@datagrok/bio 2.0.28 → 2.0.29

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Files changed (13) hide show
  1. package/dist/package-test.js +68 -38
  2. package/dist/package.js +55 -24
  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/src/analysis/sequence-activity-cliffs.ts +16 -1
  7. package/src/analysis/sequence-similarity-viewer.ts +1 -1
  8. package/src/package.ts +2 -1
  9. package/src/tests/activity-cliffs-tests.ts +2 -2
  10. package/src/tests/sequence-space-test.ts +4 -4
  11. package/src/tests/similarity-diversity-tests.ts +6 -7
  12. package/src/tests/substructure-filter-tests.ts +1 -1
  13. 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": "2.0.29",
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",
@@ -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/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';
@@ -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/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);