@datagrok/bio 2.0.3 → 2.0.5

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 (14) hide show
  1. package/dist/package-test.js +99 -91
  2. package/dist/package.js +77 -85
  3. package/files/tests/sample_MSA_data.csv +96 -0
  4. package/files/tests/sample_MSA_data_empty_vals.csv +96 -0
  5. package/package.json +1 -1
  6. package/src/__jest__/test-node.ts +1 -1
  7. package/src/package.ts +7 -6
  8. package/src/tests/activity-cliffs-tests.ts +4 -4
  9. package/src/tests/activity-cliffs-utils.ts +1 -1
  10. package/src/tests/renderers-test.ts +1 -1
  11. package/src/tests/splitters-test.ts +21 -0
  12. package/src/utils/cell-renderer.ts +64 -46
  13. package/src/utils/sequence-activity-cliffs.ts +29 -41
  14. package/{test-Bio-c5a05867bf79-cba1e171.html → test-Bio-7770371320b2-4674dcdc.html} +94 -99
package/files/tests/sample_MSA_data.csv ADDED
@@ -0,0 +1,96 @@
1
+ MSA,Activity,Embed_X_1,Embed_Y_1,sali__1,containsCliff_1
2
+ D-Tyr_Et/Tyr_ab-dehydroMe/dV/E/N/D-Orn/D-aThr//Phe_4Me,5.30751,-1.8903083801269531,-1.661839246749878,0,false
3
+ meI/hHis/Aca/Cys_SEt/T/dK/Thr_PO3H2/Aca/Tyr_PO3H2/D-Chg/dV/Phe_ab-dehydro/N/D-Orn/D-aThr//Phe_4Me,5.72388,1.561508297920227,0.3119281530380249,0,true
4
+ Lys_Boc/hHis/Aca/Cys_SEt/T/dK/Thr_PO3H2/Aca/Tyr_PO3H2/D-Chg/dV/Thr_PO3H2/N/D-Orn/D-aThr//Phe_4Me,5.18581,1.8352901935577393,0.6328232288360596,0,true
5
+ meI/hHis/Aca/Cys_SEt/T/dK/Thr_PO3H2/Aca/Tyr_PO3H2/D-Chg/dV/Thr_PO3H2/N/D-Orn/D-aThr//Phe_4Me,6.22350,1.5621939897537231,0.5008559823036194,27.671560287475586,true
6
+ Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/dV/Chg/N/D-Orn/D-aThr//Phe_4Me,3.84591,-1.6137192249298096,-1.276538610458374,0,false
7
+ meI/hHis/Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_Bn/dV/E/N/dV///Phe_4Me,3.27920,1.1405763626098633,-1.071689486503601,61.04805374145508,true
8
+ meI/hHis/Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/Aze/dV/E/N/dV///Phe_4Me,2.10585,1.1493492126464844,-1.0257583856582642,4.245477676391602,true
9
+ /D-Tyr_Et/meQ/dV/E/N/dV///Phe_4Me,1.80369,-1.874788522720337,-2.621032953262329,0,false
10
+ meI/hHis/Aca/N/T/dK/Thr_PO3H2/Aca/Oic_3aS-7aS/D-Chg/dV/E/N/D-Orn/D-aThr//Phe_4Me,6.38806,1.2151710987091064,-0.1381276398897171,19.07081413269043,true
11
+ meI/hHis/Aca/N/T/dK/Thr_PO3H2/Aca/E/N/D-Orn/D-aThr//Phe_4Me,4.44165,0.5254772305488586,-1.4159870147705078,0,false
12
+ meI/hHis/Aca/N/T/dK/Thr_PO3H2/Aca/Oic_3aS-7aS/Tyr_ab-dehydroMe/dV/E/N/D-Orn/D-aThr//Phe_4Me,5.32857,0.7058690190315247,-0.18089637160301208,36.66057586669922,true
13
+ meI/hHis//Aca/meM/Tyr_ab-dehydroMe/dV/E/N/D-Orn/D-aThr//Phe_4Me,4.70637,-1.1708372831344604,-1.661417841911316,0,false
14
+ meI/hHis/Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/D-Dap/dV/E/N/pnG///Phe_4Me,3.51582,1.225983738899231,-0.98129802942276,2.3875210285186768,true
15
+ meI//Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/dV/D-Cit/N/D-Orn/D-aThr//Phe_4Me,5.02344,0.01807424984872341,0.16467878222465515,0.8364539742469788,true
16
+ meI//Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/dV/meL/N/D-Orn/D-aThr//Phe_4Me,6.38359,-0.030419517308473587,0.20976503193378448,171.22459411621094,true
17
+ meI//Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/dV/Dsu/N/D-Orn/D-aThr//Phe_4Me,5.06602,0.022242402657866478,0.20077788829803467,2.369337797164917,true
18
+ Thr_PO3H2/D-Thz/D-Tyr_Et/Tyr_ab-dehydroMe/dV/D-Thz/N/D-Orn/D-aThr/Thz/Phe_4Me,5.05713,-2.348414897918701,-0.9183459877967834,0,false
19
+ meI//Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/dV/dE/N/D-Orn/D-aThr//Phe_4Me,4.97697,0.008319525979459286,0.3116433024406433,0,true
20
+ meI//Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/dV/meF/N/D-Orn/D-aThr//Phe_4Me,5.34730,0.01848183386027813,0.2308797389268875,21.90473747253418,true
21
+ meI/////dK/Thr_PO3H2/D-Thz/D-Tyr_Et/Tyr_ab-dehydroMe/dV/D-Thz/N/D-Orn/D-aThr//Phe_4Me,5.51508,-1.3141636848449707,0.9964643716812134,6.690232753753662,true
22
+ meI/hHis/Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/Lys_Boc/dV/E/N/dV///Phe_4Me,1.86999,1.2052497863769531,-1.024699091911316,0,true
23
+ meI//Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/N/D-Orn/D-aThr//Phe_4Me,5.65780,-0.37085768580436707,-0.28365179896354675,0,false
24
+ meI//Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/dV/pnA/N/D-Orn/D-aThr//Phe_4Me,5.55783,-0.01638980768620968,0.11942846328020096,44.641944885253906,true
25
+ meI//Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/dV/D-Thz/N/D-Orn/D-aThr//Phe_4Me,6.21246,-0.06910920888185501,0.2709718346595764,161.0983123779297,true
26
+ /Aca/D-Tyr_Et/Tyr_ab-dehydroMe/dV/D-2Pal/N/D-Orn/D-aThr//Phe_4Me,6.57811,-1.897789716720581,-1.1608996391296387,5.140321254730225,true
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
+ 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
+ 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
package/files/tests/sample_MSA_data_empty_vals.csv ADDED
@@ -0,0 +1,96 @@
1
+ MSA,Activity,Embed_X_1,Embed_Y_1,sali__1,containsCliff_1
2
+ ,-1.8903083801269531,-1.661839246749878,0,false
3
+ meI/hHis/Aca/Cys_SEt/T/dK/Thr_PO3H2/Aca/Tyr_PO3H2/D-Chg/dV/Phe_ab-dehydro/N/D-Orn/D-aThr//Phe_4Me,5.72388,1.561508297920227,0.3119281530380249,0,true
4
+ Lys_Boc/hHis/Aca/Cys_SEt/T/dK/Thr_PO3H2/Aca/Tyr_PO3H2/D-Chg/dV/Thr_PO3H2/N/D-Orn/D-aThr//Phe_4Me,5.18581,1.8352901935577393,0.6328232288360596,0,true
5
+ meI/hHis/Aca/Cys_SEt/T/dK/Thr_PO3H2/Aca/Tyr_PO3H2/D-Chg/dV/Thr_PO3H2/N/D-Orn/D-aThr//Phe_4Me,6.22350,1.5621939897537231,0.5008559823036194,27.671560287475586,true
6
+ ,3.84591,-1.6137192249298096,-1.276538610458374,0,false
7
+ meI/hHis/Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_Bn/dV/E/N/dV///Phe_4Me,3.27920,1.1405763626098633,-1.071689486503601,61.04805374145508,true
8
+ meI/hHis/Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/Aze/dV/E/N/dV///Phe_4Me,2.10585,1.1493492126464844,-1.0257583856582642,4.245477676391602,true
9
+ /D-Tyr_Et/meQ/dV/E/N/dV///Phe_4Me,1.80369,-1.874788522720337,-2.621032953262329,0,false
10
+ meI/hHis/Aca/N/T/dK/Thr_PO3H2/Aca/Oic_3aS-7aS/D-Chg/dV/E/N/D-Orn/D-aThr//Phe_4Me,6.38806,1.2151710987091064,-0.1381276398897171,19.07081413269043,true
11
+ meI/hHis/Aca/N/T/dK/Thr_PO3H2/Aca/E/N/D-Orn/D-aThr//Phe_4Me,4.44165,0.5254772305488586,-1.4159870147705078,0,false
12
+ meI/hHis/Aca/N/T/dK/Thr_PO3H2/Aca/Oic_3aS-7aS/Tyr_ab-dehydroMe/dV/E/N/D-Orn/D-aThr//Phe_4Me,5.32857,0.7058690190315247,-0.18089637160301208,36.66057586669922,true
13
+ meI/hHis//Aca/meM/Tyr_ab-dehydroMe/dV/E/N/D-Orn/D-aThr//Phe_4Me,4.70637,-1.1708372831344604,-1.661417841911316,0,false
14
+ meI/hHis/Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/D-Dap/dV/E/N/pnG///Phe_4Me,3.51582,1.225983738899231,-0.98129802942276,2.3875210285186768,true
15
+ meI//Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/dV/D-Cit/N/D-Orn/D-aThr//Phe_4Me,5.02344,0.01807424984872341,0.16467878222465515,0.8364539742469788,true
16
+ meI//Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/dV/meL/N/D-Orn/D-aThr//Phe_4Me,6.38359,-0.030419517308473587,0.20976503193378448,171.22459411621094,true
17
+ meI//Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/dV/Dsu/N/D-Orn/D-aThr//Phe_4Me,5.06602,0.022242402657866478,0.20077788829803467,2.369337797164917,true
18
+ Thr_PO3H2/D-Thz/D-Tyr_Et/Tyr_ab-dehydroMe/dV/D-Thz/N/D-Orn/D-aThr/Thz/Phe_4Me,5.05713,-2.348414897918701,-0.9183459877967834,0,false
19
+ meI//Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/dV/dE/N/D-Orn/D-aThr//Phe_4Me,4.97697,0.008319525979459286,0.3116433024406433,0,true
20
+ meI//Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/dV/meF/N/D-Orn/D-aThr//Phe_4Me,5.34730,0.01848183386027813,0.2308797389268875,21.90473747253418,true
21
+ meI/////dK/Thr_PO3H2/D-Thz/D-Tyr_Et/Tyr_ab-dehydroMe/dV/D-Thz/N/D-Orn/D-aThr//Phe_4Me,5.51508,-1.3141636848449707,0.9964643716812134,6.690232753753662,true
22
+ meI/hHis/Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/Lys_Boc/dV/E/N/dV///Phe_4Me,1.86999,1.2052497863769531,-1.024699091911316,0,true
23
+ meI//Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/N/D-Orn/D-aThr//Phe_4Me,5.65780,-0.37085768580436707,-0.28365179896354675,0,false
24
+ meI//Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/dV/pnA/N/D-Orn/D-aThr//Phe_4Me,5.55783,-0.01638980768620968,0.11942846328020096,44.641944885253906,true
25
+ meI//Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/dV/D-Thz/N/D-Orn/D-aThr//Phe_4Me,6.21246,-0.06910920888185501,0.2709718346595764,161.0983123779297,true
26
+ /Aca/D-Tyr_Et/Tyr_ab-dehydroMe/dV/D-2Pal/N/D-Orn/D-aThr//Phe_4Me,6.57811,-1.897789716720581,-1.1608996391296387,5.140321254730225,true
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
+ 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
+ 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
package/package.json CHANGED
@@ -5,7 +5,7 @@
5
5
  "name": "Leonid Stolbov",
6
6
  "email": "lstolbov@datagrok.ai"
7
7
  },
8
- "version": "2.0.3",
8
+ "version": "2.0.5",
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",
package/src/__jest__/test-node.ts CHANGED
@@ -76,7 +76,7 @@ export async function getBrowserPage(puppeteer: any): Promise<{ browser: any, pa
76
76
  }, token);
77
77
  await page.goto(url);
78
78
  try {
79
- await page.waitForSelector('.grok-preloader', { timeout: 1800000 });
79
+ // await page.waitForSelector('.grok-preloader', { timeout: 1800000 });
80
80
  await page.waitForFunction(() => document.querySelector('.grok-preloader') == null, {timeout: 3600000});
81
81
  } catch (error) {
82
82
  throw error;
package/src/package.ts CHANGED
@@ -32,7 +32,7 @@ import {
32
32
 
33
33
  import {splitAlignedSequences} from '@datagrok-libraries/bio/src/utils/splitter';
34
34
  import * as C from './utils/constants';
35
- import {getFingerprints} from './calculations/fingerprints'
35
+ import {getFingerprints} from './calculations/fingerprints';
36
36
 
37
37
  //tags: init
38
38
  export async function initBio() {
@@ -40,8 +40,8 @@ export async function initBio() {
40
40
 
41
41
  //name: fastaSequenceCellRenderer
42
42
  //tags: cellRenderer
43
- //meta.cellType: Sequence
44
- //meta.columnTags: units=fasta
43
+ //meta.cellType: sequence
44
+ //meta.columnTags: quality=Macromolecule, units=fasta
45
45
  //output: grid_cell_renderer result
46
46
  export function fastaSequenceCellRenderer(): MacromoleculeSequenceCellRenderer {
47
47
  return new MacromoleculeSequenceCellRenderer();
@@ -49,8 +49,8 @@ export function fastaSequenceCellRenderer(): MacromoleculeSequenceCellRenderer {
49
49
 
50
50
  //name: separatorSequenceCellRenderer
51
51
  //tags: cellRenderer
52
- //meta.cellType: Sequence
53
- //meta.columnTags: units=separator
52
+ //meta.cellType: sequence
53
+ //meta.columnTags: quality=Macromolecule, units=separator
54
54
  //output: grid_cell_renderer result
55
55
  export function separatorSequenceCellRenderer(): MacromoleculeSequenceCellRenderer {
56
56
  return new MacromoleculeSequenceCellRenderer();
@@ -379,6 +379,7 @@ export function monomerCellRenderer(): MonomerCellRenderer {
379
379
  //name: MacromoleculeDifferenceCellRenderer
380
380
  //tags: cellRenderer
381
381
  //meta.cellType: MacromoleculeDifference
382
+ //meta.columnTags: quality=MacromoleculeDifference
382
383
  //output: grid_cell_renderer result
383
384
  export function macromoleculeDifferenceCellRenderer(): MacromoleculeDifferenceCellRenderer {
384
385
  return new MacromoleculeDifferenceCellRenderer();
@@ -463,7 +464,7 @@ export function getHelmMonomers(seqCol: DG.Column<string>): string[] {
463
464
  export async function macromoleculesFingerprints(mcol: DG.Column): Promise<Uint8Array[]> {
464
465
  grok.functions.call('Chem:getRdKitModule');
465
466
  const monomers = getHelmMonomers(mcol);
466
- const mols = await grok.functions.call('HELM:getMolFiles', {mcol : mcol});
467
+ const mols = await grok.functions.call('HELM:getMolFiles', {mcol: mcol});
467
468
 
468
469
  return getFingerprints(mols.toList(), monomers);
469
470
  }
package/src/tests/activity-cliffs-tests.ts CHANGED
@@ -15,9 +15,9 @@ category('activityCliffs', async () => {
15
15
 
16
16
 
17
17
  before(async () => {
18
- actCliffsDf = await readDataframe('samples/sample_MSA.csv');
18
+ actCliffsDf = await readDataframe('tests/sample_MSA_data.csv');
19
19
  actCliffsTableView = grok.shell.addTableView(actCliffsDf);
20
- actCliffsDfWithEmptyRows = await readDataframe('samples/sample_HELM_empty_vals.csv');
20
+ actCliffsDfWithEmptyRows = await readDataframe('tests/sample_MSA_data_empty_vals.csv');
21
21
  actCliffsTableViewWithEmptyRows = grok.shell.addTableView(actCliffsDfWithEmptyRows);
22
22
  });
23
23
 
@@ -29,11 +29,11 @@ category('activityCliffs', async () => {
29
29
  });
30
30
 
31
31
  test('activityCliffsOpen', async () => {
32
- await _testActivityCliffsOpen(actCliffsDf, 53, 'UMAP', 'MSA');
32
+ await _testActivityCliffsOpen(actCliffsDf, 102, 'UMAP', 'MSA');
33
33
  });
34
34
 
35
35
  test('activityCliffsOpenWithEmptyRows', async () => {
36
- await _testActivityCliffsOpen(actCliffsDfWithEmptyRows, 53, 'UMAP', 'HELM');
36
+ await _testActivityCliffsOpen(actCliffsDfWithEmptyRows, 103, 'UMAP', 'MSA');
37
37
  });
38
38
 
39
39
  });
package/src/tests/activity-cliffs-utils.ts CHANGED
@@ -9,7 +9,7 @@ export async function _testActivityCliffsOpen(df: DG.DataFrame, numberCliffs: nu
9
9
  df,
10
10
  df.col(colName)!,
11
11
  df.col('Activity')!,
12
- 80,
12
+ 90,
13
13
  method);
14
14
 
15
15
  expect(scatterPlot != null, true);
package/src/tests/renderers-test.ts CHANGED
@@ -114,7 +114,7 @@ category('renderers', () => {
114
114
  const tw = grok.shell.addTableView(df);
115
115
  await delay(100);
116
116
  const renderer = tw.dataFrame.col('SequencesDiff')?.getTag(DG.TAGS.CELL_RENDERER);
117
- if (renderer !== 'MacromoleculeDifferenceCR')
117
+ if (renderer !== 'MacromoleculeDifference') // this is value of MacromoleculeDifferenceCR.cellType
118
118
  throw new Error(`Units 'separator', separator '/' and semType 'MacromoleculeDifference' have been ` +
119
119
  `manually set on column but after df aws added as table view renderer has been reset to '${renderer}'`);
120
120
  }
package/src/tests/splitters-test.ts CHANGED
@@ -8,6 +8,20 @@ import {splitToMonomers, _package} from '../package';
8
8
  import * as C from '../utils/constants';
9
9
 
10
10
  category('splitters', () => {
11
+ let tvList: DG.TableView[];
12
+ let dfList: DG.DataFrame[];
13
+
14
+ before(async () => {
15
+ await grok.functions.call('Bio:initBio');
16
+ tvList = [];
17
+ dfList = [];
18
+ });
19
+
20
+ after(async () => {
21
+ dfList.forEach((df: DG.DataFrame) => { grok.shell.closeTable(df); });
22
+ tvList.forEach((tv: DG.TableView) => tv.close());
23
+ });
24
+
11
25
  const helm1 = 'PEPTIDE1{meI.hHis.Aca.N.T.dE.Thr_PO3H2.Aca.D-Tyr_Et.Tyr_ab-dehydroMe.dV.E.N.D-Orn.D-aThr.Phe_4Me}$$$';
12
26
 
13
27
  const helm2 = 'PEPTIDE1{meI.hHis.Hcy.Q.T.W.Q.Phe_4NH2.D-Tyr_Et.Tyr_ab-dehydroMe.dV.E.N.N.meK}$$$';
@@ -63,6 +77,13 @@ category('splitters', () => {
63
77
  seqCol.semType = semType;
64
78
  seqCol.setTag(C.TAGS.ALIGNED, C.MSA);
65
79
 
80
+ const tv: DG.TableView = grok.shell.addTableView(df);
81
+ // call to calculate 'cell.renderer' tag
82
+ await grok.data.detectSemanticTypes(df);
83
+
84
+ dfList.push(df);
85
+ tvList.push(tv);
86
+
66
87
  splitToMonomers(seqCol);
67
88
  expect(df.columns.names().includes('17'), true);
68
89
  });
package/src/utils/cell-renderer.ts CHANGED
@@ -227,18 +227,18 @@ export class MonomerCellRenderer extends DG.GridCellRenderer {
227
227
  const color = palette.get(s);
228
228
 
229
229
  g.fillStyle = color;
230
- g.fillText(s, x + (w / 2), y - (h / 2), w);
230
+ g.fillText(s, x + (w / 2), y + (h / 2), w);
231
231
  }
232
232
  }
233
233
 
234
234
  export class MacromoleculeDifferenceCellRenderer extends DG.GridCellRenderer {
235
- get name(): string {return 'MacromoleculeDifferenceCR';}
235
+ get name(): string { return 'MacromoleculeDifferenceCR'; }
236
236
 
237
- get cellType(): string {return C.SEM_TYPES.MACROMOLECULE_DIFFERENCE;}
237
+ get cellType(): string { return C.SEM_TYPES.MACROMOLECULE_DIFFERENCE; }
238
238
 
239
- get defaultHeight(): number {return 30;}
239
+ get defaultHeight(): number { return 30; }
240
240
 
241
- get defaultWidth(): number {return 230;}
241
+ get defaultWidth(): number { return 230; }
242
242
 
243
243
  /**
244
244
  * Cell renderer function.
@@ -254,51 +254,69 @@ export class MacromoleculeDifferenceCellRenderer extends DG.GridCellRenderer {
254
254
  */
255
255
  render(
256
256
  g: CanvasRenderingContext2D, x: number, y: number, w: number, h: number, gridCell: DG.GridCell,
257
- cellStyle: DG.GridCellStyle): void {
257
+ _cellStyle: DG.GridCellStyle): void {
258
258
  const grid = gridCell.grid;
259
259
  const cell = gridCell.cell;
260
-
261
- w = getUpdatedWidth(grid, g, w, x);
262
- g.save();
263
- g.beginPath();
264
- g.rect(x, y, w, h);
265
- g.clip();
266
- g.font = '12px monospace';
267
- g.textBaseline = 'top';
268
260
  const s: string = cell.value ?? '';
269
-
270
- //TODO: can this be replaced/merged with splitSequence?
271
- const [s1, s2] = s.split('#');
272
261
  const separator = gridCell.tableColumn!.tags[C.TAGS.SEPARATOR];
273
262
  const units: string = gridCell.tableColumn!.tags[DG.TAGS.UNITS];
274
- const splitter = WebLogo.getSplitter(units, separator);
275
- const subParts1 = splitter(s1);
276
- const subParts2 = splitter(s2);
277
- const [text] = processSequence(subParts1);
278
- const textSize = g.measureText(text.join(''));
279
- let updatedX = Math.max(x, x + (w - (textSize.width + subParts1.length * 4)) / 2);
280
- // 28 is the height of the two substitutions on top of each other + space
281
- const updatedY = Math.max(y, y + (h - 28) / 2);
282
-
283
- let palette: SeqPalette = UnknownSeqPalettes.Color;
284
- if (units != 'HELM')
285
- palette = getPaletteByType(units.substring(units.length - 2));
286
-
287
- const vShift = 7;
288
- for (let i = 0; i < subParts1.length; i++) {
289
- const amino1 = subParts1[i];
290
- const amino2 = subParts2[i];
291
- const color1 = palette.get(amino1);
292
-
293
- if (amino1 != amino2) {
294
- const color2 = palette.get(amino2);
295
- const subX0 = printLeftOrCentered(updatedX, updatedY - vShift, w, h, g, amino1, color1, 0, true);
296
- const subX1 = printLeftOrCentered(updatedX, updatedY + vShift, w, h, g, amino2, color2, 0, true);
297
- updatedX = Math.max(subX1, subX0);
298
- } else
299
- updatedX = printLeftOrCentered(updatedX, updatedY, w, h, g, amino1, color1, 0, true, 0.5);
300
- updatedX += 4;
301
- }
302
- g.restore();
263
+ w = getUpdatedWidth(grid, g, x, w);
264
+ drawMoleculeDifferenceOnCanvas(g, x, y, w, h, s, units, separator);
265
+ }
266
+ }
267
+
268
+ export function drawMoleculeDifferenceOnCanvas(
269
+ g: CanvasRenderingContext2D,
270
+ x: number,
271
+ y: number,
272
+ w: number,
273
+ h: number,
274
+ s: string,
275
+ units: string,
276
+ separator: string,
277
+ fullStringLength?: boolean) {
278
+
279
+ //TODO: can this be replaced/merged with splitSequence?
280
+ const [s1, s2] = s.split('#');
281
+ const splitter = WebLogo.getSplitter(units, separator);
282
+ const subParts1 = splitter(s1);
283
+ const subParts2 = splitter(s2);
284
+ const textSize1 = g.measureText(processSequence(subParts1).join(''));
285
+ const textSize2 = g.measureText(processSequence(subParts2).join(''));
286
+ const textWidth = Math.max(textSize1.width, textSize2.width);
287
+ if (fullStringLength) {
288
+ w = textWidth + subParts1.length * 4;
289
+ g.canvas.width = textWidth + subParts1.length * 4;
290
+ }
291
+ let updatedX = Math.max(x, x + (w - (textWidth + subParts1.length * 4)) / 2);
292
+ // 28 is the height of the two substitutions on top of each other + space
293
+ const updatedY = Math.max(y, y + (h - 28) / 2);
294
+
295
+ g.save();
296
+ g.beginPath();
297
+ g.rect(x, y, fullStringLength ? textWidth + subParts1.length * 4 : w, h);
298
+ g.clip();
299
+ g.font = '12px monospace';
300
+ g.textBaseline = 'top';
301
+
302
+ let palette: SeqPalette = UnknownSeqPalettes.Color;
303
+ if (units != 'HELM')
304
+ palette = getPaletteByType(units.substring(units.length - 2));
305
+
306
+ const vShift = 7;
307
+ for (let i = 0; i < subParts1.length; i++) {
308
+ const amino1 = subParts1[i];
309
+ const amino2 = subParts2[i];
310
+ const color1 = palette.get(amino1);
311
+
312
+ if (amino1 != amino2) {
313
+ const color2 = palette.get(amino2);
314
+ const subX0 = printLeftOrCentered(updatedX, updatedY - vShift, w, h, g, amino1, color1, 0, true);
315
+ const subX1 = printLeftOrCentered(updatedX, updatedY + vShift, w, h, g, amino2, color2, 0, true);
316
+ updatedX = Math.max(subX1, subX0);
317
+ } else
318
+ updatedX = printLeftOrCentered(updatedX, updatedY, w, h, g, amino1, color1, 0, true, 0.5);
319
+ updatedX += 4;
303
320
  }
321
+ g.restore();
304
322
  }
package/src/utils/sequence-activity-cliffs.ts CHANGED
@@ -6,6 +6,8 @@ import {AvailableMetrics} from '@datagrok-libraries/ml/src/typed-metrics';
6
6
  import * as grok from 'datagrok-api/grok';
7
7
  import { SplitterFunc, WebLogo } from '@datagrok-libraries/bio/src/viewers/web-logo';
8
8
  import { UnitsHandler } from '@datagrok-libraries/bio/src/utils/units-handler';
9
+ import {SEM_TYPES, TAGS} from '../utils/constants';
10
+ import { drawMoleculeDifferenceOnCanvas } from './cell-renderer';
9
11
 
10
12
  export async function getDistances(col: DG.Column, seq: string): Promise<Array<number>> {
11
13
  const stringArray = col.toList();
@@ -71,47 +73,33 @@ function moleculeInfo(df: DG.DataFrame, idx: number, seqColName: string): HTMLEl
71
73
 
72
74
 
73
75
  export function createPropPanelElement(params: ITooltipAndPanelParams): HTMLDivElement {
74
- const propPanel = ui.divV([]);
75
- const columnNames = ui.divH([
76
- ui.divText(params.seqCol.name),
77
- ui.divText(params.activityCol.name),
78
- ]);
79
- columnNames.style.fontWeight = 'bold';
80
- columnNames.style.justifyContent = 'space-between';
81
- propPanel.append(columnNames);
82
- const hosts: HTMLDivElement[] = [];
83
- params.line.mols.forEach((molIdx: number, hostIdx: number) => {
84
- const activity = ui.divText(params.activityCol.get(molIdx).toFixed(2));
85
- activity.style.paddingLeft = '15px';
86
- activity.style.paddingLeft = '10px';
87
- const molHost = ui.divText(params.seqCol.get(molIdx));
88
- if (params.df.currentRowIdx === molIdx) {
89
- molHost.style.border = 'solid 1px lightgrey';
90
- }
91
- //@ts-ignore
92
- ui.tooltip.bind(molHost, () => moleculeInfo(params.df, molIdx, params.seqCol.name));
93
- molHost.onclick = () => {
94
- const obj = grok.shell.o;
95
- molHost.style.border = 'solid 1px lightgrey';
96
- params.df.currentRowIdx = molIdx;
97
- hosts.forEach((h, i) => {
98
- if (i !== hostIdx) {
99
- h.style.border = '';
100
- }
101
- })
102
- setTimeout(() => {
103
- grok.shell.o = obj
104
- }, 1000);
105
- };
106
- propPanel.append(ui.divH([
107
- molHost,
108
- activity,
109
- ]));
110
- hosts.push(molHost);
76
+ const propPanel = ui.div();
77
+
78
+ propPanel.append(ui.divText(params.seqCol.name, { style: { fontWeight: 'bold' } }));
79
+
80
+ const sequencesArray = new Array<string>(2);
81
+ const activitiesArray = new Array<number>(2);
82
+ params.line.mols.forEach((molIdx, idx) => {
83
+ sequencesArray[idx] = params.seqCol.get(molIdx);
84
+ activitiesArray[idx] = params.activityCol.get(molIdx);
111
85
  });
112
- propPanel.append(ui.divH([
113
- ui.divText(`Cliff: `, {style: {fontWeight: 'bold', paddingRight: '5px'}}),
114
- ui.divText(params.sali!.toFixed(2))
115
- ]));
86
+ const canvas = document.createElement('canvas');
87
+ const context = canvas.getContext('2d');
88
+ canvas.height = 30;
89
+ const units = params.seqCol.getTag(DG.TAGS.UNITS);
90
+ const separator = params.seqCol.getTag(TAGS.SEPARATOR);
91
+ drawMoleculeDifferenceOnCanvas(context!, 0, 0, 0, 30, sequencesArray.join('#'), units, separator, true);
92
+ propPanel.append(ui.div(canvas, { style: { width: '300px', overflow: 'scroll' } }));
93
+
94
+ function addFiledToPropPanel(name: string, value: number) {
95
+ propPanel.append(ui.divH([
96
+ ui.divText(`${name}: `, { style: { fontWeight: 'bold', paddingRight: '5px' } }),
97
+ ui.divText(value.toFixed(2))
98
+ ], { style: { paddingTop: '5px' } }));
99
+ }
100
+
101
+ addFiledToPropPanel('Activity delta', Math.abs(activitiesArray[0] - activitiesArray[1]));
102
+ addFiledToPropPanel('Cliff', params.sali!);
103
+
116
104
  return propPanel;
117
105
  }