@datagrok/bio 1.5.10 → 1.7.1

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 (29) hide show
  1. package/detectors.js +1 -1
  2. package/dist/package-test.js +522 -475
  3. package/dist/package.js +312 -469
  4. package/files/samples/sample_FASTA.csv +0 -1
  5. package/files/samples/sample_FASTA.fasta +0 -3
  6. package/files/samples/sample_FASTA_DNA.csv +101 -0
  7. package/files/samples/sample_FASTA_PT.csv +101 -0
  8. package/files/samples/sample_FASTA_RNA.csv +101 -0
  9. package/files/{samples → tests}/peptides_complex_msa.csv +0 -0
  10. package/files/{samples → tests}/peptides_simple_msa.csv +0 -0
  11. package/files/{samples/testSmiles.csv → tests/sar-small.csv} +0 -0
  12. package/files/{samples → tests}/testDemog.csv +0 -0
  13. package/files/{samples → tests}/testHelm.csv +0 -0
  14. package/files/{samples → tests}/testId.csv +0 -0
  15. package/files/tests/testSmiles.csv +201 -0
  16. package/files/{samples → tests}/testSmiles2.csv +0 -0
  17. package/package.json +2 -2
  18. package/scripts/generate_fasta_csv_for_alphabets.R +70 -0
  19. package/src/package-test.ts +1 -0
  20. package/src/package.ts +89 -27
  21. package/src/tests/convert-test.ts +49 -8
  22. package/src/tests/detectors-test.ts +12 -6
  23. package/src/utils/cell-renderer.ts +58 -91
  24. package/src/utils/convert.ts +10 -14
  25. package/src/utils/multiple-sequence-alignment.ts +0 -1
  26. package/src/utils/notation-converter.ts +178 -65
  27. package/{test-Bio-34f75e5127b8-936bf89b.html → test-Bio-34f75e5127b8-726a0649.html} +2 -2
  28. package/src/utils/chem-palette.ts +0 -280
  29. package/src/utils/misc.ts +0 -29
package/files/samples/sample_FASTA.csv CHANGED
@@ -63,4 +63,3 @@ UPI0001614A89,37,A0A0A8VBX4; A0A0H3NXY0; A0A0G2N6K7.1 (obsolete); A0A0M1V224.1 (
63
63
  UPI000169E485,35,A0A153KQI0.1 (obsolete); A0A1J0NK41.1 (obsolete); A0A1V2DF85.1 (obsolete); K7QCB5.1 (obsolete),MHERFLRENRRSPSRVGGAIDAMPAGCGGMVVIGM,-1.5044359483896845
64
64
  UPI000169FCE1,39,A0A656IDX3; A0A6C7A0R4; C0Q053; E8XEF8; G5LRF0; G5NFQ1; M7RCS7; A0A021WPB8.1 (obsolete); A0A068IN21.1 (obsolete); A0A068PK03.1 (obsolete); A0A077YJZ3.1 (obsolete); A0A078P440.1 (obsolete); A0A078PGS7.1 (obsolete); A0A080YVC6.1 (obsolete); A0A098GTT7.1 (obsolete); A0A0A8SUG6.1 (obsolete); A0A0B7QMT4.1 (obsolete); A0A0B7QXI3.1 (obsolete); A0A0B7QYQ1.1 (obsolete); A0A0B7RM41.1 (obsolete); A0A0B7RSH2.1 (obsolete); A0A0B7RYE2.1 (obsolete); A0A0B7SSM9.1 (obsolete); A0A0B7STM0.1 (obsolete); A0A0B7T296.1 (obsolete); A0A0B7TX24.1 (obsolete); A0A0B7U1H7.1 (obsolete); A0A0B7U264.1 (obsolete); A0A0B7UC41.1 (obsolete); A0A0B7UME8.1 (obsolete); A0A0B7V6B1.1 (obsolete); A0A0B7VLT0.1 (obsolete); A0A0B7VRU2.1 (obsolete); A0A0B7W472.1 (obsolete); A0A0B7W5J9.1 (obsolete); A0A0B7WUQ0.1 (obsolete); A0A0B8K7B9.1 (obsolete); A0A0C5TXP2.1 (obsolete); A0A0E1Q441.1 (obsolete); A0A0E2MH47.1 (obsolete); A0A0F6DRT0.1 (obsolete); A0A0G2LKZ8.1 (obsolete); A0A0G2NQ03.1 (obsolete); A0A0H3RKU6.1 (obsolete); A0A0N2BI82.1 (obsolete); A0A0N2BNW2.1 (obsolete); A0A0S2WD32.1 (obsolete); A0A1M3ZBY0.1 (obsolete); A0A1M3ZIA1.1 (obsolete); A0A1M4A4L9.1 (obsolete); A0A1M4A739.1 (obsolete); A0A1W2L8M5.1 (obsolete); A0A221AY29.1 (obsolete); A0A486X7G3.1 (obsolete); A0A518UNK4.1 (obsolete); A0A5E4DW86.1 (obsolete); B5C6Q5.1 (obsolete); B5FPF5.1 (obsolete); B5MIR4.1 (obsolete); B5N1F1.1 (obsolete); E7V3X0.1 (obsolete); E8NPX9.1 (obsolete); F2FBP0.1 (obsolete); F2FSL8.1 (obsolete); G5MZY4.1 (obsolete); G7T2W4.1 (obsolete); J1I084.1 (obsolete); J1IMV6.1 (obsolete); J1J8I1.1 (obsolete); J1KGX6.1 (obsolete); J1L3A6.1 (obsolete); J1L833.1 (obsolete); J1LPB8.1 (obsolete); J1NKU7.1 (obsolete); J1PPY6.1 (obsolete); J1S5B6.1 (obsolete); J1VRL7.1 (obsolete); J1WIA4.1 (obsolete); J1WZQ3.1 (obsolete); J2AWK9.1 (obsolete); J2B6K2.1 (obsolete); J2DH55.1 (obsolete); J2DI78.1 (obsolete); J2ENS4.1 (obsolete); J2FR89.1 (obsolete); J2HHJ4.1 (obsolete); J2I9P0.1 (obsolete); K8S348.1 (obsolete); K8S5C1.1 (obsolete); K8S896.1 (obsolete); K8T7U3.1 (obsolete); K8TAY6.1 (obsolete); K8TJL1.1 (obsolete); K8UBJ3.1 (obsolete); K8ULX9.1 (obsolete); K8V3L9.1 (obsolete); K8VAJ8.1 (obsolete); K8VPG1.1 (obsolete); L5W4S4.1 (obsolete); L5WC19.1 (obsolete); L5WHP1.1 (obsolete); L5WP78.1 (obsolete); L5X276.1 (obsolete); L5XDS4.1 (obsolete); L5YA20.1 (obsolete); L5YPV3.1 (obsolete); L5YVT4.1 (obsolete); L5ZH95.1 (obsolete); L5ZKS5.1 (obsolete); L6A2S2.1 (obsolete); L6A7R6.1 (obsolete); L6APT2.1 (obsolete); L6B959.1 (obsolete); L6BV30.1 (obsolete); L6C2V7.1 (obsolete); L6CB61.1 (obsolete); L6CX95.1 (obsolete); L6D2R2.1 (obsolete); L6DYK1.1 (obsolete); L6E2G1.1 (obsolete); L6ECX2.1 (obsolete); L6F2X8.1 (obsolete); L6FBL9.1 (obsolete); L6FXC0.1 (obsolete); L6GAQ7.1 (obsolete); L6GDF3.1 (obsolete); L6GQ18.1 (obsolete); L6GUK0.1 (obsolete); L6HEM7.1 (obsolete); L6HZ42.1 (obsolete); L6IJA8.1 (obsolete); L6IKQ8.1 (obsolete); L6JAX7.1 (obsolete); L6JQW5.1 (obsolete); L6JTZ9.1 (obsolete); L6KHV2.1 (obsolete); L6KJ96.1 (obsolete); L6KPE7.1 (obsolete); L6LIS9.1 (obsolete); L6LRL1.1 (obsolete); L6M479.1 (obsolete); L6MJ49.1 (obsolete); L6MRV4.1 (obsolete); L6N4S1.1 (obsolete); L6NJT7.1 (obsolete); L6NQD7.1 (obsolete); L6NYY9.1 (obsolete); L6PTJ6.1 (obsolete); L6Q5G9.1 (obsolete); L6QG28.1 (obsolete); L6RD28.1 (obsolete); L6RT68.1 (obsolete); L6S8W2.1 (obsolete); L6SG06.1 (obsolete); L6ST86.1 (obsolete); L6TMF4.1 (obsolete); L6TTR9.1 (obsolete); L6U0S5.1 (obsolete); L6UCM0.1 (obsolete); L6UY97.1 (obsolete); L6V2H8.1 (obsolete); L6VEW0.1 (obsolete); L6VGW5.1 (obsolete); L6VM83.1 (obsolete); L6W988.1 (obsolete); L6WWB6.1 (obsolete); L6WY56.1 (obsolete); L6X469.1 (obsolete); L6Y0M1.1 (obsolete); L6YE57.1 (obsolete); L6YI25.1 (obsolete); L6Z0U5.1 (obsolete); L6ZMA5.1 (obsolete); L6ZXN5.1 (obsolete); L9Q2Z1.1 (obsolete); L9Q651.1 (obsolete); L9QWK6.1 (obsolete); L9RTY2.1 (obsolete); L9RZ23.1 (obsolete); L9RZV7.1 (obsolete); L9SPL8.1 (obsolete); L9SUR8.1 (obsolete); L9T0I1.1 (obsolete); L9T3F0.1 (obsolete); M9XM34.1 (obsolete); R7RAX9.1 (obsolete); S4HPD6.1 (obsolete); S4IA20.1 (obsolete); S4IYB2.1 (obsolete); S4JUW3.1 (obsolete); S4KAX3.1 (obsolete); S4KSA9.1 (obsolete); S4KVH5.1 (obsolete); S4LU50.1 (obsolete); S5HC55.1 (obsolete); S5IK76.1 (obsolete); S5V9L5.1 (obsolete); T1YEZ9.1 (obsolete); T2PZY7.1 (obsolete); T2QEG8.1 (obsolete); U1J3E4.1 (obsolete); U1RUM6.1 (obsolete); U3SIJ4.1 (obsolete); U6QI94.1 (obsolete); U6QL14.1 (obsolete); U6VL57.1 (obsolete); U6W0G5.1 (obsolete); U6WAX9.1 (obsolete); U6X5N2.1 (obsolete); U6XU02.1 (obsolete); U6XUE1.1 (obsolete); U6Z0B9.1 (obsolete); V0GUR1.1 (obsolete); V0JCU6.1 (obsolete); V1FK33.1 (obsolete); V1G2K9.1 (obsolete); V1GCR6.1 (obsolete); V1IGN7.1 (obsolete); V1IMQ3.1 (obsolete); V1JBW5.1 (obsolete); V1K0S1.1 (obsolete); V1KS42.1 (obsolete); V1LZZ7.1 (obsolete); V1NPU7.1 (obsolete); V1NX60.1 (obsolete); V1Q9V0.1 (obsolete); V1QHX1.1 (obsolete); V1RCP8.1 (obsolete); V1YX44.1 (obsolete); V2CQS1.1 (obsolete); V2D2U7.1 (obsolete); V2DLF9.1 (obsolete); V2F5F1.1 (obsolete); V2F5Q4.1 (obsolete); V2MGV5.1 (obsolete); V2NI96.1 (obsolete); V2NYL4.1 (obsolete); V2PHB9.1 (obsolete); V5KNP2.1 (obsolete); V5ZLN4.1 (obsolete); V7RZQ1.1 (obsolete); V7WUI4.1 (obsolete); V7X4V6.1 (obsolete); V8M2J1.1 (obsolete); V8ML76.1 (obsolete); X4RML9.1 (obsolete); X5NKI0.1 (obsolete),MFFTQNLWVERQQLIKPFILNVNIIYLKNIIIFFIIGGY,-1.194574836126887
65
65
  UPI00016B0142,38,NA,MRDTQCHSADFPVYPNVLAVGVRRALWPLPAQDANRTQ,0.44996359010503817
66
- UPI000173114C,30,B2L4W4,PADDMPTXRNGPSTTNDSDDFVDPWTVQTG,1.3068624916447211
package/files/samples/sample_FASTA.fasta CHANGED
@@ -190,7 +190,4 @@ MFFTQNLWVERQQLIKPFILNVNIIYLKNIIIFFIIGGY
190
190
  >UPI00016B0142:38
191
191
  MRDTQCHSADFPVYPNVLAVGVRRALWPLPAQDANRTQ
192
192
 
193
- >UPI000173114C:30
194
- PADDMPTXRNGPSTTNDSDDFVDPWTVQTG
195
-
196
193
 
package/files/samples/sample_FASTA_DNA.csv ADDED
@@ -0,0 +1,101 @@
1
+ id,sequence
2
+ 1,TGTCTCAGCACCATCCAATTTGCGATTCGACCC
3
+ 2,TGTCTCTCATCAAATCATCCCTATGGTGGCCCTAATT
4
+ 3,ATTTATCAACGATCATCCCAACAAAGCGAAACCGTCAT
5
+ 4,CGAGGCCAGCCCTCATCCAATAGAACACCTTCGTG
6
+ 5,TGGGTCACCCTTCATCCCCCACTCCTACTAGGA
7
+ 6,TTTATTCATCGGTCATCCACGTGCGTATACATATG
8
+ 7,GACCTCAACTGTCCTCCGGGAGACATGCCCGAAAT
9
+ 8,CTGCATCAGCTGTCATCCCCTGGTGAGGTTTCTTGTG
10
+ 9,TATTTTCACCTATCATCGTTAATGGCTAACCGGCAT
11
+ 10,CGCCTTCAGCGGACATCCTATACAGTCGGCCCACTT
12
+ 11,ACGCTTCACCCCTCATCCATAACTTTTCGTAGTC
13
+ 12,AATCCTCAACATTCATCGCGAAGTAAAGGTCCTTTA
14
+ 13,TCGCTTTCAGCGCTCATCCCCAAATCTTCCCAAAAAG
15
+ 14,CCATGTTCATCGATCATCCGTAACGTCATACTTAGT
16
+ 15,CAAACTCATCATTTATCTATAGTCTTCCGCGAT
17
+ 16,CGTTCTCAGCCTCATCCTATGTTCAGCCGGCGT
18
+ 17,GTTAGTCATCGCTCATCCTGTCGGCAACTCCTTAC
19
+ 18,GGTCGTCACCGTTCATCCTTCAGATCAGCAATGTGTAC
20
+ 19,AGACATCAACTCTCAGCCTGCAATGATTACCGATA
21
+ 20,TGTATTCATCCTCATCCCAGGTAATGTGACTATCT
22
+ 21,ATGGTCAGCGTCCATCAGGAGAATTTTACATACG
23
+ 22,TATCTTCAGCGGACATCCTATGTCGCGCACAGACAT
24
+ 23,CCATACTCAGCTAGCATCCCAGACCGATCTCATCTC
25
+ 24,TCCCTTCAGCTTTCATCCAGACGACTGTTCAAAAA
26
+ 25,TCCGTTCAACACGCATCCTCTGACGAGACTCAAGA
27
+ 26,CGCATCAGCGATCCTCCGGCAGTGTGGCCCGCTGA
28
+ 27,TGCGCTCAACTTTCATCCTGGCGTCCAGGCGAG
29
+ 28,TTTCTTCAGCGCTCATCAAAAGGTCCCAGCCATA
30
+ 29,TCACGTCACCCATCATCCATCGGACAGACCCCCC
31
+ 30,GATTGTTCAACCCTTATCTGAGCGTTATCCCGGCGAG
32
+ 31,GAGCTTCATCCGTCATCCCACGAGAAGTACTGGTA
33
+ 32,CCTGTTCATCCTTCATCCTGAGGTACAAACCCCCT
34
+ 33,AGACGTCAGCCTTCACCGAGATTCTATTCCACATTA
35
+ 34,GTGCGTCAGCAGTCATCCTTCTGAACCGGCGGATC
36
+ 35,TTTGGTCAGCGATCATCCGTGCGATTGTTACGTCGG
37
+ 36,TTGTTTCAGCTGTCATCCAACAAGCTGGCCTATC
38
+ 37,CGGTGTCAGCCATCATTCGAACGAGTAGCCGCGGC
39
+ 38,TGGGTTCACTCCTTCATCGGGTACGGACCCCAAGCA
40
+ 39,CCTATTCATCCCCTCATCGAACAGATTAGCCGAAAC
41
+ 40,GGAGGTCACCCTTCATCCTGGTACTGGCAAGA
42
+ 41,GGCACTCAGCTCTCATCACGACTATTCGGCAGAGG
43
+ 42,CGGTATCAACGGTCATCTAACTTGATGATTCCCTCA
44
+ 43,GACTTTCACCAATCATCAGAGGGGTAGCACCTCGAA
45
+ 44,AGACGTCAACCCGCATCAAACTGGTTGCACACCA
46
+ 45,CAGTTCAGCAAATCATCCCTCTTGTACGACCCTAG
47
+ 46,CCAAATCACCGATCATCTAAACCCCTAGACAGCGC
48
+ 47,TCTGGTAAACCCTCATCCCCGATAAAGCAGCTATAA
49
+ 48,ACTATTCAACCTCATCCGAGAGCCCGCTACGT
50
+ 49,TACAAGTCAGCGGCCATCCGCCGATGTGCACTCAGC
51
+ 50,TTTAGGTTCAGCAGTTTATCCTCCAAGTTTTTCCTCA
52
+ 51,TCTATCTCAGCCTTCATCCAGAACGGTAGTCCTTGTT
53
+ 52,GGGAGCTCAGCTCTCATCAAGATAGATCACCGATT
54
+ 53,TGACTTCATCACTCATCCGACAGATCACCACTAA
55
+ 54,GCTATCAGCCCTCATCAACTAAGGCGAGCGGAAA
56
+ 55,TTTAATCAGCGGTCATCAACCCAGCGCGCACACACCG
57
+ 56,TGGCATTCATCCGTCATCCAAACGTCCGCGACCATCA
58
+ 57,TATGGTCAGCAGTCATCCGCAGCAGCAAACATGGA
59
+ 58,AAGCTCATCGGTCAGCCGACGGTAAATACTAAAG
60
+ 59,CCGTTCAGCCGACAACCGGGATTCCGCACAGCCT
61
+ 60,TTAGTCATCGATCATCCGGGATCTTACGCGTTAT
62
+ 61,GGTATCAGCATTCATCCCACAAACCAATAGCCCTCTA
63
+ 62,TACCATCAGCTGTCATCGCGTGTAGGCAGACCACCTC
64
+ 63,AGTTGTCAACCTCATCCAGACCTCCCTTCCTGAGA
65
+ 64,ACCAGTCAGCGATCATCCGCATCTGTTCCCCCGCC
66
+ 65,CTGGACCAGCTCACACCCTAGCGAGCAGGCAGGGAG
67
+ 66,CTATCGTTCAGCGATCATCCACTGGCGGATCCTTGGG
68
+ 67,AGATATCAGCGATCATCGCCGTGTCACACCTAGAC
69
+ 68,GCGGTTCAGCATCATCCGTAAGTCGATTCCGACT
70
+ 69,CCGCTTCATCGCTCATCCCTGGGGGGACGCAGAAT
71
+ 70,GATTTCAACGATCATCCTCATCGACGTTGCCAGA
72
+ 71,TGCCCTCAGCGATCATCCGATGGTGCAGGCCTCGG
73
+ 72,CGTTATCAGGCCGTCATCCACGCTGGCTACGAGCCT
74
+ 73,GCTGTTCACCGCTCATCCGATGGGTGATACATCGC
75
+ 74,TGCCCTCAGCACCCATCCCAACGGTTAGTCCGGA
76
+ 75,TGTCATCAGCGTTCATCTTTCGACCCGTACCAAAGC
77
+ 76,GGTCCCAGCATTCATCTATTTCAGGCGTACTCGG
78
+ 77,CCCTGTCAGCGGTCATCCCAGGGACGATCCGTACA
79
+ 78,CGGGTTCAGCACTCATCCTGTTGGTTTACCGACTTA
80
+ 79,TACAATCAGCGTTCATCCCGGGTTTTTCTCCTGCT
81
+ 80,CGGCATCAGCTTCATCCATTGGGTTTGTCTTGA
82
+ 81,CTCAATCAGGCTGTCATCCTCTGGGTTAGCCAATGG
83
+ 82,TGCAATCAACGATTCATCCGGCTTCCTCCTCGGAT
84
+ 83,AGGCTTCAGCTTTCATTAGGCAGACATTGCCATCCGA
85
+ 84,CCTAGTCAGTAATTCATCACAAATGAAAGAACAGTC
86
+ 85,TTCATTCAGCCCTCATCAGCCATGCCCCTCCGTC
87
+ 86,GTCATCAACTCTCATCACTAACATCAAGCGAAT
88
+ 87,GGTCTTCAACCATCATCCTGGGGATACACCTACT
89
+ 88,TCGTCTCAGCCCTCATCCCACAGTCGATACCCCCC
90
+ 89,AGAACTCAACCCTCAACCGGACAGGACCACTC
91
+ 90,AGCCGTCAGCTATCATCCTCCTTATTTGTCATAGC
92
+ 91,CGTTCAACGGTCATCCGTACCTGATCTCCTTGA
93
+ 92,CGTTCTTCATCCCTCATCCGACATGGTAGACTGGGCC
94
+ 93,TAGATTCAACGGTCATCCAGACCTACGTTCCCGACA
95
+ 94,TCTGTCAGCCATCATCCGAGTCACCATCCTTGT
96
+ 95,GGTTCTCAGCGTTCAGCCTGCCTGAGCCCGCGGCCA
97
+ 96,AGTGTTCAGCATCATCCGAATAAGGCTGCAACTT
98
+ 97,TTCGATCATCGGGCATCGCGGGGATTGTCCGACTG
99
+ 98,TTTCATCAGCGTTCATCGAGGTGTGTACCCCAACTC
100
+ 99,GTGCTTCAGCTCTCATCAGACGAAAGGGACGAGG
101
+ 100,TCCGTTCATCAGTCATCTAGCGGCGCTATCGTAGTG
package/files/samples/sample_FASTA_PT.csv ADDED
@@ -0,0 +1,101 @@
1
+ id,sequence
2
+ 1,MFITMFCMFWLFIFILMMLIFFMEAMIKPML
3
+ 2,AQMTMFCIMFFLMLMFIIMIMFMILEAMKKMLNAI
4
+ 3,ILMTMFCICWMIMIFFLLLIMFMLMAMMKMLIFL
5
+ 4,FQMTMICMLFFLMMFMFDLIILFIMMEAMMKPDLMFI
6
+ 5,LLMTMFCFFMMLLMFFMFMIMFMYFEAMKKFFILF
7
+ 6,AMMTMFCFMLIMMFILLFIDIIMEAMLKLDNFI
8
+ 7,LLMTMFCMILISMIMILMMIMFLMEAMKKIFFAV
9
+ 8,LIMTMFCMLILIFMLMDFMIIMIFFEAMFKMLFLMF
10
+ 9,FQMTMFCLMIFMWIFMMMMILDIFIEAMIKFINLFM
11
+ 10,FLMTMFCILINIMIIWMIIMLMFEAMFKLDIIF
12
+ 11,FFMTMFCMMIFLLLIMIIIMIMDMIMEAMKKMMDIII
13
+ 12,IMMTMFCICLLFWLLFMLLIMDMMFEAMLKFIMMI
14
+ 13,MQMTMFCFMLLLMFFMDIMIIMLLDEAMLKLDLIL
15
+ 14,LQMTMFCIFWMLFMLFMLFIFFLFLEAMLKFINLI
16
+ 15,IIMTMFCMIMIISIFFIIMIMLFIFEAMIKLDIIAM
17
+ 16,FLMTMLCMCFILFFFLFMFIMLSFFLEALIKILILI
18
+ 17,FQMTMFCMMIFLFIMWMIIFIIFFIFEAMKMLLLL
19
+ 18,MFMTMFCMCIMFWIFDIIIIILFLIEAMLKLFFIIV
20
+ 19,IMLMTMFCMFFFMWIFMFMLIIFSLILEAMMKPDIII
21
+ 20,AFLTMFCFMWLLMLMFLFLIMIIIDEAMIKLFFL
22
+ 21,FQMTMFCFLLMSFLMIIMIFILMFFDEAMFKILNFI
23
+ 22,MIMTMFCMLMNLLMFFMLIILILMIEAMLKLMMAI
24
+ 23,MIMTMFCMIILMFHMMMFLIFILYEAMKKLFNMIV
25
+ 24,LFTMFCMCWMIMIFWIIILMIMIFLAMKKPMFLF
26
+ 25,AFLMTMFCICWFLFFLFMILIMLMFFEAMKKFFLV
27
+ 26,LLMTMFCMCMNMMMFMLIMMILMSYIEAMFKFFLI
28
+ 27,LQLTMFCFILLIFLMILLILMILFEAMMKMFFAL
29
+ 28,IQMTMFCMMMMFLMLFFIDIMFLMMEMMFKMDLMFF
30
+ 29,MMTMFCIWIFMMILDMMFFIIMIIAMMMFLLIIV
31
+ 30,FQMTMFCMMLFMFILWDIFIMISMLEAMMKLDIIM
32
+ 31,LFMTMFCMMMNFMIFWLILIFFSLFEAMKKLILAM
33
+ 32,AFMTMFCMFLWFILHLWIFFIMMLIMIEAMIKIDIAV
34
+ 33,LLTMFCMILIFWHFMFMDIMMMMIFEAMLMIFIMI
35
+ 34,IMMTMFCFCFLIFHMMIFDIMISMIEAMKKIIMLL
36
+ 35,FMMTMFCMMMLFIIMFLIMMIDILLFIDEAMMKDFIL
37
+ 36,IMMTMFCMIILFMFMFMMIIIMLFFMLEAMFKMMFF
38
+ 37,LLMTMFCMLWMMLFIFFIMLIFISLFEAMKKIFIIM
39
+ 38,FIMTMFCMMLLLFFFIILDIMLMFIEAMKKLLLL
40
+ 39,IMMTMFCFMMMSMMFFFLIIIILFMFDMAMKILLI
41
+ 40,MFMTMFCMFILILLLWIIDIMFMLDEAMKKPDFL
42
+ 41,LIMTMFCMCMFLILWMMFIMLIIIEAMKKPIILI
43
+ 42,AFMTMFCFMMMFMHFMLIFIFMIFMEAMKKFFLFLM
44
+ 43,AFIQMTMLCMCMLLMFFLDIFIIIIFLDEAMMKPLMLL
45
+ 44,LQMTMFCMFMIILFDMIMMMMMEAMLKIMIF
46
+ 45,ALMTMFCFIWNSIFIFIFDILMILLIEAMFKMDNII
47
+ 46,LMMTMFCLMLFSWLMWLMIIFIIMMILEAMLKPLFAFV
48
+ 47,FFMTMFCMFFIMFLIFFLLLIMLFMMEAMLKIFL
49
+ 48,LMMMTMFCIFMLLFFFFMFIMMMFDEAMFKMDMIL
50
+ 49,QITMFCIFFMFIIMWLFFFLFFLFEAMLKMIMAL
51
+ 50,IIMTMFCIMLILWIFLFIIIIMILIAMKKLILLL
52
+ 51,ILMTMFCMMLIIFFFMLFFILIILDFFFEAMLKIDMMI
53
+ 52,FIMTMFCMCWFILLIMMIIIFLIDEAMMKMFLMM
54
+ 53,FIMTMFCMLLMFSLMFFMMMILIFYIEAMIKMMLFI
55
+ 54,IQMTMFCMCWMFLHMMFLDILFIFLDEAMLKMIIFL
56
+ 55,FMMTMFCMLILMMHLFFFIIMDMIEAMLKMDMLV
57
+ 56,LMMTMFCMFINSMLLMMFILILMMLFEAMKKPFMIM
58
+ 57,MLMTMFCLIMNFFMFLMFMIMMMEAMFKMLM
59
+ 58,ILMTMFCLFFFSFFFILIMMIYIEAMLKIMMIL
60
+ 59,IIMMTMFCMCLLMLMFWIIMIMISFLMEAMKKFLIAM
61
+ 60,IFMTMFCMMFNSFLIFWIILMFFLLILEAMMKPLNLV
62
+ 61,IFITMFCMILLSMLFILFDIFFIIMEIMKKFIIAF
63
+ 62,IMMTMFCFCMIMFMFILFLILFLDEAMMKMLIL
64
+ 63,IFMTMFCMFLMFMIMLLFDIFLSFFEAMKKFFIAV
65
+ 64,IQMTMFCMIFFSMMFFMDMDIMIFIIEAMFKMNMLL
66
+ 65,LFMTMFCMFLLMFILFFIIMDFYFFEAMKKPMLILL
67
+ 66,AMMTMFCMLLMMFHMLDFIFDFFMEAMKKMMML
68
+ 67,AIMTMFCMFLNLMLMMFIFMMIDEAMIKFLLFI
69
+ 68,MFMTMFCMFIIFLIIMMDLIIMIIMLEAMIFILILLL
70
+ 69,IFMTMFFMFMMIIFWLMWDLMIIFSIMIMAMIKLMMAL
71
+ 70,ILMTMFCMMLFLLFFFLIIIIFSMMEAMMKPDIMM
72
+ 71,FFMTMFCMFFIFLHMIFFDIFLFFYLEAMMKPMFFI
73
+ 72,MFMTMFCMLWMFMLHIMFFLIMMMLFEAMFKFMLAF
74
+ 73,AIMTMFCMMIMMIMLFFLLILMFLIEAMFKFIFFM
75
+ 74,MMMTMFCMLMFWIIFIIFLIFILMIEAMFKMINIV
76
+ 75,LLMTMFCMLIMLIMLWLMDIMMMLIEAMKKPLMFFL
77
+ 76,LQITMFIMMWILLFMIFIFILFFEAMMKFMLF
78
+ 77,ILMTMFCIFFIFFMFMFMFFIMFFLIEAMKKLDIML
79
+ 78,MLMTMLCMMMFSLLIFIFLDIIIFILEAMLKFMMI
80
+ 79,ILMTMFCMCMMMIMMIIIIMDSFLEAMKKPMMMI
81
+ 80,QMTMFCMMFFIIHMMIIFFMDLIMMLAMKKPDMAI
82
+ 81,LLMTMICILFFMFMFLMMLIIMFLYFEAMMKMLNII
83
+ 82,MMMMFCMFIFFIHFMLILIMLIYMMIMKIMMNML
84
+ 83,ALMTMFCMFIFFMLMMMIIIFFFFEAMMKMFIFV
85
+ 84,ALMTMFCMWLILMWFMIIILMMDEAMKKLLNIL
86
+ 85,LIIMTMFCMMLLLIIMMFLIFIFLLEAMIKFLLFLL
87
+ 86,MLMTMFCMLLMFHFLIMMILISYFEAMKKLIFML
88
+ 87,FIMTMFCMMIFIFFFMFDIILSMMAMFKIDLIM
89
+ 88,FMTMFCMMWLSLFFMFLILFFIFIEAMFKLMNFV
90
+ 89,MMMTMMCMLLIMFLFMFIMFIFMLIEAMKKLDLLI
91
+ 90,AFMTMFCFMFISWMMIIFMLIMFILFEAMMKMFFFL
92
+ 91,LIMTMFCMIWFIMHFLILMLIMILYLEAMFKPLIFF
93
+ 92,MIMTMFCMFINLWIFFLLDIFFLIMEAMKLDMIM
94
+ 93,LLMTMFCMFIIMLFFLFMFLIMFFIDEAMFKPLFIM
95
+ 94,FFMTMFCIFFMSLHLFMLLIIFMFDEAMKKMLLFI
96
+ 95,IFFTMFLIFLLFIMMMIDMIIFILLEAMKKPMFII
97
+ 96,MFMMTMFCFMIIFFMMMDIMIIMDFILEAMLKIFLIII
98
+ 97,IIMTMFCMIINMLFFDLLIIILLEAMLKFDMFF
99
+ 98,MLMTMFCMLLIMFMILILMFIFLLYDEAMKKMLMLI
100
+ 99,LFMTMFCMLINSLIMIFFDIIIFLEAMFKFFLILL
101
+ 100,FLMTMFCMMMFSMMMMFIIFMLLIEAMLKIFNAL
package/files/samples/sample_FASTA_RNA.csv ADDED
@@ -0,0 +1,101 @@
1
+ id,sequence
2
+ 1,AAGGCCAGCAAAGUCUUCACGAGAGCGCGGAAACUU
3
+ 2,AGGCCAUACGACUAAUUCUGAAUCUGCGGAAAUCA
4
+ 3,GUGCCCGCAUCUUCAGUGGUGUAAUUUGCGGAUGCUCG
5
+ 4,GGGCCAGAAUACAUAGCUAAGCAGCUGCGAACGGUA
6
+ 5,CUGCCAGCCUUGAAAAGGCGGUCGCGCGGAGCUAA
7
+ 6,AGGCCAGCUUCUCACUGUCUCGUUCGCGGAUAGCA
8
+ 7,UAGCCAGCAAUAUUAGUAGGAAUAGCGGAGGCCA
9
+ 8,ACGCCAGUACCGCGCAUAGGAGCAGCGUACCCUA
10
+ 9,AUGCCAGCUCAUCACCAUAGCCCUGCGGAUGGCCG
11
+ 10,ACGCCAGCAAUAGCACCUAGUCCCUUGCGGACAUCA
12
+ 11,CGGCCAGCUGCUCUCGGGGACUAGCGAAUGGGG
13
+ 12,CUCCCAGCCAGACAUGCGUGAGUCUAGCGUAACAC
14
+ 13,GGGCCAGCCUGAUUUGGCGCGAACGAGCGGAACGA
15
+ 14,CUGUCCAGCAUUUGGGAGCAGUUCUAGCGCACGGCG
16
+ 15,GCGCCAGCUCGUUUUGCGGUGUGCGUGCGGAACUA
17
+ 16,UCGCCGGCCGUUGUUACCGGACAUGCGGCAAGUCU
18
+ 17,GGGCCAGCGGUAACCGGAGGCGUGUGCGUAUGCUA
19
+ 18,UGGCCAGUGUUAUCAUUGAUGGGCGCACAAAA
20
+ 19,GGGCCAGCAAAUCGUAGGAAGUAAAUGCGCAUCCCA
21
+ 20,GGGCCAGGAAUCAAUAAGUGCAGGAGCGUAACAU
22
+ 21,UAUGCCAGCGGGCGAUGUGAAUAAUUCGCGGACCGGU
23
+ 22,GUACCAGAAUAGAAUGCUAGAUACGGCGAAUUGCA
24
+ 23,CGGCCAGCCCGCGGCAGCGCGUUAGCGGACGCGU
25
+ 24,GUGCCAGCUCUGUUCCUCCGCUUAGGCGAAUCUG
26
+ 25,GUGCCAGCGCAAUUCGCGAGCCAUGUGCGCAGCACG
27
+ 26,AAGCCAGCCACGCCUGAGAGGCAUCCUCGCGGACGCC
28
+ 27,UGCCUGUCGACGGCCGAGCGGCGGCGUACGAGC
29
+ 28,CGGCCAGCGAUCUUUUUGUGGGGGGGCGCACAAAU
30
+ 29,CAAGCCAGCAAGCUACAUAGGGUGUGCGGAGGUA
31
+ 30,CGGCCAGCCCCACUUACGUAGUGUAGCGCAUUCUA
32
+ 31,GGCCCAGCAACGUUCGAAUGCACCGGCGUAACCGC
33
+ 32,UAGCCAGCUUCUUAACACAUGCACGAGCGAAGAACG
34
+ 33,GAGGUAGCCUAACAAGGAUUAGUUUGGGCGGAUGACU
35
+ 34,UGGCCUGACGUAACCAUUCGAACAGCGGACGCGG
36
+ 35,GGCCAGCUUGUCUUAACCGAAUGAGCGAAAGUUU
37
+ 36,GUGCCAGCGCGCGGCGACGCAACAGCGGUAGCGU
38
+ 37,UUGCCAGCGUGUGGAGCCGAUUUGCGCAAUGUA
39
+ 38,GACGCCAGCUCGGAGAUAGUGAUGAUGCGGAUAGGG
40
+ 39,CAGCCAGAUCAUCGUAAGAGAGUGCGGAACCA
41
+ 40,UUGCCAGGUAGCAUUCGCUGAGGGGCGGAGAGAA
42
+ 41,CGGCCGGCGUGAGUAAGGUGCACUUGCGGAGUUGG
43
+ 42,UGACCAGCCAGGCCCUGAUGAAUGCGGCGGAAUCUU
44
+ 43,CAGCCAGCCCCGGCAAGGUAGCGUCAGCGGAUUGGA
45
+ 44,AGGCCAGCAAGAAGCGCAGCACGCCGGGGACCAC
46
+ 45,UCGCCAGCUAGUUGACAUAGAAUACGCGGACAAGUA
47
+ 46,GUGCCUGCUUCAAAAGAGGGUCCGCGCACCCGG
48
+ 47,GAGCCAGAUGGGCCAGGUGUAGUUGAGGACCCG
49
+ 48,UGGCCUGCGGGCAUGUCAAGGUCAAGCGGAUAUA
50
+ 49,GCGCCAGUGACCGUCUUAUGACUUAACGGGCUCA
51
+ 50,GGCCAGAUGUCACGGUUUGCUGAGGCGGACGGA
52
+ 51,ACGCCAGAUAUUCACGACCCGGGGCCGCGGAAGGUU
53
+ 52,CUGCCAGCUUUUAUAAGCAGGUAUGUGCGCAUCAAUG
54
+ 53,ACGCCAGUUACUGCAAAACGCACAGCGCACCCAC
55
+ 54,GCGCCAGACUCGUAGGCUCGCUGGGUGCGGAUGUAA
56
+ 55,GAGCCAGCAGUAGCGAUAGGUUGCCGCGGAGCCGG
57
+ 56,AGGCCUGCUUGCCCCGGGAAUGGGCCUGCGUAGCUG
58
+ 57,UAGCCAAGUGACAACUGUAGGUCGCGCGAAUGCCC
59
+ 58,CAGCCAGCUGUUCUCAGCGUGGGAGCGGAAGCAG
60
+ 59,CCUCCAGGUAUAUGGACGGCAGCUGCGGAUAUGA
61
+ 60,CCGCCAGCGAACUAAAAAGGACGGCAGCGAAAUCUG
62
+ 61,ACGCCAGCAAAAAACGGGUGUGUGUGCGGAUUUGA
63
+ 62,GGACCAGUUAUGAUGUAGAGGAAGAGCAGAACAAUA
64
+ 63,GGGCCAGCCGGUUCACCGGACGGUGCGGAAGGC
65
+ 64,GGACCAGCGGCAGACCGACGCCUGUGCGUAUUAAA
66
+ 65,GUGCCAGCGGUCUCCGCCAGUAUCGGCGUAUCUCA
67
+ 66,UAGCCAGCUAAAUACUCACGGGUUUGCGGAACCCG
68
+ 67,GUGCCAGCGCGGUUACAGGGCAGCAGGCGGACGACA
69
+ 68,UGGCCAGCAGCCGACUCGCCAGUGCGGACUAC
70
+ 69,GGCCACCGAGCACGGGUUGUACGUGCGGAUGAGCG
71
+ 70,UAGCCAGCCCUAGUCAGACGAGAACGCGAAUAUGUGG
72
+ 71,UUGGCCAGCGCAGCGUCAUCGCCGCGCGCAUGUG
73
+ 72,CAGCCAGCCGCUCAUGAAAGCUGAGCGUAUUAA
74
+ 73,CGGCCAGCUGUGAACACGCAGUAGCUGCGCAGUCC
75
+ 74,AAGCCAGGUUUCGUCGCCCUGCUGGAUCGCAUCGCAG
76
+ 75,UAGCCAGCUAGCUUUAGCGAAGGCAAGCGGCCGGAAC
77
+ 76,GAGCCGGUAAAUGCCGCCGAGCAGCACCGGAUUAGC
78
+ 77,CCAGCCAGCCAUGAUCACGCGUUCUCAGCGGAUGCGA
79
+ 78,GGGCCAGCCUUUUACGCGUCCCCGCGUAGAAA
80
+ 79,GGGCCAGCUUCACGAUGUACGACCCGGGGGAACCUG
81
+ 80,GACCGUUGGCCGGUGAAGCAUCUGCGGAUGCAA
82
+ 81,AGGCCAGGAAAUUCCUGAGAGAUAUCCGGACGCCC
83
+ 82,AGGCCAGCCAUCAUACCCCUGUUGAAAAGGCGGAUAUGA
84
+ 83,CAGCCAGGUGUCAUAAGCGGCCUCCGCGAAAGGA
85
+ 84,GCGCCGGCGGUUGCAUCGGACCUAGCGCAUGCGC
86
+ 85,GGGCCAGCGUGUUAAUUGUGAUCACGCGUAAAGUGU
87
+ 86,UAGCCAGCUAUGGGACAAGUAAGGCGAACGCAU
88
+ 87,GUGCCAGCAAUAAUACCUAAGAUUCAGCGGAGGAU
89
+ 88,AGCCCCAGAUUUGUACCUCAGUCUGCGGCGGAGUGA
90
+ 89,UGGCCAGUCUCAACGCAUGAGCACGCGAACGACA
91
+ 90,AAGCCAGCCUUCGCUGGAUGGAUUUGCGCAACCUA
92
+ 91,GUGCCAGUGAUUAACGGAUUCUGCUGCGGACUCCC
93
+ 92,GGGCCGGAUACUCUGAUGCUGCAGAAGCGAAGUGAU
94
+ 93,UUCGCCAGGAGAUAUCCUAUGGGUGGUGCGCAACAA
95
+ 94,UAGCCACCUCAAUAUGCAAUGGUGCAGCGGAGGCGA
96
+ 95,GCGCCAGCUAUUCUGGUGGGUCUCUGCGGAUACUG
97
+ 96,GAGCCAGGGUACCUCAUUCGCCGCACGCGUAGCCUGA
98
+ 97,GAGCCAGGAGGUUCGUUAGGAAUCUGCGGAAGGGA
99
+ 98,AAACCAGGAUCAAUAACAAGAAGACGCGCACAGCGC
100
+ 99,GAGCCAGCGGGUUUUUGAGGAGAUCUGCGGACGUUC
101
+ 100,GAGCCAGCUACCGAAAGGGCACAGCGGACUUUACG
package/files/{samples → tests}/peptides_simple_msa.csv RENAMED
File without changes
package/files/{samples → tests}/testDemog.csv RENAMED
File without changes
package/files/{samples → tests}/testHelm.csv RENAMED
File without changes
package/files/{samples → tests}/testId.csv RENAMED
File without changes
package/files/tests/testSmiles.csv ADDED
@@ -0,0 +1,201 @@
1
+ smiles
2
+ O=C1CN=C(c2ccccc2N1)C3CCCCC3
3
+ CN1C(=O)CN=C(c2ccccc12)C3CCCCC3
4
+ CCCCN1C(=O)CN=C(c2ccccc12)C3CCCCC3
5
+ CC(C)CCN1C(=O)CN=C(c2ccccc12)C3CCCCC3
6
+ O=C1CN=C(c2ccccc2N1CC3CCCCC3)C4CCCCC4
7
+ O=C1CN=C(c2cc(Cl)ccc2N1)C3CCCCC3
8
+ CN1C(=O)CN=C(c2cc(Cl)ccc12)C3CCCCC3
9
+ CCCCN1C(=O)CN=C(c2cc(Cl)ccc12)C3CCCCC3
10
+ CC(C)CCN1C(=O)CN=C(c2cc(Cl)ccc12)C3CCCCC3
11
+ O=C1CN=C(c2cc(Cl)ccc2N1CC3CCCCC3)C4CCCCC4
12
+ N#Cc1ccc2NC(=O)CN=C(c2c1)C3CCCCC3
13
+ CN1C(=O)CN=C(c2cc(C#N)ccc12)C3CCCCC3
14
+ CCCCN1C(=O)CN=C(c2cc(C#N)ccc12)C3CCCCC3
15
+ CC(C)CCN1C(=O)CN=C(c2cc(C#N)ccc12)C3CCCCC3
16
+ N#Cc1ccc2c(c1)C(=NCC(=O)N2CC3CCCCC3)C4CCCCC4
17
+ CN(C)c1ccc2NC(=O)CN=C(c2c1)C3CCCCC3
18
+ CN(C)c1ccc2c(c1)C(=NCC(=O)N2C)C3CCCCC3
19
+ CCCCN1C(=O)CN=C(c2cc(ccc12)N(C)C)C3CCCCC3
20
+ CC(C)CCN1C(=O)CN=C(c2cc(ccc12)N(C)C)C3CCCCC3
21
+ CN(C)c1ccc2c(c1)C(=NCC(=O)N2CC3CCCCC3)C4CCCCC4
22
+ O=C1CN=C(c2cc(F)ccc2N1)C3CCCCC3
23
+ CN1C(=O)CN=C(c2cc(F)ccc12)C3CCCCC3
24
+ CCCCN1C(=O)CN=C(c2cc(F)ccc12)C3CCCCC3
25
+ CC(C)CCN1C(=O)CN=C(c2cc(F)ccc12)C3CCCCC3
26
+ O=C1CN=C(c2cc(F)ccc2N1CC3CCCCC3)C4CCCCC4
27
+ O=C1CN=C(c2cc(Br)ccc2N1)C3CCCCC3
28
+ CN1C(=O)CN=C(c2cc(Br)ccc12)C3CCCCC3
29
+ CCCCN1C(=O)CN=C(c2cc(Br)ccc12)C3CCCCC3
30
+ CC(C)CCN1C(=O)CN=C(c2cc(Br)ccc12)C3CCCCC3
31
+ O=C1CN=C(c2cc(Br)ccc2N1CC3CCCCC3)C4CCCCC4
32
+ O=C1CN=C(c2cc(I)ccc2N1)C3CCCCC3
33
+ CN1C(=O)CN=C(c2cc(I)ccc12)C3CCCCC3
34
+ CCCCN1C(=O)CN=C(c2cc(I)ccc12)C3CCCCC3
35
+ CC(C)CCN1C(=O)CN=C(c2cc(I)ccc12)C3CCCCC3
36
+ O=C1CN=C(c2cc(I)ccc2N1CC3CCCCC3)C4CCCCC4
37
+ NC(=O)c1ccc2NC(=O)CN=C(c2c1)C3CCCCC3
38
+ CN1C(=O)CN=C(c2cc(ccc12)C(N)=O)C3CCCCC3
39
+ CCCCN1C(=O)CN=C(c2cc(ccc12)C(N)=O)C3CCCCC3
40
+ CC(C)CCN1C(=O)CN=C(c2cc(ccc12)C(N)=O)C3CCCCC3
41
+ NC(=O)c1ccc2c(c1)C(=NCC(=O)N2CC3CCCCC3)C4CCCCC4
42
+ O=C1CN=C(c2cc(ccc2N1)[N+](=O)[O-])C3CCCCC3
43
+ CN1C(=O)CN=C(c2cc(ccc12)[N+](=O)[O-])C3CCCCC3
44
+ CCCCN1C(=O)CN=C(c2cc(ccc12)[N+](=O)[O-])C3CCCCC3
45
+ CC(C)CCN1C(=O)CN=C(c2cc(ccc12)[N+](=O)[O-])C3CCCCC3
46
+ O=C1CN=C(c2cc(ccc2N1CC3CCCCC3)[N+](=O)[O-])C4CCCCC4
47
+ O=C1CN=C(c2ccccc2)c3ccccc3N1
48
+ CN1C(=O)CN=C(c2ccccc2)c3ccccc13
49
+ CCCCN1C(=O)CN=C(c2ccccc2)c3ccccc13
50
+ CC(C)CCN1C(=O)CN=C(c2ccccc2)c3ccccc13
51
+ O=C1CN=C(c2ccccc2)c3ccccc3N1CC4CCCCC4
52
+ O=C1CN=C(c2ccccc2)c3cc(Cl)ccc3N1
53
+ CN1C(=O)CN=C(c2ccccc2)c3cc(Cl)ccc13
54
+ CCCCN1C(=O)CN=C(c2ccccc2)c3cc(Cl)ccc13
55
+ CC(C)CCN1C(=O)CN=C(c2ccccc2)c3cc(Cl)ccc13
56
+ O=C1CN=C(c2ccccc2)c3cc(Cl)ccc3N1CC4CCCCC4
57
+ N#Cc1ccc2NC(=O)CN=C(c3ccccc3)c2c1
58
+ CN1C(=O)CN=C(c2ccccc2)c3cc(C#N)ccc13
59
+ CCCCN1C(=O)CN=C(c2ccccc2)c3cc(C#N)ccc13
60
+ CC(C)CCN1C(=O)CN=C(c2ccccc2)c3cc(C#N)ccc13
61
+ N#Cc1ccc2c(c1)C(=NCC(=O)N2CC3CCCCC3)c4ccccc4
62
+ CN(C)c1ccc2NC(=O)CN=C(c3ccccc3)c2c1
63
+ CN(C)c1ccc2c(c1)C(=NCC(=O)N2C)c3ccccc3
64
+ CCCCN1C(=O)CN=C(c2ccccc2)c3cc(ccc13)N(C)C
65
+ CC(C)CCN1C(=O)CN=C(c2ccccc2)c3cc(ccc13)N(C)C
66
+ CN(C)c1ccc2c(c1)C(=NCC(=O)N2CC3CCCCC3)c4ccccc4
67
+ O=C1CN=C(c2ccccc2)c3cc(F)ccc3N1
68
+ CN1C(=O)CN=C(c2ccccc2)c3cc(F)ccc13
69
+ CCCCN1C(=O)CN=C(c2ccccc2)c3cc(F)ccc13
70
+ CC(C)CCN1C(=O)CN=C(c2ccccc2)c3cc(F)ccc13
71
+ O=C1CN=C(c2ccccc2)c3cc(F)ccc3N1CC4CCCCC4
72
+ O=C1CN=C(c2ccccc2)c3cc(Br)ccc3N1
73
+ CN1C(=O)CN=C(c2ccccc2)c3cc(Br)ccc13
74
+ CCCCN1C(=O)CN=C(c2ccccc2)c3cc(Br)ccc13
75
+ CC(C)CCN1C(=O)CN=C(c2ccccc2)c3cc(Br)ccc13
76
+ O=C1CN=C(c2ccccc2)c3cc(Br)ccc3N1CC4CCCCC4
77
+ O=C1CN=C(c2ccccc2)c3cc(I)ccc3N1
78
+ CN1C(=O)CN=C(c2ccccc2)c3cc(I)ccc13
79
+ CCCCN1C(=O)CN=C(c2ccccc2)c3cc(I)ccc13
80
+ CC(C)CCN1C(=O)CN=C(c2ccccc2)c3cc(I)ccc13
81
+ O=C1CN=C(c2ccccc2)c3cc(I)ccc3N1CC4CCCCC4
82
+ NC(=O)c1ccc2NC(=O)CN=C(c3ccccc3)c2c1
83
+ CN1C(=O)CN=C(c2ccccc2)c3cc(ccc13)C(N)=O
84
+ CCCCN1C(=O)CN=C(c2ccccc2)c3cc(ccc13)C(N)=O
85
+ CC(C)CCN1C(=O)CN=C(c2ccccc2)c3cc(ccc13)C(N)=O
86
+ NC(=O)c1ccc2c(c1)C(=NCC(=O)N2CC3CCCCC3)c4ccccc4
87
+ O=C1CN=C(c2ccccc2)c3cc(ccc3N1)[N+](=O)[O-]
88
+ CN1C(=O)CN=C(c2ccccc2)c3cc(ccc13)[N+](=O)[O-]
89
+ CCCCN1C(=O)CN=C(c2ccccc2)c3cc(ccc13)[N+](=O)[O-]
90
+ CC(C)CCN1C(=O)CN=C(c2ccccc2)c3cc(ccc13)[N+](=O)[O-]
91
+ O=C1CN=C(c2ccccc2)c3cc(ccc3N1CC4CCCCC4)[N+](=O)[O-]
92
+ COc1ccc(cc1)C2=NCC(=O)Nc3ccccc23
93
+ COc1ccc(cc1)C2=NCC(=O)N(C)c3ccccc23
94
+ CCCCN1C(=O)CN=C(c2ccc(cc2)OC)c3ccccc13
95
+ COc1ccc(cc1)C2=NCC(=O)N(CCC(C)C)c3ccccc23
96
+ COc1ccc(cc1)C2=NCC(=O)N(CC3CCCCC3)c4ccccc24
97
+ COc1ccc(cc1)C2=NCC(=O)Nc3ccc(Cl)cc23
98
+ COc1ccc(cc1)C2=NCC(=O)N(C)c3ccc(Cl)cc23
99
+ CCCCN1C(=O)CN=C(c2ccc(cc2)OC)c3cc(Cl)ccc13
100
+ COc1ccc(cc1)C2=NCC(=O)N(CCC(C)C)c3ccc(Cl)cc23
101
+ COc1ccc(cc1)C2=NCC(=O)N(CC3CCCCC3)c4ccc(Cl)cc24
102
+ COc1ccc(cc1)C2=NCC(=O)Nc3ccc(C#N)cc23
103
+ COc1ccc(cc1)C2=NCC(=O)N(C)c3ccc(C#N)cc23
104
+ CCCCN1C(=O)CN=C(c2ccc(cc2)OC)c3cc(C#N)ccc13
105
+ COc1ccc(cc1)C2=NCC(=O)N(CCC(C)C)c3ccc(C#N)cc23
106
+ COc1ccc(cc1)C2=NCC(=O)N(CC3CCCCC3)c4ccc(C#N)cc24
107
+ COc1ccc(cc1)C2=NCC(=O)Nc3ccc(cc23)N(C)C
108
+ COc1ccc(cc1)C2=NCC(=O)N(C)c3ccc(cc23)N(C)C
109
+ CCCCN1C(=O)CN=C(c2ccc(cc2)OC)c3cc(ccc13)N(C)C
110
+ COc1ccc(cc1)C2=NCC(=O)N(CCC(C)C)c3ccc(cc23)N(C)C
111
+ COc1ccc(cc1)C2=NCC(=O)N(CC3CCCCC3)c4ccc(cc24)N(C)C
112
+ COc1ccc(cc1)C2=NCC(=O)Nc3ccc(F)cc23
113
+ COc1ccc(cc1)C2=NCC(=O)N(C)c3ccc(F)cc23
114
+ CCCCN1C(=O)CN=C(c2ccc(cc2)OC)c3cc(F)ccc13
115
+ COc1ccc(cc1)C2=NCC(=O)N(CCC(C)C)c3ccc(F)cc23
116
+ COc1ccc(cc1)C2=NCC(=O)N(CC3CCCCC3)c4ccc(F)cc24
117
+ COc1ccc(cc1)C2=NCC(=O)Nc3ccc(Br)cc23
118
+ COc1ccc(cc1)C2=NCC(=O)N(C)c3ccc(Br)cc23
119
+ CCCCN1C(=O)CN=C(c2ccc(cc2)OC)c3cc(Br)ccc13
120
+ COc1ccc(cc1)C2=NCC(=O)N(CCC(C)C)c3ccc(Br)cc23
121
+ COc1ccc(cc1)C2=NCC(=O)N(CC3CCCCC3)c4ccc(Br)cc24
122
+ COc1ccc(cc1)C2=NCC(=O)Nc3ccc(I)cc23
123
+ COc1ccc(cc1)C2=NCC(=O)N(C)c3ccc(I)cc23
124
+ CCCCN1C(=O)CN=C(c2ccc(cc2)OC)c3cc(I)ccc13
125
+ COc1ccc(cc1)C2=NCC(=O)N(CCC(C)C)c3ccc(I)cc23
126
+ COc1ccc(cc1)C2=NCC(=O)N(CC3CCCCC3)c4ccc(I)cc24
127
+ COc1ccc(cc1)C2=NCC(=O)Nc3ccc(cc23)C(N)=O
128
+ COc1ccc(cc1)C2=NCC(=O)N(C)c3ccc(cc23)C(N)=O
129
+ CCCCN1C(=O)CN=C(c2ccc(cc2)OC)c3cc(ccc13)C(N)=O
130
+ COc1ccc(cc1)C2=NCC(=O)N(CCC(C)C)c3ccc(cc23)C(N)=O
131
+ COc1ccc(cc1)C2=NCC(=O)N(CC3CCCCC3)c4ccc(cc24)C(N)=O
132
+ COc1ccc(cc1)C2=NCC(=O)Nc3ccc(cc23)[N+](=O)[O-]
133
+ COc1ccc(cc1)C2=NCC(=O)N(C)c3ccc(cc23)[N+](=O)[O-]
134
+ CCCCN1C(=O)CN=C(c2ccc(cc2)OC)c3cc(ccc13)[N+](=O)[O-]
135
+ COc1ccc(cc1)C2=NCC(=O)N(CCC(C)C)c3ccc(cc23)[N+](=O)[O-]
136
+ COc1ccc(cc1)C2=NCC(=O)N(CC3CCCCC3)c4ccc(cc24)[N+](=O)[O-]
137
+ CC1N=C(c2ccccc2NC1=O)C3CCCCC3
138
+ CC1N=C(c2ccccc2N(C)C1=O)C3CCCCC3
139
+ CCCCN1C(=O)C(C)N=C(c2ccccc12)C3CCCCC3
140
+ CC(C)CCN1C(=O)C(C)N=C(c2ccccc12)C3CCCCC3
141
+ CC1N=C(c2ccccc2N(CC3CCCCC3)C1=O)C4CCCCC4
142
+ CC1N=C(c2cc(Cl)ccc2NC1=O)C3CCCCC3
143
+ CC1N=C(c2cc(Cl)ccc2N(C)C1=O)C3CCCCC3
144
+ CCCCN1C(=O)C(C)N=C(c2cc(Cl)ccc12)C3CCCCC3
145
+ CC(C)CCN1C(=O)C(C)N=C(c2cc(Cl)ccc12)C3CCCCC3
146
+ CC1N=C(c2cc(Cl)ccc2N(CC3CCCCC3)C1=O)C4CCCCC4
147
+ CC1N=C(c2cc(C#N)ccc2NC1=O)C3CCCCC3
148
+ CC1N=C(c2cc(C#N)ccc2N(C)C1=O)C3CCCCC3
149
+ CCCCN1C(=O)C(C)N=C(c2cc(C#N)ccc12)C3CCCCC3
150
+ CC(C)CCN1C(=O)C(C)N=C(c2cc(C#N)ccc12)C3CCCCC3
151
+ CC1N=C(c2cc(C#N)ccc2N(CC3CCCCC3)C1=O)C4CCCCC4
152
+ CC1N=C(c2cc(ccc2NC1=O)N(C)C)C3CCCCC3
153
+ CC1N=C(c2cc(ccc2N(C)C1=O)N(C)C)C3CCCCC3
154
+ CCCCN1C(=O)C(C)N=C(c2cc(ccc12)N(C)C)C3CCCCC3
155
+ CC(C)CCN1C(=O)C(C)N=C(c2cc(ccc12)N(C)C)C3CCCCC3
156
+ CC1N=C(c2cc(ccc2N(CC3CCCCC3)C1=O)N(C)C)C4CCCCC4
157
+ CC1N=C(c2cc(F)ccc2NC1=O)C3CCCCC3
158
+ CC1N=C(c2cc(F)ccc2N(C)C1=O)C3CCCCC3
159
+ CCCCN1C(=O)C(C)N=C(c2cc(F)ccc12)C3CCCCC3
160
+ CC(C)CCN1C(=O)C(C)N=C(c2cc(F)ccc12)C3CCCCC3
161
+ CC1N=C(c2cc(F)ccc2N(CC3CCCCC3)C1=O)C4CCCCC4
162
+ CC1N=C(c2cc(Br)ccc2NC1=O)C3CCCCC3
163
+ CC1N=C(c2cc(Br)ccc2N(C)C1=O)C3CCCCC3
164
+ CCCCN1C(=O)C(C)N=C(c2cc(Br)ccc12)C3CCCCC3
165
+ CC(C)CCN1C(=O)C(C)N=C(c2cc(Br)ccc12)C3CCCCC3
166
+ CC1N=C(c2cc(Br)ccc2N(CC3CCCCC3)C1=O)C4CCCCC4
167
+ CC1N=C(c2cc(I)ccc2NC1=O)C3CCCCC3
168
+ CC1N=C(c2cc(I)ccc2N(C)C1=O)C3CCCCC3
169
+ CCCCN1C(=O)C(C)N=C(c2cc(I)ccc12)C3CCCCC3
170
+ CC(C)CCN1C(=O)C(C)N=C(c2cc(I)ccc12)C3CCCCC3
171
+ CC1N=C(c2cc(I)ccc2N(CC3CCCCC3)C1=O)C4CCCCC4
172
+ CC1N=C(c2cc(ccc2NC1=O)C(N)=O)C3CCCCC3
173
+ CC1N=C(c2cc(ccc2N(C)C1=O)C(N)=O)C3CCCCC3
174
+ CCCCN1C(=O)C(C)N=C(c2cc(ccc12)C(N)=O)C3CCCCC3
175
+ CC(C)CCN1C(=O)C(C)N=C(c2cc(ccc12)C(N)=O)C3CCCCC3
176
+ CC1N=C(c2cc(ccc2N(CC3CCCCC3)C1=O)C(N)=O)C4CCCCC4
177
+ CC1N=C(c2cc(ccc2NC1=O)[N+](=O)[O-])C3CCCCC3
178
+ CC1N=C(c2cc(ccc2N(C)C1=O)[N+](=O)[O-])C3CCCCC3
179
+ CCCCN1C(=O)C(C)N=C(c2cc(ccc12)[N+](=O)[O-])C3CCCCC3
180
+ CC(C)CCN1C(=O)C(C)N=C(c2cc(ccc12)[N+](=O)[O-])C3CCCCC3
181
+ CC1N=C(c2cc(ccc2N(CC3CCCCC3)C1=O)[N+](=O)[O-])C4CCCCC4
182
+ CC1N=C(c2ccccc2)c3ccccc3NC1=O
183
+ CC1N=C(c2ccccc2)c3ccccc3N(C)C1=O
184
+ CCCCN1C(=O)C(C)N=C(c2ccccc2)c3ccccc13
185
+ CC(C)CCN1C(=O)C(C)N=C(c2ccccc2)c3ccccc13
186
+ CC1N=C(c2ccccc2)c3ccccc3N(CC4CCCCC4)C1=O
187
+ CC1N=C(c2ccccc2)c3cc(Cl)ccc3NC1=O
188
+ CC1N=C(c2ccccc2)c3cc(Cl)ccc3N(C)C1=O
189
+ CCCCN1C(=O)C(C)N=C(c2ccccc2)c3cc(Cl)ccc13
190
+ CC(C)CCN1C(=O)C(C)N=C(c2ccccc2)c3cc(Cl)ccc13
191
+ CC1N=C(c2ccccc2)c3cc(Cl)ccc3N(CC4CCCCC4)C1=O
192
+ CC1N=C(c2ccccc2)c3cc(C#N)ccc3NC1=O
193
+ CC1N=C(c2ccccc2)c3cc(C#N)ccc3N(C)C1=O
194
+ CCCCN1C(=O)C(C)N=C(c2ccccc2)c3cc(C#N)ccc13
195
+ CC(C)CCN1C(=O)C(C)N=C(c2ccccc2)c3cc(C#N)ccc13
196
+ CC1N=C(c2ccccc2)c3cc(C#N)ccc3N(CC4CCCCC4)C1=O
197
+ CC1N=C(c2ccccc2)c3cc(ccc3NC1=O)N(C)C
198
+ CC1N=C(c2ccccc2)c3cc(ccc3N(C)C1=O)N(C)C
199
+ CCCCN1C(=O)C(C)N=C(c2ccccc2)c3cc(ccc13)N(C)C
200
+ CC(C)CCN1C(=O)C(C)N=C(c2ccccc2)c3cc(ccc13)N(C)C
201
+ CC1N=C(c2ccccc2)c3cc(ccc3N(CC4CCCCC4)C1=O)N(C)C
package/files/{samples → tests}/testSmiles2.csv RENAMED
File without changes
package/package.json CHANGED
@@ -2,7 +2,7 @@
2
2
  "name": "@datagrok/bio",
3
3
  "beta": false,
4
4
  "friendlyName": "Bio",
5
- "version": "1.5.10",
5
+ "version": "1.7.1",
6
6
  "description": "Bio is a [package](https://datagrok.ai/help/develop/develop#packages) for the [Datagrok](https://datagrok.ai) platform",
7
7
  "repository": {
8
8
  "type": "git",
@@ -11,7 +11,7 @@
11
11
  },
12
12
  "dependencies": {
13
13
  "@biowasm/aioli": ">=2.4.0",
14
- "@datagrok-libraries/bio": "^2.4.2",
14
+ "@datagrok-libraries/bio": "^2.5.0",
15
15
  "@datagrok-libraries/utils": "^1.0.0",
16
16
  "@datagrok-libraries/ml": "^2.0.9",
17
17
  "cash-dom": "latest",
package/scripts/generate_fasta_csv_for_alphabets.R ADDED
@@ -0,0 +1,70 @@
1
+ require(tidyverse)
2
+ library(random)
3
+
4
+ alphabetDna <- c('A','C','G','T')
5
+ alphabetRna <- c('A','C','G','U')
6
+ alphabetPt <- c('G', 'L', 'Y', 'S', 'E', 'Q', 'D', 'N', 'F', 'A',
7
+ 'K', 'R', 'H', 'C', 'V', 'P', 'W', 'I', 'M', 'T',)
8
+
9
+ toAlphabet <- function(v, a;ph){
10
+ paste(sapply(v, function(ci){ alph[ci]; }), collapse = '')
11
+ }
12
+
13
+ mutateString <- function(s, p){
14
+
15
+ }
16
+
17
+ seq <- toAlphabet(sample.int(4, 35, replace=TRUE), alphabet);
18
+ seqPt <- toAlphabet(sample.int(20, 35, replace=TRUE), alphabetPt);
19
+ seqDna <- toAlphabet(sample.int(4, 35, replace=TRUE), alphabetDna);
20
+ seqRna <- toAlphabet(sample.int(4, 35, replace=TRUE), alphabetRna);
21
+ # probability to mutate
22
+ seq_p1 <- c(100, 100, 100, 100, 100, 5, 2, 2, 50, 3,
23
+ 100, 100, 7, 2, 2, 7, 2, 33, 100, 100,
24
+ 100, 100, 100, 100, 100, 100, 100, 100, 100, 2,
25
+ 100, 100, 100, 100, 100)
26
+ seq_p2 <- c(100, 100, 7, 2, 2, 7, 2, 33, 100, 100,
27
+ 100, 100, 100, 100, 100, 100, 100, 100, 100, 2,
28
+ 100, 100, 100, 100, 100, 5, 2, 2, 50, 3,
29
+ 100, 100, 100, 100, 100)
30
+
31
+ # mutate string s with probability p and alphabet
32
+ seq_mutate <- function(s, p, alphabet){
33
+ # s <- seqDna
34
+ # p <- seq_p
35
+ # alphabet <- alphabetDna
36
+ res_s <- s
37
+ res_p <- p
38
+ for (i in 1:(str_length(res_s)*2)) {
39
+ pos <- sample.int(str_length(res_s), 1)
40
+ if (sample.int(100, 1) < res_p[pos]) {
41
+ cast <- sample.int(100, 1) # mutation type probabilty
42
+ if (0 < cast && cast <= 2 ) {
43
+ #insertion
44
+ res_s <- paste(substr(res_s, 1, pos), alphabet[sample.int(4, 1)], substr(res_s, pos+1, str_length(res_s)), collapse='', sep='')
45
+ res_p <- c(res_p[1:pos], c(100), res_p[(pos+1):length(res_p)])
46
+ #cat('insertion');
47
+ } else if (2 < cast && cast <= 4 ) {
48
+ # deletion
49
+ res_s <- paste(substr(res_s, 1, pos-1), substr(res_s, pos+1, str_length(res_s)), collapse = '', sep='')
50
+ res_p <- c(res_p[1: (pos-1)], res_p[(pos+1):length(res_p)])
51
+ #cat('deletion');
52
+ } else {
53
+ # replace
54
+ res_s <- paste(substr(res_s, 1, pos-1), alphabet[sample.int(4, 1)], substr(res_s, pos+1, str_length(res_s)), collapse='', sep='')
55
+ #cat('replace')
56
+ }
57
+ #cat(res, '\n')
58
+ }
59
+ }
60
+ res_s;
61
+ }
62
+
63
+ fastaDna_df <- data.frame(id = 1:100, sequence = sapply(1:100, function(id){ seq_mutate(seqDna, seq_p1, alphabetDna)}));
64
+ write_csv(fastaDna_df, 'D:/HOME/atanas/Datagrok/projs/public/packages/Bio/files/samples/sample_FASTA_DNA.csv');
65
+
66
+ fastaRna_df <- data.frame(id = 1:100, sequence = sapply(1:100, function(id){ seq_mutate(seqRna, seq_p2, alphabetRna)}));
67
+ write_csv(fastaRna_df, 'D:/HOME/atanas/Datagrok/projs/public/packages/Bio/files/samples/sample_FASTA_RNA.csv');
68
+
69
+ fastaPt_df <- data.frame(id = 1:100, sequence = sapply(1:100, function(id){ seq_mutate(seqPt, seq_p2, alphabetPt)}));
70
+ write_csv(fastaPt_df, 'D:/HOME/atanas/Datagrok/projs/public/packages/Bio/files/samples/sample_FASTA_PT.csv');
package/src/package-test.ts CHANGED
@@ -10,6 +10,7 @@ import './tests/sequence-space-test';
10
10
  import './tests/activity-cliffs-tests';
11
11
  import './tests/splitter-test';
12
12
  import './tests/renderer-test';
13
+ import './tests/convert-test';
13
14
 
14
15
  export const _package = new DG.Package();
15
16
  export {tests};