHis/Aca/N/T/dK/Thr_PO3H2/Aca/Met_O/Tyr_ab-dehydroMe/dV/Thr_PO3H2/N/D-Orn/D-aThr//Phe_4Me,4.86407,0.8048027753829956,0.18814975023269653,2.629258871078491,true
49
- meI/hHis/Aca/N/T/dK/Thr_PO3H2/Aca/His_1Me/Tyr_ab-dehydroMe/dV/Thr_PO3H2/N/D-Orn/D-aThr//Phe_4Me,4.71800,0.8228142261505127,0.2221541851758957,0,true
50
- meI////D-Thz/dK/Thr_PO3H2/NMe2Abz/D-Tyr_Et/Tyr_ab-dehydroMe/dV/NMe2Abz/N/D-Orn/D-aThr//Phe_4Me,6.20951,-1.4961341619491577,0.6778771877288818,0,false
51
- D-Bmt//Hcy/N/T/W/Q/Phe_4NH2/Tyr_PO3H2/Tyr_ab-dehydroMe/dV/Cys_SEt/N/D-Orn/D-aThr//Phe_4Me,3.81322,0.08868088573217392,2.597508668899536,0,false
52
- aHyp//Hcy/N/T/W/Q/Phe_4NH2/D-Tyr_Et/Tyr_ab-dehydroMe/dV/Cys_SEt/N/D-Orn/D-aThr//Phe_4Me,7.90369,-0.3908594846725464,2.2342283725738525,0,false
53
- meI/aMePro/Hcy/N/T/W/Q/Phe_4NH2/D-Tyr_Et/Tyr_ab-dehydroMe/dV/Aad/N/D-Orn/D-aThr//Phe_4Me,7.39222,-0.0022207542788237333,2.1672749519348145,0,false
54
- meI/hHis/Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/dV/E/N/A/D-aThr//Phe_4Me,3.88637,0.5533066987991333,-0.46762487292289734,28.333782196044922,true
55
- meI/hHis/Aca/N/T/Tyr_Me/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/dV/E/N/dV///Phe_4Me,4.66975,0.8956347107887268,-1.2199956178665161,0,false
56
- /hHis/Aca/N/T/dK/Thr_PO3H2/Aca/seC/Tyr_ab-dehydroMe/dV/E/N/D-Orn/D-aThr//Phe_4Me,6.38815,1.072934865951538,-0.0661509782075882,2.116978645324707,true
57
- meI/hHis/Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/Thr_PO3H2/dV/E/N/pnG///Phe_4Me,3.38318,1.237688660621643,-0.9708142876625061,0,true
58
- meI/hHis/Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/D-Chg/dV/E/N/D-aMeAbu/D-aThr//Phe_4Me,3.59309,1.0994300842285156,-0.40876659750938416,0,true
59
- meI/hHis/Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/dV/E/N/Thz/D-aThr//Phe_4Me,2.87946,0.5648310780525208,-0.45618200302124023,0,true
60
- meI/hHis/Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/D-Chg/dV/E/N/3Abz/D-aThr//Phe_4Me,7.60253,1.1164917945861816,-0.46195703744888306,149.2701416015625,true
61
- meI/hHis/Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/dV/E/N/meM///Phe_4Me,2.98472,0.8085882663726807,-0.8359185457229614,17.12320899963379,true
62
- D-Phg/hHis/Aca/N/T/dK/Thr_PO3H2/Aca/seC/Tyr_ab-dehydroMe/dV/E/N/D-Orn/D-aThr//Phe_4Me,6.27054,1.0916587114334106,0.019979439675807953,0,true
63
- meI/hHis/Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/A/dV/E/N/D-Orn/D-aThr//Phe_4Me,2.72803,0.6214887499809265,-0.36722248792648315,0,false
64
- meI/hHis/Aca/N/T/dK/Thr_PO3H2/Aca/A/Tyr_ab-dehydroMe/dV/E/N/D-Orn/D-aThr//Phe_4Me,3.71966,0.684988796710968,-0.22345584630966187,0,true
65
- meI/dE/Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/dV/D-Thz/N/D-Orn/D-aThr//Phe_4Me,5.06373,0.24633337557315826,0.2890184819698334,0,true
66
- meI////Pip/dK/Thr_PO3H2/pnT/D-Tyr_Et/Tyr_ab-dehydroMe/dV/Cys_SEt/N/D-Orn/D-aThr//Phe_4Me,4.58898,-1.1358332633972168,1.2197506427764893,0,false
67
- meI/D-2Thi/Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/dV/Thr_PO3H2/N/D-Orn/D-aThr//Phe_4Me,5.49809,0.3402663469314575,0.35587310791015625,0,true
68
- meI//D-Hyp/N/T/dK/Thr_PO3H2/Trp_Ome/D-Tyr_Et/Tyr_ab-dehydroMe/dV/E/N/D-Orn/D-aThr//Phe_4Me,3.07080,-0.5990715026855469,0.006005885545164347,0,false
69
- "meI////Pip/dK/Thr_PO3H2/L-hArg(Et,Et)/D-Tyr_Et/Tyr_ab-dehydroMe/dV/E/N/D-Orn/D-aThr//Phe_4Me",4.44629,-1.2494760751724243,0.3289206922054291,0,false
70
- meI////T/dK/Thr_PO3H2/D-Thz/D-Tyr_Et/Tyr_ab-dehydroMe/dV/D-Thz/N/D-Orn/xiHyp//Phe_4Me,6.32360,-1.2599071264266968,0.913629412651062,50.43183135986328,true
71
- meI/1Nal/Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/dV/Thr_PO3H2/N/D-Orn/D-aThr//Phe_4Me,5.90846,0.33817559480667114,0.40676024556159973,7.38666296005249,true
72
- meI/hHis/Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/Phe_4Sdihydroorotamido/dV/E/N/dV///Phe_4Me,2.47020,1.2842589616775513,-0.869986891746521,17.36207389831543,true
73
- meI//Aca/N/T/W/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/dV/Thr_PO3H2/N/D-Orn/D-aThr//Phe_4Me,5.84633,-0.11631345003843307,0.5462477803230286,0,false
74
- N/T/dK/Thr_PO3H2/Trp_Ome/D-Tyr_Et/Tyr_ab-dehydroMe/dV/E/N/D-Orn/D-aThr//Phe_4Me,4.39002,-0.704487681388855,-1.0367000102996826,0,false
75
- meI/hHis/D-Thz/N/Pip/dK/Thr_PO3H2/D-Thz/D-Tyr_Et/Tyr_ab-dehydroMe/dV/D-Thz/N/D-Orn/D-aThr//Phe_4Me,2.92846,-0.39414742588996887,1.315218210220337,0,false
76
- meI//Aca/D-Tyr_Et/Tyr_ab-dehydroMe/dV/E/N/Tyr_3OH///Phe_4Me,2.66868,-1.1101311445236206,-2.1285560131073,0,false
77
- meI/hHis/Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/dV/E/N/D-Orn/Orn//Phe_4Me,5.71958,0.48867273330688477,-0.448117196559906,0,false
78
- Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/dV/E/N/D-Orn/Oic_3aR-7aS//Phe_4Me,5.90143,-0.0903714969754219,-1.0966628789901733,0,false
79
- meI/hHis/Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/dV/E/N/D-Phe_4Cl///Phe_4Me,2.03343,0.7943960428237915,-0.8285616636276245,0,true
80
- meI/hHis/Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/dV/E/N/D-1Nal///Phe_4Me,4.29826,0.8097547292709351,-0.8324390053749084,64.41063690185547,true
81
- meI/hHis/Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/dV/E/N/D-xiIle/D-aThr//Phe_4Me,5.90934,0.6005289554595947,-0.5086122155189514,137.57411193847656,true
82
- D-1Nal/hHis/Aca/N/T/dK/Thr_PO3H2/Aca/Tyr_PO3H2/Tyr_ab-dehydroMe/dV/Cys_SEt/N/D-Orn/D-aThr//Phe_4Me,1.37957,0.9966986775398254,0.7701456546783447,0,false
83
- Phe_2F//Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/dV/Cys_SEt/N/D-Orn///Phe_4Me,5.54611,0.19441579282283783,0.8366346955299377,0,false
84
- meI//Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/dV/E/N/D-2Pal///meF,4.38201,0.40358930826187134,-1.3779624700546265,0,false
85
- meI////T/dK/dR/D-Thz/D-Tyr_Et/Tyr_ab-dehydroMe/dR/Thr_PO3H2/N/D-Orn/D-aThr//Phe_4Me,4.59437,-1.206743597984314,1.6398860216140747,0,false
86
- meI//Aca/N/T/dK/D-Thz/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/D-Thz/Thr_PO3H2/N/D-Orn/D-aThr//Phe_4Me,5.81956,0.40751710534095764,1.2538228034973145,0,false
87
- meI/Tyr_26diMe/Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/D-Dap/D-Thz/N/D-Orn/D-aThr//Phe_4Me,4.49219,0.41388168931007385,0.8675658702850342,0,false
88
- meI////T/dK/Thr_PO3H2/dR/D-Tyr_Et/Tyr_ab-dehydroMe/dV/dR/N/D-Orn/D-aThr//Phe_4Me,3.56886,-0.9029757976531982,0.8573476076126099,0,false
89
- meI//Aca/N/Pip/dK/D-Thz/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/D-Thz/Thr_PO3H2/N/D-Orn///Phe_4Me,1.92623,1.1478890180587769,1.5433778762817383,0,false
90
- D-Tic////////D-Tyr_Et/Tyr_ab-dehydroMe/dV/Cys_SEt/N/D-Orn/D-aThr//Phe_4Me,2.45736,-2.073575735092163,1.6658960580825806,0,false
91
- Phe_2F/////////Tyr_ab-dehydroMe/dV/Aca/N/D-Orn/D-aThr//Phe_4Me,0.41856,-2.535810947418213,1.5070313215255737,0,false
92
- meI/hHis/Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/dV/E/N/3Abz/D-aThr//Phe_4Me,3.31918,0.6050193309783936,-0.39509856700897217,7.914954662322998,true
93
- Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/dV/E/N/D-Trp_2Me/D-aThr//Phe_4Me,5.73646,0.046205081045627594,-1.0987070798873901,0,false
94
- Phe_4Sdihydroorotamido/hHis/Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/dV/E/N/D-Orn/D-aThr//Phe_4Me,5.47681,0.36598652601242065,-0.3528278172016144,0,false
95
- dK/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/dV/E/N/Phe_3Cl/meK//Phe_4Me,3.68756,-0.782490074634552,-2.2279326915740967,0,false
96
- meI/hHis/Aca/N/T/dK/Thr_PO3H2/Aca/Sta_3S4S/Tyr_ab-dehydroMe/dV/E/N/D-Orn/D-aThr//Phe_4Me,4.90078,0.6861110925674438,-0.1880904883146286,21.26015281677246,true
30
+ meI//Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/dV/Trp_Me/N/D-Orn/D-aThr//Phe_4Me,5.15504,0.007045681122690439,0.28774088621139526,7.176403522491455,true
package/files/tests/sample_MSA_data_empty_vals.csv CHANGED
@@ -27,70 +27,4 @@ meI//Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/dV/D-Thz/N/D-Orn/D-aThr/
27
27
  meI////T/dK/Thr_PO3H2/D-Thz/D-Tyr_Et/Tyr_ab-dehydroMe/dV/D-Thz/N/D-Orn/D-Nle//Phe_4Me,6.93933,-1.21695876121521,0.9705945253372192,104.92483520507812,true
28
28
  meI/////dK/Thr_PO3H2/D-Thz/D-Tyr_Et/Tyr_ab-dehydroMe/dV/D-Thz/N/D-Orn/D-Nle//Phe_4Me,5.14340,-1.609805703163147,1.0245943069458008,0,true
29
29
  meI//Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/Phe_4NO2/Thr_PO3H2/N/D-Orn/D-aThr//Phe_4Me,5.90818,0.06358370929956436,0.709276020526886,0,true
30
- meI//Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/dV/Trp_Me/N/D-Orn/D-aThr//Phe_4Me,5.15504,0.007045681122690439,0.28774088621139526,7.176403522491455,true
31
- meI/hHis/Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/dV/Thr_PO3H2/N/D-Orn/D-Nle//Phe_4Me,5.33149,0.7007661461830139,0.25986868143081665,0,false
32
- dD/hHis/Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/dV/Trp_Me/N/D-Orn/D-aThr//Phe_4Me,6.14884,0.6452232599258423,0.39612022042274475,0,false
33
- hPhe/hHis/Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/dV/Phe_ab-dehydro/N/D-Orn/D-aThr//Phe_4Me,6.40426,0.7010866403579712,0.3945997357368469,0,true
34
- dI/hHis/Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/dV/Thz/N/D-Orn/D-aThr//Phe_4Me,4.57459,0.2392749786376953,-0.23711872100830078,0,false
35
- /D-Tic/Hcy/N/T/dK/Thr_PO3H2/Phe_4NH2/D-Tyr_Et/Tyr_ab-dehydroMe/dV/Cys_SEt/N/D-2Pal/D-aThr//Phe_4Me,5.75670,0.2600181996822357,1.9668617248535156,0,false
36
- meI//Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/dV/Tyr_Bn/N/D-Orn/D-aThr//Phe_4Me,5.29810,-0.04338091239333153,0.13291242718696594,17.476734161376953,true
37
- meI//Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/dV/D-hArg/N/D-Orn/D-aThr//Phe_4Me,5.94887,-0.013414794579148293,0.18237340450286865,97.71964263916016,true
38
- meI//Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/4Abz/Thr_PO3H2/N/D-Orn/D-aThr//Phe_4Me,6.05301,0.1423971801996231,0.6929029226303101,2.6069343090057373,true
39
- /Thr_PO3H2/Aca/Tyr_ab-dehydroMe/dV/D-Pip/N/D-Orn/D-aThr//Phe_4Me,5.58673,-1.874976396560669,-1.1251744031906128,0,false
40
- meI//Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/dV/dK/N/D-Orn/D-aThr//Phe_4Me,6.60328,0.022662760689854622,0.2533372938632965,214.72315979003906,true
41
- meI//Aca/N/T/dK/Tyr_ab-dehydroMe/dV/D-Phg/N/D-Orn/D-aThr//Phe_4Me,6.21215,-0.944249153137207,-0.5838506817817688,0,false
42
- meI//Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/dV/Gly_allyl/N/D-Orn/D-aThr//Phe_4Me,5.73739,-0.024882297962903976,0.2659182548522949,67.26651763916016,true
43
- meI////T/dK/Thr_PO3H2/D-Thz/D-Tyr_Et/Tyr_ab-dehydroMe/dV/D-Thz/N/D-Orn/Oic_3aR-7aS//Phe_4Me,3.52183,-1.289717674255371,0.796217679977417,0,true
44
- Oic_3axi-7axi//Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/dV/Cys_SEt/N/D-2Pal/D-aThr//Phe_4Me,4.94922,0.6311581134796143,1.0401051044464111,0,false
45
- meI/hHis/Trp_Ome/N/T/dK/Thr_PO3H2/D-Hyp/D-Tyr_Et/Tyr_ab-dehydroMe/dV/E/N/D-Orn/D-aThr//Phe_4Me,5.58059,-0.0681256651878357,-0.6029895544052124,0,false
46
- /Aca/D-Tyr_Et/Tyr_ab-dehydroMe/dV/Thz/N/D-Orn/D-aThr//Phe_4Me,6.14975,-1.911975622177124,-0.9528587460517883,0,true
47
- meI/hHis/Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/dV/Phe_ab-dehydro/N/D-Orn/D-aThr//Phe_4Me,6.93447,0.4047900140285492,0.0385725237429142,9.54377555847168,true
48
- meI/hHis/Aca/N/T/dK/Thr_PO3H2/Aca/Met_O/Tyr_ab-dehydroMe/dV/Thr_PO3H2/N/D-Orn/D-aThr//Phe_4Me,4.86407,0.8048027753829956,0.18814975023269653,2.629258871078491,true
49
- meI/hHis/Aca/N/T/dK/Thr_PO3H2/Aca/His_1Me/Tyr_ab-dehydroMe/dV/Thr_PO3H2/N/D-Orn/D-aThr//Phe_4Me,4.71800,0.8228142261505127,0.2221541851758957,0,true
50
- meI////D-Thz/dK/Thr_PO3H2/NMe2Abz/D-Tyr_Et/Tyr_ab-dehydroMe/dV/NMe2Abz/N/D-Orn/D-aThr//Phe_4Me,6.20951,-1.4961341619491577,0.6778771877288818,0,false
51
- D-Bmt//Hcy/N/T/W/Q/Phe_4NH2/Tyr_PO3H2/Tyr_ab-dehydroMe/dV/Cys_SEt/N/D-Orn/D-aThr//Phe_4Me,3.81322,0.08868088573217392,2.597508668899536,0,false
52
- aHyp//Hcy/N/T/W/Q/Phe_4NH2/D-Tyr_Et/Tyr_ab-dehydroMe/dV/Cys_SEt/N/D-Orn/D-aThr//Phe_4Me,7.90369,-0.3908594846725464,2.2342283725738525,0,false
53
- meI/aMePro/Hcy/N/T/W/Q/Phe_4NH2/D-Tyr_Et/Tyr_ab-dehydroMe/dV/Aad/N/D-Orn/D-aThr//Phe_4Me,7.39222,-0.0022207542788237333,2.1672749519348145,0,false
54
- meI/hHis/Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/dV/E/N/A/D-aThr//Phe_4Me,3.88637,0.5533066987991333,-0.46762487292289734,28.333782196044922,true
55
- meI/hHis/Aca/N/T/Tyr_Me/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/dV/E/N/dV///Phe_4Me,4.66975,0.8956347107887268,-1.2199956178665161,0,false
56
- /hHis/Aca/N/T/dK/Thr_PO3H2/Aca/seC/Tyr_ab-dehydroMe/dV/E/N/D-Orn/D-aThr//Phe_4Me,6.38815,1.072934865951538,-0.0661509782075882,2.116978645324707,true
57
- meI/hHis/Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/Thr_PO3H2/dV/E/N/pnG///Phe_4Me,3.38318,1.237688660621643,-0.9708142876625061,0,true
58
- meI/hHis/Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/D-Chg/dV/E/N/D-aMeAbu/D-aThr//Phe_4Me,3.59309,1.0994300842285156,-0.40876659750938416,0,true
59
- meI/hHis/Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/dV/E/N/Thz/D-aThr//Phe_4Me,2.87946,0.5648310780525208,-0.45618200302124023,0,true
60
- meI/hHis/Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/D-Chg/dV/E/N/3Abz/D-aThr//Phe_4Me,7.60253,1.1164917945861816,-0.46195703744888306,149.2701416015625,true
61
- meI/hHis/Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/dV/E/N/meM///Phe_4Me,2.98472,0.8085882663726807,-0.8359185457229614,17.12320899963379,true
62
- D-Phg/hHis/Aca/N/T/dK/Thr_PO3H2/Aca/seC/Tyr_ab-dehydroMe/dV/E/N/D-Orn/D-aThr//Phe_4Me,6.27054,1.0916587114334106,0.019979439675807953,0,true
63
- meI/hHis/Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/A/dV/E/N/D-Orn/D-aThr//Phe_4Me,2.72803,0.6214887499809265,-0.36722248792648315,0,false
64
- meI/hHis/Aca/N/T/dK/Thr_PO3H2/Aca/A/Tyr_ab-dehydroMe/dV/E/N/D-Orn/D-aThr//Phe_4Me,3.71966,0.684988796710968,-0.22345584630966187,0,true
65
- meI/dE/Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/dV/D-Thz/N/D-Orn/D-aThr//Phe_4Me,5.06373,0.24633337557315826,0.2890184819698334,0,true
66
- meI////Pip/dK/Thr_PO3H2/pnT/D-Tyr_Et/Tyr_ab-dehydroMe/dV/Cys_SEt/N/D-Orn/D-aThr//Phe_4Me,4.58898,-1.1358332633972168,1.2197506427764893,0,false
67
- meI/D-2Thi/Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/dV/Thr_PO3H2/N/D-Orn/D-aThr//Phe_4Me,5.49809,0.3402663469314575,0.35587310791015625,0,true
68
- meI//D-Hyp/N/T/dK/Thr_PO3H2/Trp_Ome/D-Tyr_Et/Tyr_ab-dehydroMe/dV/E/N/D-Orn/D-aThr//Phe_4Me,3.07080,-0.5990715026855469,0.006005885545164347,0,false
69
- "meI////Pip/dK/Thr_PO3H2/L-hArg(Et,Et)/D-Tyr_Et/Tyr_ab-dehydroMe/dV/E/N/D-Orn/D-aThr//Phe_4Me",4.44629,-1.2494760751724243,0.3289206922054291,0,false
70
- meI////T/dK/Thr_PO3H2/D-Thz/D-Tyr_Et/Tyr_ab-dehydroMe/dV/D-Thz/N/D-Orn/xiHyp//Phe_4Me,6.32360,-1.2599071264266968,0.913629412651062,50.43183135986328,true
71
- meI/1Nal/Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/dV/Thr_PO3H2/N/D-Orn/D-aThr//Phe_4Me,5.90846,0.33817559480667114,0.40676024556159973,7.38666296005249,true
72
- meI/hHis/Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/Phe_4Sdihydroorotamido/dV/E/N/dV///Phe_4Me,2.47020,1.2842589616775513,-0.869986891746521,17.36207389831543,true
73
- meI//Aca/N/T/W/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/dV/Thr_PO3H2/N/D-Orn/D-aThr//Phe_4Me,5.84633,-0.11631345003843307,0.5462477803230286,0,false
74
- N/T/dK/Thr_PO3H2/Trp_Ome/D-Tyr_Et/Tyr_ab-dehydroMe/dV/E/N/D-Orn/D-aThr//Phe_4Me,4.39002,-0.704487681388855,-1.0367000102996826,0,false
75
- meI/hHis/D-Thz/N/Pip/dK/Thr_PO3H2/D-Thz/D-Tyr_Et/Tyr_ab-dehydroMe/dV/D-Thz/N/D-Orn/D-aThr//Phe_4Me,2.92846,-0.39414742588996887,1.315218210220337,0,false
76
- meI//Aca/D-Tyr_Et/Tyr_ab-dehydroMe/dV/E/N/Tyr_3OH///Phe_4Me,2.66868,-1.1101311445236206,-2.1285560131073,0,false
77
- meI/hHis/Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/dV/E/N/D-Orn/Orn//Phe_4Me,5.71958,0.48867273330688477,-0.448117196559906,0,false
78
- Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/dV/E/N/D-Orn/Oic_3aR-7aS//Phe_4Me,5.90143,-0.0903714969754219,-1.0966628789901733,0,false
79
- meI/hHis/Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/dV/E/N/D-Phe_4Cl///Phe_4Me,2.03343,0.7943960428237915,-0.8285616636276245,0,true
80
- meI/hHis/Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/dV/E/N/D-1Nal///Phe_4Me,4.29826,0.8097547292709351,-0.8324390053749084,64.41063690185547,true
81
- meI/hHis/Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/dV/E/N/D-xiIle/D-aThr//Phe_4Me,5.90934,0.6005289554595947,-0.5086122155189514,137.57411193847656,true
82
- D-1Nal/hHis/Aca/N/T/dK/Thr_PO3H2/Aca/Tyr_PO3H2/Tyr_ab-dehydroMe/dV/Cys_SEt/N/D-Orn/D-aThr//Phe_4Me,1.37957,0.9966986775398254,0.7701456546783447,0,false
83
- Phe_2F//Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/dV/Cys_SEt/N/D-Orn///Phe_4Me,5.54611,0.19441579282283783,0.8366346955299377,0,false
84
- meI//Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/dV/E/N/D-2Pal///meF,4.38201,0.40358930826187134,-1.3779624700546265,0,false
85
- meI////T/dK/dR/D-Thz/D-Tyr_Et/Tyr_ab-dehydroMe/dR/Thr_PO3H2/N/D-Orn/D-aThr//Phe_4Me,4.59437,-1.206743597984314,1.6398860216140747,0,false
86
- meI//Aca/N/T/dK/D-Thz/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/D-Thz/Thr_PO3H2/N/D-Orn/D-aThr//Phe_4Me,5.81956,0.40751710534095764,1.2538228034973145,0,false
87
- meI/Tyr_26diMe/Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/D-Dap/D-Thz/N/D-Orn/D-aThr//Phe_4Me,4.49219,0.41388168931007385,0.8675658702850342,0,false
88
- meI////T/dK/Thr_PO3H2/dR/D-Tyr_Et/Tyr_ab-dehydroMe/dV/dR/N/D-Orn/D-aThr//Phe_4Me,3.56886,-0.9029757976531982,0.8573476076126099,0,false
89
- meI//Aca/N/Pip/dK/D-Thz/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/D-Thz/Thr_PO3H2/N/D-Orn///Phe_4Me,1.92623,1.1478890180587769,1.5433778762817383,0,false
90
- D-Tic////////D-Tyr_Et/Tyr_ab-dehydroMe/dV/Cys_SEt/N/D-Orn/D-aThr//Phe_4Me,2.45736,-2.073575735092163,1.6658960580825806,0,false
91
- Phe_2F/////////Tyr_ab-dehydroMe/dV/Aca/N/D-Orn/D-aThr//Phe_4Me,0.41856,-2.535810947418213,1.5070313215255737,0,false
92
- meI/hHis/Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/dV/E/N/3Abz/D-aThr//Phe_4Me,3.31918,0.6050193309783936,-0.39509856700897217,7.914954662322998,true
93
- Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/dV/E/N/D-Trp_2Me/D-aThr//Phe_4Me,5.73646,0.046205081045627594,-1.0987070798873901,0,false
94
- Phe_4Sdihydroorotamido/hHis/Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/dV/E/N/D-Orn/D-aThr//Phe_4Me,5.47681,0.36598652601242065,-0.3528278172016144,0,false
95
- dK/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/dV/E/N/Phe_3Cl/meK//Phe_4Me,3.68756,-0.782490074634552,-2.2279326915740967,0,false
96
- meI/hHis/Aca/N/T/dK/Thr_PO3H2/Aca/Sta_3S4S/Tyr_ab-dehydroMe/dV/E/N/D-Orn/D-aThr//Phe_4Me,4.90078,0.6861110925674438,-0.1880904883146286,21.26015281677246,true
30
+ meI//Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/dV/Trp_Me/N/D-Orn/D-aThr//Phe_4Me,5.15504,0.007045681122690439,0.28774088621139526,7.176403522491455,true
package/package.json CHANGED
@@ -5,7 +5,7 @@
5
5
  "name": "Leonid Stolbov",
6
6
  "email": "lstolbov@datagrok.ai"
7
7
  },
8
- "version": "2.0.27",
8
+ "version": "2.0.29",
9
9
  "description": "Bio is a [package](https://datagrok.ai/help/develop/develop#packages) for the [Datagrok](https://datagrok.ai) platform",
10
10
  "repository": {
11
11
  "type": "git",
@@ -14,9 +14,9 @@
14
14
  },
15
15
  "dependencies": {
16
16
  "@biowasm/aioli": "^3.1.0",
17
- "@datagrok-libraries/bio": "^5.5.0",
17
+ "@datagrok-libraries/bio": "^5.7.0",
18
18
  "@datagrok-libraries/chem-meta": "1.0.1",
19
- "@datagrok-libraries/ml": "^6.2.0",
19
+ "@datagrok-libraries/ml": "^6.2.1",
20
20
  "@datagrok-libraries/utils": "^1.11.1",
21
21
  "cash-dom": "^8.0.0",
22
22
  "datagrok-api": "^1.7.0",
package/scripts/admet-run.py ADDED
@@ -0,0 +1,27 @@
1
+ #!/usr/bin/env python2
2
+ # -*- coding: utf-8 -*-
3
+ """
4
+ Created on Mon Feb 19 17:30:46 2018
5
+
6
+ @author: cbdd
7
+ """
8
+ from sklearn.externals import joblib
9
+ import numpy as np
10
+ import pandas as pd
11
+ import os
12
+
13
+ ###################################### Load model ##########
14
+ # current_path = os.path.split(os.path.realpath(__file__))[0]
15
+ cf = joblib.load('CYP3A4-substrate.pkl')
16
+
17
+ ###################################### Load descriptors ##########
18
+ fingerprint_content = pd.read_csv('des.csv').ix[:, 1:]
19
+ des_list = np.array(fingerprint_content)
20
+
21
+ ###################################### Prediction ##########
22
+ y_predict_label = cf.predict(des_list)
23
+ y_predict_proba = cf.predict_proba(des_list)
24
+ print('#' * 10 + 'Results labels' + '#' * 10)
25
+ print(y_predict_label)
26
+ print('#' * 10 + 'Results probabilities' + '#' * 10)
27
+ print(y_predict_proba)
package/src/analysis/sequence-activity-cliffs.ts CHANGED
@@ -8,6 +8,8 @@ import {getSimilarityFromDistance} from '@datagrok-libraries/utils/src/similarit
8
8
  import {AvailableMetrics} from '@datagrok-libraries/ml/src/typed-metrics';
9
9
  import {TAGS} from '../utils/constants';
10
10
  import {drawMoleculeDifferenceOnCanvas} from '../utils/cell-renderer';
11
+ import * as C from '../utils/constants';
12
+ import { GridColumn } from 'datagrok-api/dg';
11
13
 
12
14
  export async function getDistances(col: DG.Column, seq: string): Promise<Array<number>> {
13
15
  const stringArray = col.toList();
@@ -103,7 +105,7 @@ function createPropPanelField(name: string, value: number): HTMLDivElement {
103
105
  return ui.divH([
104
106
  ui.divText(`${name}: `, {style: {fontWeight: 'bold', paddingRight: '5px'}}),
105
107
  ui.divText(value.toFixed(2))
106
- ], {style: {paddingTop: '5px'}});
108
+ ], {style: {paddingTop: '10px'}});
107
109
  }
108
110
 
109
111
  export function createDifferenceCanvas(
@@ -138,3 +140,16 @@ export function createDifferencesWithPositions(
138
140
  }
139
141
  return div;
140
142
  }
143
+
144
+ export function createLinesGrid(df: DG.DataFrame, colNames: string[]): DG.Grid {
145
+ const seqDiffCol = DG.Column.string('seq_diff', df.rowCount)
146
+ .init((i) => `${df.get(colNames[0], i)}#${df.get(colNames[1], i)}`);
147
+ seqDiffCol.semType = 'MacromoleculeDifference';
148
+ seqDiffCol.setTag(DG.TAGS.UNITS, df.col(colNames[0])!.getTag(DG.TAGS.UNITS));
149
+ seqDiffCol.setTag(C.TAGS.SEPARATOR, df.col(colNames[0])!.getTag(C.TAGS.SEPARATOR));
150
+ df.columns.add(seqDiffCol);
151
+ const grid = df.plot.grid();
152
+ grid.col(colNames[0])!.visible = false;
153
+ grid.col(colNames[1])!.visible = false;
154
+ return grid;
155
+ }
package/src/analysis/sequence-similarity-viewer.ts CHANGED
@@ -8,7 +8,6 @@ import {getMonomericMols} from '../calculations/monomerLevelMols';
8
8
  import * as C from '../utils/constants';
9
9
  import {createDifferenceCanvas, createDifferencesWithPositions} from './sequence-activity-cliffs';
10
10
  import {updateDivInnerHTML} from '../utils/ui-utils';
11
- import {TableView} from 'datagrok-api/dg';
12
11
  import {Subject} from 'rxjs';
13
12
 
14
13
  export class SequenceSimilarityViewer extends SequenceSearchBaseViewer {
@@ -62,7 +61,7 @@ export class SequenceSimilarityViewer extends SequenceSearchBaseViewer {
62
61
  const resDf = DG.DataFrame.fromColumns([this.idxs!, this.molCol!, this.scores!]);
63
62
  resDf.onCurrentRowChanged.subscribe((_) => {
64
63
  this.dataFrame.currentRowIdx = resDf.col('indexes')!.get(resDf.currentRowIdx);
65
- this.createPropertyPanel(resDf);
64
+ setTimeout(() => { this.createPropertyPanel(resDf); }, 1000);
66
65
  this.gridSelect = true;
67
66
  });
68
67
  const grid = resDf.plot.grid();
@@ -70,7 +69,7 @@ export class SequenceSimilarityViewer extends SequenceSearchBaseViewer {
70
69
  const targetMolRow = this.idxs?.getRawData().findIndex((it) => it == this.targetMoleculeIdx);
71
70
  const targetScoreCell = grid.cell('score', targetMolRow!);
72
71
  targetScoreCell.cell.value = null;
73
- (grok.shell.v as TableView).grid.root.addEventListener('click', (event: MouseEvent) => {
72
+ (grok.shell.v as DG.TableView).grid.root.addEventListener('click', (event: MouseEvent) => {
74
73
  this.gridSelect = false;
75
74
  });
76
75
  updateDivInnerHTML(this.root, grid.root);
package/src/package.ts CHANGED
@@ -12,7 +12,7 @@ import {runKalign, testMSAEnoughMemory} from './utils/multiple-sequence-alignmen
12
12
  import {SequenceAlignment, Aligned} from './seq_align';
13
13
  import {getEmbeddingColsNames, sequenceSpace} from './analysis/sequence-space';
14
14
  import {getActivityCliffs} from '@datagrok-libraries/ml/src/viewers/activity-cliffs';
15
- import {createPropPanelElement, createTooltipElement, getSimilaritiesMarix} from './analysis/sequence-activity-cliffs';
15
+ import {createLinesGrid, createPropPanelElement, createTooltipElement, getSimilaritiesMarix} from './analysis/sequence-activity-cliffs';
16
16
  import {createJsonMonomerLibFromSdf, encodeMonomers, getMolfilesFromSeq} from '@datagrok-libraries/bio/src/utils/monomer-utils';
17
17
  import {HELM_CORE_LIB_FILENAME} from '@datagrok-libraries/bio/src/utils/const';
18
18
  import {getMacroMol} from './utils/atomic-works';
@@ -195,6 +195,7 @@ export async function activityCliffs(df: DG.DataFrame, macroMolecule: DG.Column,
195
195
  getSimilaritiesMarix,
196
196
  createTooltipElement,
197
197
  createPropPanelElement,
198
+ createLinesGrid,
198
199
  (options as any)[methodName]);
199
200
  return sp;
200
201
  }
package/src/substructure-search/substructure-search.ts CHANGED
@@ -5,12 +5,11 @@ import * as bio from '@datagrok-libraries/bio';
5
5
 
6
6
  import * as C from '../utils/constants';
7
7
  import {getMonomericMols} from '../calculations/monomerLevelMols';
8
- import {BitSet} from 'datagrok-api/dg';
9
8
  import {updateDivInnerHTML} from '../utils/ui-utils';
10
9
 
11
10
  export const MONOMER_MOLS_COL = 'monomeric-mols';
12
11
 
13
- const enum MONOMERIC_COL_TAGS{
12
+ const enum MONOMERIC_COL_TAGS {
14
13
  MONOMERIC_MOLS = 'monomeric-mols',
15
14
  LAST_INVALIDATED_VERSION = 'last-invalidated-version',
16
15
  MONOMERS_DICT = 'monomers-dict'
@@ -64,7 +63,7 @@ export function substructureSearchDialog(col: DG.Column): void {
64
63
  const colExists = col.dataFrame.columns.names()
65
64
  .filter((it) => it.toLocaleLowerCase() === matchesColName.toLocaleLowerCase()).length > 0;
66
65
  if (!colExists) {
67
- let matches: BitSet;
66
+ let matches: DG.BitSet;
68
67
  if (units === bio.NOTATION.HELM)
69
68
  matches = await helmSubstructureSearch(substructure, col);
70
69
  else
@@ -92,13 +91,13 @@ function prepareSubstructureRegex(substructure: string, separator: string) {
92
91
  const endsWithSep = substructure.charAt(substructure.length - 1) === separator;
93
92
  const substrWithoutSep = substructure.replace(new RegExp(`^${char}|${char}$`, 'g'), '');
94
93
  const re = startsWithSep ? endsWithSep ? `${char}${substrWithoutSep}${char}` :
95
- `${char}${substrWithoutSep}${char}|${char}${substrWithoutSep}$` :
94
+ `${char}${substrWithoutSep}${char}|${char}${substrWithoutSep}$` :
96
95
  endsWithSep ? `^${substrWithoutSep}${char}|${char}${substrWithoutSep}${char}` :
97
96
  `^${substrWithoutSep}${char}|${char}${substrWithoutSep}${char}|${char}${substrWithoutSep}$`;
98
97
  return re;
99
98
  }
100
99
 
101
- export async function helmSubstructureSearch(substructure: string, col: DG.Column): Promise<BitSet> {
100
+ export async function helmSubstructureSearch(substructure: string, col: DG.Column): Promise<DG.BitSet> {
102
101
  if (col.version !== col.temp[MONOMERIC_COL_TAGS.LAST_INVALIDATED_VERSION])
103
102
  await invalidateHelmMols(col);
104
103
  const substructureCol = DG.Column.string('helm', 1).init((i) => substructure);
package/src/tests/activity-cliffs-tests.ts CHANGED
@@ -16,7 +16,7 @@ category('activityCliffs', async () => {
16
16
  test('activityCliffsOpens', async () => {
17
17
  actCliffsDf = await readDataframe('tests/sample_MSA_data.csv');
18
18
  actCliffsTableView = grok.shell.addTableView(actCliffsDf);
19
- await _testActivityCliffsOpen(actCliffsDf, 102, 'UMAP', 'MSA');
19
+ await _testActivityCliffsOpen(actCliffsDf, 36, 'UMAP', 'MSA');
20
20
  grok.shell.closeTable(actCliffsDf);
21
21
  actCliffsTableView.close();
22
22
  });
@@ -24,7 +24,7 @@ category('activityCliffs', async () => {
24
24
  test('activityCliffsWithEmptyRows', async () => {
25
25
  actCliffsDfWithEmptyRows = await readDataframe('tests/sample_MSA_data_empty_vals.csv');
26
26
  actCliffsTableViewWithEmptyRows = grok.shell.addTableView(actCliffsDfWithEmptyRows);
27
- await _testActivityCliffsOpen(actCliffsDfWithEmptyRows, 103, 'UMAP', 'MSA');
27
+ await _testActivityCliffsOpen(actCliffsDfWithEmptyRows, 37, 'UMAP', 'MSA');
28
28
  grok.shell.closeTable(actCliffsDfWithEmptyRows);
29
29
  actCliffsTableViewWithEmptyRows.close();
30
30
  });
package/src/tests/checkInputColumn-tests.ts CHANGED
@@ -7,8 +7,6 @@ import * as bio from '@datagrok-libraries/bio';
7
7
  import {after, before, category, test, expect, expectArray} from '@datagrok-libraries/utils/src/test';
8
8
 
9
9
  import {checkInputColumn, multipleSequenceAlignmentAny} from '../package';
10
- import {UNITS} from 'datagrok-api/dg';
11
- import {ALPHABET, NOTATION} from '@datagrok-libraries/bio/src/utils/macromolecule';
12
10
 
13
11
  category('checkInputColumn', () => {
14
12
  const csv = `seq
@@ -41,7 +39,7 @@ seq4`;
41
39
  const df: DG.DataFrame = DG.DataFrame.fromCsv(csv);
42
40
  const col: DG.Column = df.getCol('seq');
43
41
  col.semType = DG.SEMTYPE.MACROMOLECULE;
44
- col.setTag(DG.TAGS.UNITS, NOTATION.HELM);
42
+ col.setTag(DG.TAGS.UNITS, bio.NOTATION.HELM);
45
43
  col.setTag(bio.TAGS.alphabetSize, '11');
46
44
  col.setTag(bio.TAGS.alphabetIsMultichar, 'true');
47
45
 
@@ -56,7 +54,7 @@ seq4`;
56
54
  const df: DG.DataFrame = DG.DataFrame.fromCsv(csv);
57
55
  const col: DG.Column = df.getCol('seq');
58
56
  col.semType = DG.SEMTYPE.MACROMOLECULE;
59
- col.setTag(DG.TAGS.UNITS, NOTATION.FASTA);
57
+ col.setTag(DG.TAGS.UNITS, bio.NOTATION.FASTA);
60
58
  col.setTag(bio.TAGS.alphabet, 'UN');
61
59
  col.setTag(bio.TAGS.alphabetSize, '11');
62
60
  col.setTag(bio.TAGS.alphabetIsMultichar, 'true');
package/src/tests/sequence-space-test.ts CHANGED
@@ -11,17 +11,17 @@ category('sequenceSpace', async () => {
11
11
  let testHelmWithEmptyRowsTableView: DG.TableView;
12
12
 
13
13
  test('sequenceSpaceOpens', async () => {
14
- testFastaDf = await readDataframe('samples/sample_FASTA.csv');
14
+ testFastaDf = await readDataframe('tests/sample_MSA_data.csv');
15
15
  testFastaTableView = grok.shell.addTableView(testFastaDf);
16
- await _testSequenceSpaceReturnsResult(testFastaDf, 'UMAP', 'Sequence');
16
+ await _testSequenceSpaceReturnsResult(testFastaDf, 'UMAP', 'MSA');
17
17
  grok.shell.closeTable(testFastaDf);
18
18
  testFastaTableView.close();
19
19
  });
20
20
 
21
21
  test('sequenceSpaceWithEmptyRows', async () => {
22
- testHelmWithEmptyRows = await readDataframe('data/sample_HELM_empty_vals.csv');
22
+ testHelmWithEmptyRows = await readDataframe('tests/sample_MSA_data_empty_vals.csv');
23
23
  testHelmWithEmptyRowsTableView = grok.shell.addTableView(testHelmWithEmptyRows);
24
- await _testSequenceSpaceReturnsResult(testHelmWithEmptyRows, 'UMAP', 'HELM');
24
+ await _testSequenceSpaceReturnsResult(testHelmWithEmptyRows, 'UMAP', 'MSA');
25
25
  grok.shell.closeTable(testHelmWithEmptyRows);
26
26
  testHelmWithEmptyRowsTableView.close();
27
27
  });
package/src/tests/similarity-diversity-tests.ts CHANGED
@@ -14,7 +14,7 @@ category('similarity/diversity', async () => {
14
14
  });
15
15
 
16
16
  async function _testSimilaritySearchViewer() {
17
- const molecules = await createTableView('samples/sample_MSA.csv');
17
+ const molecules = await createTableView('tests/sample_MSA_data.csv');
18
18
  const viewer = molecules.addViewer('SequenceSimilaritySearchViewer');
19
19
  await delay(100);
20
20
  const similaritySearchviewer = getSearchViewer(viewer, 'SequenceSimilaritySearchViewer');
@@ -25,11 +25,11 @@ async function _testSimilaritySearchViewer() {
25
25
  expect(similaritySearchviewer.scores!.get(0), DG.FLOAT_NULL);
26
26
  expect(similaritySearchviewer.idxs!.get(0), 0);
27
27
  expect(similaritySearchviewer.molCol!.get(0),
28
- 'meI/hHis/Aca/N/T/dE/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/dV/E/N/D-Orn/D-aThr//Phe_4Me');
29
- expect(similaritySearchviewer.scores!.get(1), 0.6603773832321167);
30
- expect(similaritySearchviewer.idxs!.get(1), 100);
28
+ 'D-Tyr_Et/Tyr_ab-dehydroMe/dV/E/N/D-Orn/D-aThr//Phe_4Me');
29
+ expect(similaritySearchviewer.scores!.get(1), 0.4722222089767456);
30
+ expect(similaritySearchviewer.idxs!.get(1), 11);
31
31
  expect(similaritySearchviewer.molCol!.get(1),
32
- 'meI/hHis/Aca/N/T/W/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/dV/E/N/D-Orn/D-aThr//Phe_4Me');
32
+ 'meI/hHis//Aca/meM/Tyr_ab-dehydroMe/dV/E/N/D-Orn/D-aThr//Phe_4Me');
33
33
  molecules.dataFrame.currentRowIdx = 1;
34
34
  await delay(100);
35
35
  await waitForCompute(similaritySearchviewer);
@@ -42,7 +42,7 @@ async function _testSimilaritySearchViewer() {
42
42
 
43
43
 
44
44
  async function _testDiversitySearchViewer() {
45
- const molecules = await createTableView('samples/sample_MSA.csv');
45
+ const molecules = await createTableView('tests/sample_MSA_data.csv');
46
46
  const viewer = molecules.addViewer('SequenceDiversitySearchViewer');
47
47
  await delay(10);
48
48
  const diversitySearchviewer = getSearchViewer(viewer, 'SequenceDiversitySearchViewer');
@@ -67,7 +67,6 @@ async function waitForCompute(viewer: SequenceSimilarityViewer) {
67
67
  const t = new Promise((resolve, reject) => {
68
68
  viewer.computeCompleted.subscribe(async (_: any) => {
69
69
  try {
70
- console.log(`!@#$%^&*()`+viewer.targetMoleculeIdx);
71
70
  resolve(true);
72
71
  } catch (error) {
73
72
  reject(error);
package/src/tests/substructure-filter-tests.ts CHANGED
@@ -47,7 +47,7 @@ category('substructureFilters', async () => {
47
47
  filter.attach(helm);
48
48
  (filter.bioFilter! as HelmFilter).helmSubstructure = 'PEPTIDE1{C}$$$$V2.0';
49
49
  filter.bioFilter!.onChanged.next();
50
- await delay(1000);
50
+ await delay(2000);
51
51
  expect(filter.dataFrame!.filter.trueCount, 2);
52
52
  expect(filter.dataFrame!.filter.get(0), true);
53
53
  expect(filter.dataFrame!.filter.get(3), true);