@datagrok/bio 2.8.0 → 2.8.2

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Files changed (22) hide show
  1. package/CHANGELOG.md +32 -7
  2. package/dist/package-test.js +1 -1
  3. package/dist/package-test.js.map +1 -1
  4. package/dist/package.js +1 -1
  5. package/dist/package.js.map +1 -1
  6. package/files/samples/FASTA.csv +65 -0
  7. package/files/samples/HELM.csv +541 -0
  8. package/files/samples/HELM_cyclic.tsv +42 -0
  9. package/files/samples/MSA.csv +541 -0
  10. package/files/samples/natural-sequences.csv +5063 -0
  11. package/files/samples/synthetic-sequences.csv +5044 -0
  12. package/package.json +3 -3
  13. package/scripts/sequence_generator.py +6 -3
  14. package/src/demo/bio03-atomic-level.ts +1 -1
  15. package/src/demo/bio05-helm-msa-sequence-space.ts +1 -1
  16. package/src/package.ts +1 -1
  17. package/src/tests/bio-tests.ts +33 -3
  18. package/src/tests/detectors-tests.ts +3 -3
  19. package/src/tests/renderers-monomer-placer.ts +7 -7
  20. package/src/tests/renderers-test.ts +1 -1
  21. package/src/tests/splitters-test.ts +1 -1
  22. package/src/utils/monomer-cell-renderer.ts +2 -2
package/files/samples/HELM_cyclic.tsv ADDED
@@ -0,0 +1,42 @@
1
+ cluster sequence_id sequence activity is_cliff
2
+ 0 c0_s000 PEPTIDE1{[dI].[Trp_Ome].[Asp_OMe].[D-Cit].[meG].[Phe_4NH2].[Phe_34diCl].[meY].[Pro_4Me3OH].[Met_O].[NMe2Abz].[Tyr_Ph4OH].[3Pal].[xiIle].[Tyr_35diI].[Ala_tBu]}$PEPTIDE1,PEPTIDE1,16:R2-1:R1$$$V2.0 0.6989112531216086 False
3
+ 0 c0_s001 PEPTIDE1{[Phe_4Me].[Cap].[Phe_4NO2].[Hyp].[meG].[Phe_4Sdihydroorotamido].[Lys_iPr].[meA].[Tyr_3OH].[Ser_Bn].[NMe2Abz].G.[3Pal].[dT].[Tyr_35diI].[Tyr_3OH]}$PEPTIDE1,PEPTIDE1,16:R2-1:R1$$$V2.0 1.4985718624090099 False
4
+ 0 c0_s002 PEPTIDE1{[meT].[D-aHyp].[Pqa].[dP].[meG].[D-Tyr_Me].[meV].[Tza].[D-Phe_4F].[Dha].[NMe2Abz].[Tyr_Ph4OH].[3Pal].[dT].[Tyr_35diI].[D-hArg_Et2]}$PEPTIDE1,PEPTIDE1,16:R2-1:R1$$$V2.0 0.5150783500101226 False
5
+ 0 c0_s003 PEPTIDE1{[D-Chg].[Phe_4F].[xiHyp].[bAla].[Bmt_E].[D-Hyp].[D-Abu].[Cap].[hPhe].[D-2Nal].[NMe2Abz].[Tyr_Ph4OH].[3Pal].[dT].[Tyr_35diI].[Tyr_Ph4OH]}$PEPTIDE1,PEPTIDE1,16:R2-1:R1$$$V2.0 0.7940753498433123 False
6
+ 0 c0_s004 PEPTIDE1{[D-Hyp].[Trp_Ome].L.[dP].[dW].[App].[seC].[dN].[Oic_3aR-7aS].[D-hArg].[NMe2Abz].G.[3Pal].[xiIle].[Tyr_35diI].[D-Thz]}$PEPTIDE1,PEPTIDE1,16:R2-1:R1$$$V2.0 0.37518373535618516 False
7
+ 0 c0_s005 PEPTIDE1{[Lys_Ac].[dA].A.R.[meG].[meL].[Tyr_Ph4OH].[meA].[Sta_3xi4xi].[aMeTyr_3OH].[NMe2Abz].[Tyr_Ph4OH].[3Pal].[dT].[Tyr_35diI].[Tyr_ab-dehydroMe]}$PEPTIDE1,PEPTIDE1,16:R2-1:R1$$$V2.0 0.2625075567183839 False
8
+ 0 c0_s006 PEPTIDE1{[hPhe].[dH].[Met_O].[Dip].[dW].[Gly_cPr].[Asp_Ph2NH2].[Phe_ab-dehydro_3NO2].[meQ].[D-Phg].[NMe2Abz].[Tyr_Ph4OH].[3Pal].[xiIle].[Tyr_35diI].[His_3Me]}$PEPTIDE1,PEPTIDE1,16:R2-1:R1$$$V2.0 -0.9749877867291488 False
9
+ 0 c0_s007 PEPTIDE1{[xiHyp].[Cys_SEt].[Cit].[Phe_4F].[dW].[Bip].[Dip].[dW].[Phe_4F].[Phe_2F].[NMe2Abz].G.[3Pal].[dT].[Tyr_35diI].[Phe_ab-dehydro]}$PEPTIDE1,PEPTIDE1,16:R2-1:R1$$$V2.0 -0.3982472646989369 False
10
+ 0 c0_s008 PEPTIDE1{[bAla].[aMeTyr].[pnT].[D-2Nal].[meG].[Chg].[seC].[Tyr_35diI].[Phe_4Br].[aMePhe].[NMe2Abz].G.[3Pal].[xiIle].[Tyr_35diI].[meR]}$PEPTIDE1,PEPTIDE1,16:R2-1:R1$$$V2.0 1.1539007174211635 False
11
+ 0 c0_s009 PEPTIDE1{[meQ].[xiIle].[D-Cit].[Sta_3S4S].[Bmt_E].[Trp_5OH].[Trp_5OH].[His_1Bn].[D-Pip].[Cha].[NMe2Abz].G.[3Pal].[xiIle].[Tyr_35diI].[D-hPhe]}$PEPTIDE1,PEPTIDE1,16:R2-1:R1$$$V2.0 -0.23113695525866756 False
12
+ 1 c1_s000 PEPTIDE1{[Tyr_Me].[Ac5c].[D-Bmt].[Dsu].[Asp_Ph2NH2].[Dip].[Bux].[Ser_PO3H2].[D-2Thi].[Tyr_Bn].[Pyr].[aMePhe].[Phe_4Cl].[Tyr_Me].[dM].[Bmt].[Phe_3F]}$PEPTIDE1,PEPTIDE1,17:R2-1:R1$$$V2.0 6.045737896576041 False
13
+ 1 c1_s001 PEPTIDE1{[Chg].[aMePro].[D-Thz].[D-Phe_4F].[Dpm].[Dip].[D-Phe_4F].[Ser_PO3H2].[D-2Thi].[dN].[Pyr].[aMePhe].[hHis].[Tyr_Me].[Bmt_E].[Bmt].V}$PEPTIDE1,PEPTIDE1,17:R2-1:R1$$$V2.0 5.219601040516435 False
14
+ 1 c1_s002 PEPTIDE1{[3Pal].[dV].[Phe_ab-dehydro_3NO2].[aMeTyr].[Pyr].[Dip].[Pip].[Ser_PO3H2].[D-2Thi].[3Pal].[Pyr].[Wil].[hHis].[Tyr_Me].[seC].[Phe_34diCl].[Dpm]}$PEPTIDE1,PEPTIDE1,17:R2-1:R1$$$V2.0 3.662550519162843 False
15
+ 1 c1_s003 PEPTIDE1{[Phe_3Cl].[Tyr_Me].[Bip].[aMeTyr].[Pyr].[Dip].[Lys_iPr].[Ser_PO3H2].[D-2Thi].[Tyr_Bn].[Phe_2F].[Wil].[hHis].[Tyr_Me].[Val_3OH].[Bmt].[meH]}$PEPTIDE1,PEPTIDE1,17:R2-1:R1$$$V2.0 5.9161320298313225 False
16
+ 1 c1_s004 PEPTIDE1{[Pip].[D-Cha].[dP].[D-Phe_4F].[Pyr].[Dip].[Oic_3aS-7aS].[Ser_PO3H2].[D-2Thi].[dN].[Phe_2F].[aMePhe].[hHis].[Tyr_Me].S.[Bmt].[meI]}$PEPTIDE1,PEPTIDE1,17:R2-1:R1$$$V2.0 5.4089315459726715 False
17
+ 1 c1_s005 PEPTIDE1{[Phe_bbdiMe].[Bmt].[Ser_Bn].[aMeTyr].[Dpm].[Dip].[Ser_Bn].[Ser_PO3H2].[D-2Thi].[3Pal].[Pyr].[Wil].[hHis].[Tyr_Me].[D-Bmt].[Phe_34diCl].[Aze]}$PEPTIDE1,PEPTIDE1,17:R2-1:R1$$$V2.0 4.434030084971981 False
18
+ 1 c1_s006 PEPTIDE1{[D-Nle].[pnG].[Phe_34diCl].[aMeTyr].[Dpm].[Dip].[Tyr_35diI].[Ser_PO3H2].[D-2Thi].[Tyr_Bn].[Lys_Ac].[Wil].[hArg].[Tyr_Me].[dA].[dR].[Ac5c]}$PEPTIDE1,PEPTIDE1,17:R2-1:R1$$$V2.0 3.907674936385215 False
19
+ 1 c1_s007 PEPTIDE1{[dT].[Iva].[D-Cit].[D-Phe_4F].[Dpm].[Dip].[Sta_3xi4xi].[Ser_PO3H2].[D-2Thi].[Tyr_Bn].[Pyr].[aMePhe].[hArg].[Tyr_Me].T.[dR].[xiHyp]}$PEPTIDE1,PEPTIDE1,17:R2-1:R1$$$V2.0 6.520266620622154 False
20
+ 1 c1_s008 PEPTIDE1{[D-Hyp].[Dpm].[Wil].[Dsu].[Asp_Ph2NH2].[Dip].[Dpm].[Ser_PO3H2].[D-2Thi].[3Pal].[Phe_2F].[Wil].[Phe_4Cl].[Tyr_Me].[Chg].[Phe_34diCl].[meR]}$PEPTIDE1,PEPTIDE1,17:R2-1:R1$$$V2.0 5.402193118045193 False
21
+ 1 c1_s009 PEPTIDE1{[Phe_2F].F.[Hse].[aMeTyr].[Asp_Ph2NH2].[Dip].[dH].[Ser_PO3H2].[D-2Thi].[dN].[Phe_2F].[aMePhe].[Phe_4Cl].[Tyr_Me].[Sta_3S4S].[Phe_34diCl].[D-Hyp]}$PEPTIDE1,PEPTIDE1,17:R2-1:R1$$$V2.0 4.666820384459672 False
22
+ 2 c2_s000 PEPTIDE1{[Cha].[seC].[Tyr_PO3H2].[Oic_3axi-7axi].[D-Pip].[Nva].[Aze].[Tyr_Me].[hArg].[meV].[Bmt].V.[Phe_4Br].[Bip].[Azi].[meI].[Thr_PO3H2].[D-2Thi].[meI].[Oic_3aR-7aS]}$PEPTIDE1,PEPTIDE1,20:R2-1:R1$$$V2.0 0.771686672097168 False
23
+ 2 c2_s001 PEPTIDE1{[Nva].[Ala_tBu].[Tyr_3OH].[Oic_3axi-7axi].[D-Pip].[Nva].[Aze].[Phe_3F].[hArg].[dP].[Bmt].V.[Phe_4Br].[Bip].[Nva].[L-hArg(Et,Et)].[xiIle].[hArg].[D-Chg].Q}$PEPTIDE1,PEPTIDE1,20:R2-1:R1$$$V2.0 1.347410199221249 False
24
+ 2 c2_s002 PEPTIDE1{[D-aHyp].[D-Phe_4F].[Tyr_PO3H2].[Tyr_Bn].[D-Pip].[Nva].[D-Ser_tBu].[Asp_Ph2NH2].[hArg].[dP].[dR].[D-Trp_For].[Tyr_SO3H].[Bip].[D-2Nal].[Val_3OH].[Cys_SEt].[Lys_Boc].[aMeTyr_3OH].[Sta_3xi4xi]}$PEPTIDE1,PEPTIDE1,20:R2-1:R1$$$V2.0 0.7554731959981444 False
25
+ 2 c2_s003 PEPTIDE1{[Thz].[Phe_bbdiMe].[Tyr_PO3H2].[Hyl_5xi].[D-Pip].[Nva].[Gly_cPr].[meR].[hArg].[dP].[dR].V.[4Pal].[Bip].[meQ].[Gly_allyl].[Tyr_ab-dehydroMe].[Ser_tBu].[Bmt_E].[Aze]}$PEPTIDE1,PEPTIDE1,20:R2-1:R1$$$V2.0 0.7805206435258067 False
26
+ 2 c2_s004 PEPTIDE1{[dW].[Azi].[Tyr_3OH].[Hyl_5xi].[D-Pip].[Nva].[Gly_cPr].[D-Phe_4ureido].[hArg].[meV].[Bmt].[D-Trp_For].[Phe_4Br].[Bip].[D-2Nal].[aMeTyr].[NMe2Abz].[D-2Thi].[Phe_4NO2].[Bip]}$PEPTIDE1,PEPTIDE1,20:R2-1:R1$$$V2.0 1.8989987188920898 False
27
+ 2 c2_s005 PEPTIDE1{[aMeTyr].[dN].[Tyr_3OH].[Tyr_Bn].[D-Pip].[Nva].[Aze].[Phe_4NH2].[hArg].[meV].[Bmt].[D-Trp_For].[Phe_4Br].[Bip].[Phe_4Br].[meI].[App].[Pqa].[dN].[hArg]}$PEPTIDE1,PEPTIDE1,20:R2-1:R1$$$V2.0 -0.6137287416175345 False
28
+ 2 c2_s006 PEPTIDE1{[aMeTyr].[dN].[Tyr_3OH].[Tyr_Bn].[D-Pip].[Nva].[Aze].[Phe_4NH2].[hArg].[meV].[Bmt].[dQ].[Phe_4Br].[Bip].[Phe_4Br].[meI].[App].[Pqa].[dN].[hArg]}$PEPTIDE1,PEPTIDE1,20:R2-1:R1$$$V2.0 4.3976930106356855 True
29
+ 2 c2_s006 PEPTIDE1{[nTyr].[D-xiIle].[Tyr_3OH].[Hyl_5xi].[D-Pip].[Nva].[Aze].[D-Bmt].[hArg].[dP].[Bmt].[D-Trp_For].[Tyr_SO3H].[Bip].[Met_O].G.[Tyr_26diMe].G.[aIle].[D-Dip]}$PEPTIDE1,PEPTIDE1,20:R2-1:R1$$$V2.0 0.6629616282433224 False
30
+ 2 c2_s007 PEPTIDE1{[Iva].[Phg].[Tyr_3OH].[Hyl_5xi].[D-Pip].[Nva].[D-Ser_tBu].[Phe_4I].[hArg].[dP].[Bmt].V.[4Pal].[Bip].[Lys_Ac].[Phe_34diCl].[Cit].[Dsu].[Phe_4Cl].[Trp_Ome]}$PEPTIDE1,PEPTIDE1,20:R2-1:R1$$$V2.0 0.888842415673488 False
31
+ 2 c2_s008 PEPTIDE1{[pnA].[D-xiIle].[Tyr_3OH].[Tyr_Bn].[D-Pip].[Nva].[Aze].[3Abz].[hArg].[meV].[Bmt].[D-Trp_For].[4Pal].[Bip].[meV].[D-aThr].[4Pal].[xiThr].[D-Dip].[Tyr_Me]}$PEPTIDE1,PEPTIDE1,20:R2-1:R1$$$V2.0 0.8955501360380549 False
32
+ 2 c2_s009 PEPTIDE1{[Bip].[dM].[Tyr_3OH].[Hyl_5xi].[D-Pip].[Nva].[Gly_cPr].[aMeTyr].[hArg].[meV].[dR].[D-Trp_For].[4Pal].[Bip].[Phe_2F].[Met_O2].[D-aHyp].[Thz].[Phe_34diCl].[Dha]}$PEPTIDE1,PEPTIDE1,20:R2-1:R1$$$V2.0 0.5164178845203717 False
33
+ 3 c3_s000 PEPTIDE1{[Ala_tBu].[meM].[Phe_2F].[Cha].[Tyr_Me].[Cys_Me].[Met_O2].[Phe_4Sdihydroorotamido].[dI].I.[Gly_allyl].[Tyr_SO3H].[Thr_PO3H2].[meT].[meT].[Asp_OMe].[Aoda].[Pyl].W.[Trp_Ome].[xiThr]}$PEPTIDE1,PEPTIDE1,21:R2-1:R1$$$V2.0 7.678155736110394 False
34
+ 3 c3_s001 PEPTIDE1{[xiHyp].[Phe_4Br].[Phe_2F].[pnT].[D-2Nal].[D-Abu].[Tyr_Bn].[Phe_bbdiMe].[dI].I.[Gly_allyl].[D-Phe_4Cl].[Thr_PO3H2].[D-aHyp].[His_3Me].[Asp_OMe].[Met_O2].[Tyr_Me].[Iva].[Tic].[D-aMeAbu]}$PEPTIDE1,PEPTIDE1,21:R2-1:R1$$$V2.0 7.8761846386016465 False
35
+ 3 c3_s002 PEPTIDE1{P.N.[Phe_2F].M.[Bmt].[Tyr_tBu].[Met_O2].[Phe_bbdiMe].[dI].[D-Nle].[Gly_allyl].[xiHyp].[pnT].[Tyr_tBu].[meS].[Asp_OMe].[D-1Nal].[App].[D-Trp_For].[4Abz].[Phe_4Br]}$PEPTIDE1,PEPTIDE1,21:R2-1:R1$$$V2.0 7.9631382469800975 False
36
+ 3 c3_s003 PEPTIDE1{[dF].[aThr].[Phe_2F].[D-Nva].[seC].[Gly_allyl].[Tyr_Bn].[Phe_bbdiMe].[dI].I.[Gly_allyl].[aMeTyr_3OH].[pnT].[meL].[meS].[Asp_OMe].[Sta_3S4S].[Phe_4Cl].S.[Ser_tBu].V}$PEPTIDE1,PEPTIDE1,21:R2-1:R1$$$V2.0 7.569167343227839 False
37
+ 3 c3_s004 PEPTIDE1{[meL].[His_3Me].[Phe_2F].[D-Nva].[D-hArg_Et2].[Phe_bbdiMe].[Tyr_Bn].[Phe_4Sdihydroorotamido].[D-2Nal].[D-Nle].[Gly_allyl].[Phe_4F].[pnT].[1Nal].[meS].[Asp_OMe].[xiIle].[D-Bmt].[3Abz].[NMe2Abz].[1Nal]}$PEPTIDE1,PEPTIDE1,21:R2-1:R1$$$V2.0 7.803130685790769 False
38
+ 3 c3_s005 PEPTIDE1{[Thr_PO3H2].[aMePro].[Phe_2F].[Abu_23dehydro].[Dpm].[D-2Nal].[Met_O2].[Phe_bbdiMe].[dI].I.[Gly_allyl].[dR].[Met_O].[Tyr_Bn].[meT].[Asp_OMe].[Tyr_tBu].[Trp_Ome].[aIle].[4Abz].[meS]}$PEPTIDE1,PEPTIDE1,21:R2-1:R1$$$V2.0 7.900881750721562 False
39
+ 3 c3_s006 PEPTIDE1{[meL].[Bip].[Phe_2F].[Tyr_3NO2].[xiHyp].[dV].[Tic].[Phe_4Sdihydroorotamido].[dI].[D-Nle].[Gly_allyl].[D-2Nal].[pnT].[dP].[meS].[Asp_OMe].[xiThr].[Aze].[Ala_tBu].[Tyr_tBu].[Azi]}$PEPTIDE1,PEPTIDE1,21:R2-1:R1$$$V2.0 7.75533340153031 False
40
+ 3 c3_s007 PEPTIDE1{[Asp_Ph2NH2].[xiThr].[Phe_2F].[pnT].[meG].[Phe_2Me].[Tyr_Bn].[Phe_4Sdihydroorotamido].[dI].I.[Gly_allyl].[dM].[Thr_PO3H2].[aThr].[His_3Me].[Asp_OMe].[Ac3c].[Lys_Me3].[Lys_Ac].[D-Chg].[Ac6c]}$PEPTIDE1,PEPTIDE1,21:R2-1:R1$$$V2.0 8.034711714296089 False
41
+ 3 c3_s008 PEPTIDE1{[Phe_4Br].[3Abz].[Phe_2F].[meA].H.[Phe_4F].[Met_O2].[Phe_bbdiMe].[dI].[D-Nle].[Gly_allyl].[dA].[Thr_PO3H2].[Tyr_Me].[His_3Me].[Asp_OMe].[xiIle].[dN].[D-Phe_4ureido].[Tyr_tBu].[4Pal]}$PEPTIDE1,PEPTIDE1,21:R2-1:R1$$$V2.0 7.890930587616866 False
42
+ 3 c3_s009 PEPTIDE1{[xiThr].[2Abz].[Phe_2F].[aHyp].[D-hArg_Et2].[D-Nle].[Tic].[Phe_4Sdihydroorotamido].[dI].I.[Gly_allyl].[Ac3c].[Met_O].[Lys_iPr].[meT].[Asp_OMe].[Gly_cPr].[meI].[Ac6c].[His_1Me].L}$PEPTIDE1,PEPTIDE1,21:R2-1:R1$$$V2.0 7.938066330332129 False