@datagrok/bio 2.4.18 → 2.4.23

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Files changed (26) hide show
  1. package/.eslintrc.json +2 -8
  2. package/dist/864.js +1 -1
  3. package/dist/864.js.map +1 -1
  4. package/dist/package-test.js +1 -1
  5. package/dist/package-test.js.map +1 -1
  6. package/dist/package.js +1 -1
  7. package/dist/package.js.map +1 -1
  8. package/files/data/sample_FASTA_PT_activity.csv +100 -0
  9. package/files/tests/to-atomic-level-dna-fasta-input.csv +11 -0
  10. package/files/tests/to-atomic-level-dna-output.csv +15299 -0
  11. package/files/tests/to-atomic-level-msa-output.csv +3594 -0
  12. package/files/tests/to-atomic-level-msa-separator-input.csv +12 -0
  13. package/files/tests/to-atomic-level-peptides-fasta-input.csv +65 -0
  14. package/files/tests/to-atomic-level-peptides-output.csv +34901 -0
  15. package/package.json +4 -4
  16. package/src/demo/bio01-similarity-diversity.ts +15 -9
  17. package/src/demo/bio01a-hierarchical-clustering-and-sequence-space.ts +18 -10
  18. package/src/demo/bio01b-hierarchical-clustering-and-activity-cliffs.ts +16 -14
  19. package/src/demo/bio03-atomic-level.ts +25 -3
  20. package/src/demo/bio05-helm-msa-sequence-space.ts +10 -8
  21. package/src/demo/utils.ts +0 -12
  22. package/src/package-test.ts +2 -0
  23. package/src/package.ts +18 -8
  24. package/src/tests/converters-test.ts +24 -24
  25. package/src/tests/mm-distance-tests.ts +138 -0
  26. package/src/tests/to-atomic-level-tests.ts +187 -0
package/files/tests/to-atomic-level-msa-separator-input.csv ADDED
@@ -0,0 +1,12 @@
1
+ sequence
2
+ meI/hHis/Aca/N/T/dE/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/dV/E/N/D-Orn/D-aThr//Phe_4Me
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
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
+ 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
+ meI/hHis/Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/dV/Chg/N/D-Orn/D-aThr//Phe_4Me
7
+ meI/hHis/Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_Bn/dV/E/N/dV///Phe_4Me
8
+ meI/hHis/Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/Aze/dV/E/N/dV///Phe_4Me
9
+ meI/hHis/Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/meQ/dV/E/N/dV///Phe_4Me
10
+ meI/hHis/Aca/N/T/dK/Thr_PO3H2/Aca/Oic_3aS-7aS/D-Chg/dV/E/N/D-Orn/D-aThr//Phe_4Me
11
+ meI/hHis/Aca/N/T/dK/Thr_PO3H2/Aca/meM/D-Chg/dV/E/N/D-Orn/D-aThr//Phe_4Me
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
package/files/tests/to-atomic-level-peptides-fasta-input.csv ADDED
@@ -0,0 +1,65 @@
1
+ sequence
2
+ MDYKETLLMPKTDFPMRGGLPNKEPQIQEKW
3
+ MIEVFLFGIVLGLIPITLAGLFVTAYLQYRRGDQLDL
4
+ MMELVLKTIIGPIVVGVVLRIVDKWLNKDK
5
+ MDRTDEVSNHTHDKPTLTWFEEIFEEYHSPFHN
6
+ MKSTKEEIQTIKTLLKDSRTAKYHKRLQIVL
7
+ MHAILRYFIRRLFYHIFYKIYSLISKKHQSLPSDVRQF
8
+ MSNFHNEHVMQFYRNNLKTKGVFGRQ
9
+ MPNSEPASLLELFNSIATQGELVRSLKAGNASK
10
+ IRVVGRYLIEVWKAAGMDMDKVLFLWSSDEI
11
+ MLRCLDPWRRQLLSCSWSRLCPLKHSMFTMKLQ
12
+ MSPLCLSLVGSGLHLSVMHLLFHVFLFLFDSFLRP
13
+ MIGIADVKLLNLGMLFPFVEVES
14
+ MSNFHNEHVMQFYRNNLKNFGILGFKK
15
+ MNIQNLISIDIKKALINSGAPKNCDPLIFRTV
16
+ IPKFDGQYYRVEDGDRSLFLIPTAEVVLNGFHSQEI
17
+ IRGSVANRTRTAPYPPIPNRNQI
18
+ EAGYQFERTGYFCIDNKDSTPEALVFNRTVGLRDTWEG
19
+ MAFQIPRGTQDVLPGDSEKWQYVEHIARSLC
20
+ DLDRLSPLSQERYHANLLRILDSKEPEDQE
21
+ MNYLFAKHYNGSFIVRIEDTDLARNVEG
22
+ MNIKLKLKQHIVQSLTRNGIENNNNLLISNTYQKK
23
+ LTVQDNEKTLEENEINAVIQAVLAELATRFNAVLRD
24
+ FAMLRYNVNDLRLFFDNDLNFLKQFK
25
+ FAMLRYNVNDLRLFFDNDLNFLKQFAK
26
+ FGIGLDRFAMLRYNVNDLRLFFDNDLNFLKQFAK
27
+ GIGLDRFAMLRYNVNDLRLFFDNDLNFLKQFAK
28
+ MAYSLTFQNPNDNLTDEEVAKYMEKITKALTEKIGAEVR
29
+ MEVNILAFIATALFILVPTAFLLIIYVKTVSQSD
30
+ MSSAATVDPNEAFGLITKNLQEVLNPQIIKDVLEVQ
31
+ MPLLGLLPRRAWASLLSQLLRPPCASCTGAVRCQSQ
32
+ MAERAALEELVKLQGERVRGLKQQKASAEL
33
+ ERQRYILRIRTLTKAVAEAYYASREALGFPMCNKDK
34
+ MRIGQYQLRNRLIAAPMAGITDRPF
35
+ MEAKAAPKPAASGACSVSAEETEKWMEEAMHMEIFL
36
+ TGASDVKMEEGSMRIDTNISIRPAG
37
+ EFMVDDPTLWASPSTVLGGGRYNHLVEEF
38
+ EFWMMEPEMAWMHQDESLDLQ
39
+ NAGIRPINNVVDATNYVMLLTGQPMHAYDAKLFDKTKKI
40
+ GEEVRLAGWCNTYRDHGGVVFIDLRDKSG
41
+ MIDGKKVLFSGMQATGTLTLGNYLGALKNWGDFK
42
+ MLQSYRKVVGAELSERMVYEIN
43
+ MKMIVGLGNIGTRYDETRHNTGFMVV
44
+ MPRQRGLKNVELDVSMPNRSRVTSGSACTGN
45
+ MPDLLLELFSEEIPALPSARSEARTDKLNNVHAEGVR
46
+ MIWSLFYKSGLFYFSSRMPALLHSSRSFSSSFPGRDES
47
+ MLNEYRNRRAVVSDGFRQVRTRRQALAQFTVKIGK
48
+ MLIKPKWYFSLRKQCHWEIRKKITYSRIRTCVVEVL
49
+ MKMALSTQLLLLIFWFLELGNSLEEASEKNDTIS
50
+ MNTQSIAEARALLDEFEAQMDEDVKIEL
51
+ MGGQGAGGKADFARGGAPDATKAQAGLGAVKAALAG
52
+ MAHFVSASLLCASDLDSTQTALRDFPVCAMGNDLSKDH
53
+ MSKDLANGWYQVAVQGNGLSFAKIVSGTLKNGFPKGLRF
54
+ MVVQWLPSLENYQNEDGSVTIPEVLRPYMGGVEVIKP
55
+ GWWRSWLARRSHRILRSRVRASLTP
56
+ MPTPAPASEDLSASRPIQKPTGVPGPVPGQGEW
57
+ MAHFVSASLLCASDLDSTQTALRDFPVCAMGNGLSKDH
58
+ MKFYAYFSLRILILVFYIFCHYFCLNLHKFIIFCIFI
59
+ MSESLRIIFAGTPDFAARHLDALLSSGHNVVGVFIDRN
60
+ MLWRKLYWLKSPKNAERLKRAISDFEENKNFRNWI
61
+ MRYLTHNNHTVTILTNFAPCRAEAPHLQENTINAITQ
62
+ MDFVVLVKKGVADLDNRALTEALEKLWRRHCRQAPAS
63
+ MHERFLRENRRSPSRVGGAIDAMPAGCGGMVVIGM
64
+ MFFTQNLWVERQQLIKPFILNVNIIYLKNIIIFFIIGGY
65
+ MRDTQCHSADFPVYPNVLAVGVRRALWPLPAQDANRTQ