@datagrok/bio 2.0.28 → 2.0.30

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 (16) hide show
  1. package/dist/package-test.js +140 -87
  2. package/dist/package.js +127 -73
  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 +2 -2
  6. package/scripts/admet-requirements.txt +7 -0
  7. package/src/analysis/sequence-activity-cliffs.ts +16 -1
  8. package/src/analysis/sequence-similarity-viewer.ts +1 -1
  9. package/src/package.ts +32 -8
  10. package/src/substructure-search/substructure-search.ts +8 -4
  11. package/src/tests/activity-cliffs-tests.ts +2 -2
  12. package/src/tests/sequence-space-test.ts +4 -4
  13. package/src/tests/similarity-diversity-tests.ts +6 -7
  14. package/src/tests/substructure-filter-tests.ts +1 -1
  15. package/src/widgets/bio-substructure-filter.ts +3 -3
  16. package/test-Bio-49ff04f38f57-8ab13d10.html +0 -385
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
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/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": "2.0.28",
8
+ "version": "2.0.30",
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",
@@ -16,7 +16,7 @@
16
16
  "@biowasm/aioli": "^3.1.0",
17
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-requirements.txt ADDED
@@ -0,0 +1,7 @@
1
+ numpy==1.16.6
2
+ pandas==0.24.2
3
+ python-dateutil==2.8.2
4
+ pytz==2022.5
5
+ scikit-learn==0.17.1
6
+ scipy==1.2.3
7
+ six==1.16.0
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
@@ -61,7 +61,7 @@ export class SequenceSimilarityViewer extends SequenceSearchBaseViewer {
61
61
  const resDf = DG.DataFrame.fromColumns([this.idxs!, this.molCol!, this.scores!]);
62
62
  resDf.onCurrentRowChanged.subscribe((_) => {
63
63
  this.dataFrame.currentRowIdx = resDf.col('indexes')!.get(resDf.currentRowIdx);
64
- this.createPropertyPanel(resDf);
64
+ setTimeout(() => { this.createPropertyPanel(resDf); }, 1000);
65
65
  this.gridSelect = true;
66
66
  });
67
67
  const grid = resDf.plot.grid();
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';
@@ -34,9 +34,11 @@ import {splitAlignedSequences} from '@datagrok-libraries/bio/src/utils/splitter'
34
34
  import * as C from './utils/constants';
35
35
  import {SequenceSimilarityViewer} from './analysis/sequence-similarity-viewer';
36
36
  import {SequenceDiversityViewer} from './analysis/sequence-diversity-viewer';
37
- import {substructureSearchDialog} from './substructure-search/substructure-search';
37
+ import {invalidateMols, MONOMERIC_COL_TAGS, substructureSearchDialog} from './substructure-search/substructure-search';
38
38
  import {saveAsFastaUI} from './utils/save-as-fasta';
39
39
  import {BioSubstructureFilter} from './widgets/bio-substructure-filter';
40
+ import { getMonomericMols } from './calculations/monomerLevelMols';
41
+ import { delay } from '@datagrok-libraries/utils/src/test';
40
42
 
41
43
  //tags: init
42
44
  export async function initBio() {
@@ -195,6 +197,7 @@ export async function activityCliffs(df: DG.DataFrame, macroMolecule: DG.Column,
195
197
  getSimilaritiesMarix,
196
198
  createTooltipElement,
197
199
  createPropPanelElement,
200
+ createLinesGrid,
198
201
  (options as any)[methodName]);
199
202
  return sp;
200
203
  }
@@ -204,13 +207,35 @@ export async function activityCliffs(df: DG.DataFrame, macroMolecule: DG.Column,
204
207
  //input: dataframe table
205
208
  //input: column macroMolecule { semType: Macromolecule }
206
209
  //input: string methodName { choices:["UMAP", "t-SNE", "SPE"] }
207
- //input: string similarityMetric { choices:["Levenshtein", "Tanimoto"] }
210
+ //input: string similarityMetric { choices:["Tanimoto", "Asymmetric", "Cosine", "Sokal"] }
208
211
  //input: bool plotEmbeddings = true
209
212
  export async function sequenceSpaceTopMenu(table: DG.DataFrame, macroMolecule: DG.Column, methodName: string,
210
- similarityMetric: string = 'Levenshtein', plotEmbeddings: boolean): Promise<DG.Viewer | undefined> {
211
- if (!checkInputColumnUi(macroMolecule, 'Activity Cliffs'))
213
+ similarityMetric: string = 'Tanimoto', plotEmbeddings: boolean): Promise<DG.Viewer | undefined> {
214
+ //delay is required for initial function dialog to close before starting invalidating of molfiles. Otherwise dialog is freezing
215
+ await delay(10);
216
+ if (!checkInputColumnUi(macroMolecule, 'Sequence space'))
212
217
  return;
213
- const encodedCol = encodeMonomers(macroMolecule);
218
+
219
+ if (macroMolecule.version !== macroMolecule.temp[MONOMERIC_COL_TAGS.LAST_INVALIDATED_VERSION])
220
+ await invalidateMols(macroMolecule, false);
221
+ const embedColsNames = getEmbeddingColsNames(table);
222
+
223
+ await grok.functions.call('Chem:getChemSpaceEmbeddings', {
224
+ table: table,
225
+ col: macroMolecule.temp[MONOMERIC_COL_TAGS.MONOMERIC_MOLS],
226
+ methodName: methodName,
227
+ similarityMetric: similarityMetric,
228
+ xAxis: embedColsNames[0],
229
+ yAxis: embedColsNames[1]
230
+ });
231
+
232
+ if (plotEmbeddings) {
233
+ return grok.shell
234
+ .tableView(table.name)
235
+ .scatterPlot({x: embedColsNames[0], y: embedColsNames[1], title: 'Sequence space'});
236
+ };
237
+
238
+ /* const encodedCol = encodeMonomers(macroMolecule);
214
239
  if (!encodedCol)
215
240
  return;
216
241
  const embedColsNames = getEmbeddingColsNames(table);
@@ -236,8 +261,7 @@ export async function sequenceSpaceTopMenu(table: DG.DataFrame, macroMolecule: D
236
261
  if (v.name === table.name)
237
262
  sp = (v as DG.TableView).scatterPlot({x: embedColsNames[0], y: embedColsNames[1], title: 'Sequence space'});
238
263
  }
239
- }
240
- return sp;
264
+ } */
241
265
  };
242
266
 
243
267
  //top-menu: Bio | To Atomic Level...
package/src/substructure-search/substructure-search.ts CHANGED
@@ -6,10 +6,11 @@ import * as bio from '@datagrok-libraries/bio';
6
6
  import * as C from '../utils/constants';
7
7
  import {getMonomericMols} from '../calculations/monomerLevelMols';
8
8
  import {updateDivInnerHTML} from '../utils/ui-utils';
9
+ import { delay } from '@datagrok-libraries/utils/src/test';
9
10
 
10
11
  export const MONOMER_MOLS_COL = 'monomeric-mols';
11
12
 
12
- const enum MONOMERIC_COL_TAGS {
13
+ export const enum MONOMERIC_COL_TAGS {
13
14
  MONOMERIC_MOLS = 'monomeric-mols',
14
15
  LAST_INVALIDATED_VERSION = 'last-invalidated-version',
15
16
  MONOMERS_DICT = 'monomers-dict'
@@ -99,7 +100,7 @@ function prepareSubstructureRegex(substructure: string, separator: string) {
99
100
 
100
101
  export async function helmSubstructureSearch(substructure: string, col: DG.Column): Promise<DG.BitSet> {
101
102
  if (col.version !== col.temp[MONOMERIC_COL_TAGS.LAST_INVALIDATED_VERSION])
102
- await invalidateHelmMols(col);
103
+ await invalidateMols(col, true);
103
104
  const substructureCol = DG.Column.string('helm', 1).init((i) => substructure);
104
105
  substructureCol.setTag(DG.TAGS.UNITS, bio.NOTATION.HELM);
105
106
  const substructureMolsCol =
@@ -112,10 +113,13 @@ export async function helmSubstructureSearch(substructure: string, col: DG.Colum
112
113
  return matchesCol.get(0);
113
114
  }
114
115
 
115
- export async function invalidateHelmMols(col: DG.Column) {
116
+ export async function invalidateMols(col: DG.Column, pattern: boolean) {
117
+ const progressBar = DG.TaskBarProgressIndicator.create(`Invalidating molfiles for ${col.name}`);
118
+ await delay(10);
116
119
  const monomersDict = new Map();
117
- const monomericMolsCol = await getMonomericMols(col, true, monomersDict);
120
+ const monomericMolsCol = await getMonomericMols(col, pattern, monomersDict);
118
121
  col.temp[MONOMERIC_COL_TAGS.MONOMERIC_MOLS] = monomericMolsCol;
119
122
  col.temp[MONOMERIC_COL_TAGS.MONOMERS_DICT] = monomersDict;
120
123
  col.temp[MONOMERIC_COL_TAGS.LAST_INVALIDATED_VERSION] = col.version;
124
+ progressBar.close();
121
125
  }
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/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);
package/src/widgets/bio-substructure-filter.ts CHANGED
@@ -207,12 +207,12 @@ export class HelmFilter extends BioFilterBase {
207
207
  await ui.tools.waitForElementInDom(this._filterPanel);
208
208
  this.updateFilterPanel();
209
209
  this._filterPanel.addEventListener('click', (event: MouseEvent) => {
210
+ const {editorDiv, webEditor} = this.helmEditor.createWebEditor(this.helmSubstructure);
210
211
  //@ts-ignore
211
212
  ui.dialog({showHeader: false, showFooter: true})
212
- .add(this.helmEditor.editorView)
213
+ .add(editorDiv)
213
214
  .onOK(() => {
214
- const helmString = this.helmEditor
215
- .webEditor.canvas.getHelm(true).replace(/<\/span>/g, '').replace(/<span style='background:#bbf;'>/g, '');
215
+ const helmString = webEditor.canvas.getHelm(true).replace(/<\/span>/g, '').replace(/<span style='background:#bbf;'>/g, '');
216
216
  this.helmSubstructure = helmString;
217
217
  this.updateFilterPanel(this.substructure);
218
218
  setTimeout(() => { this.onChanged.next(); }, 10);