@datagrok/sequence-translator 1.0.9 → 1.0.11

package/src/structures-works/mol-transformations.ts

@@ -78,6 +78,480 @@ M  V30 END COLLECTION
 M  V30 END CTAB
 M  END`;
 
+const GALNAC = `
+Datagrok monomer library Nucleotides                            
+
+0  0  0     0  0            999 V3000
+M  V30 BEGIN CTAB
+M  V30 COUNTS 111 113 0 0 0
+M  V30 BEGIN ATOM
+M  V30 1 O -20.7313 -0.7027 0 0
+M  V30 2 C -19.3976 0.0673 0 0
+M  V30 3 C -18.0638 -0.7027 0 0
+M  V30 4 C -16.7303 0.0673 0 0
+M  V30 5 N -15.3965 -0.7027 0 0
+M  V30 6 C -14.0628 0.0673 0 0
+M  V30 7 C -12.7293 -0.7027 0 0
+M  V30 8 C -11.3955 0.0673 0 0
+M  V30 9 C -10.062 -0.7027 0 0
+M  V30 10 C -8.7283 0.0673 0 0
+M  V30 11 N -7.3947 -0.7027 0 0
+M  V30 12 O -18.0638 -2.2427 0 0
+M  V30 13 O -14.0628 1.6073 0 0
+M  V30 14 O -8.7283 1.6073 0 0
+M  V30 15 C -5.8547 -0.7027 0 0
+M  V30 16 C -5.8547 0.8373 0 0
+M  V30 17 C -5.8547 -2.2427 0 0
+M  V30 18 C -3.4848 -3.0127 0 0
+M  V30 19 C -2.4544 -4.157 0 0
+M  V30 20 C -0.948 -3.8368 0 0
+M  V30 21 N 0.0824 -4.9813 0 0
+M  V30 22 C 1.5888 -4.6612 0 0
+M  V30 23 C 2.6192 -5.8056 0 0
+M  V30 24 C 4.1256 -5.4855 0 0
+M  V30 25 N 5.156 -6.6297 0 0
+M  V30 26 C 6.6624 -6.3096 0 0
+M  V30 27 C 7.6928 -7.4541 0 0
+M  V30 28 C 9.1992 -7.1339 0 0
+M  V30 29 C 10.2296 -8.2784 0 0
+M  V30 30 C 11.736 -7.9583 0 0
+M  V30 31 O 12.7664 -9.1027 0 0
+M  V30 32 O -0.4722 -2.3723 0 0
+M  V30 33 O 7.1382 -4.845 0 0
+M  V30 34 C 14.2728 -8.7824 0 0
+M  V30 35 C 15.3032 -9.9267 0 0
+M  V30 36 C 16.8098 -9.6065 0 0
+M  V30 37 C 17.2856 -8.1421 0 0
+M  V30 38 C 16.2552 -6.9975 0 0
+M  V30 39 O 14.7486 -7.3178 0 0
+M  V30 40 C 16.7312 -5.5329 0 0
+M  V30 41 O 18.7918 -7.8218 0 0
+M  V30 42 O 17.8404 -10.751 0 0
+M  V30 43 N 14.8274 -11.3914 0 0
+M  V30 44 C 15.7325 -12.6372 0 0
+M  V30 45 C 15.2567 -14.1018 0 0
+M  V30 46 O 17.2537 -12.3963 0 0
+M  V30 47 O 18.2628 -5.372 0 0
+M  V30 48 O -4.9494 -3.4885 0 0
+M  V30 49 C -4.521 0.0673 0 0
+M  V30 50 C -1.9414 0.2026 0 0
+M  V30 51 C -0.6077 -0.5674 0 0
+M  V30 52 C 0.726 0.2026 0 0
+M  V30 53 N 2.0596 -0.5674 0 0
+M  V30 54 C 3.3933 0.2026 0 0
+M  V30 55 C 4.7271 -0.5674 0 0
+M  V30 56 C 6.0606 0.2026 0 0
+M  V30 57 N 7.3943 -0.5674 0 0
+M  V30 58 C 8.7281 0.2026 0 0
+M  V30 59 C 10.0618 -0.5674 0 0
+M  V30 60 C 11.3953 0.2026 0 0
+M  V30 61 C 14.0628 0.2026 0 0
+M  V30 62 O 15.3964 -0.5674 0 0
+M  V30 63 O 0.726 1.7426 0 0
+M  V30 64 O 8.7281 1.7426 0 0
+M  V30 65 C 16.7301 0.2026 0 0
+M  V30 66 C 18.0638 -0.5676 0 0
+M  V30 67 C 19.3976 0.2026 0 0
+M  V30 68 C 19.3974 1.7426 0 0
+M  V30 69 C 18.0638 2.5126 0 0
+M  V30 70 O 16.7301 1.7426 0 0
+M  V30 71 C 18.064 4.0526 0 0
+M  V30 72 O 20.7311 2.5126 0 0
+M  V30 73 O 20.7313 -0.5674 0 0
+M  V30 74 N 18.0638 -2.1076 0 0
+M  V30 75 C 19.3096 -3.0127 0 0
+M  V30 76 C 19.3096 -4.5527 0 0
+M  V30 77 O 20.6818 -2.3135 0 0
+M  V30 78 O 19.4709 4.6791 0 0
+M  V30 79 O -3.1872 -0.7027 0 0
+M  V30 80 C 12.7291 -0.5674 0 0
+M  V30 81 C -3.919 3.2277 0 0
+M  V30 82 C -2.4126 2.9076 0 0
+M  V30 83 C -1.3822 4.0519 0 0
+M  V30 84 N 0.1242 3.7317 0 0
+M  V30 85 C 1.1546 4.8762 0 0
+M  V30 86 C 2.661 4.5561 0 0
+M  V30 87 C 3.6914 5.7005 0 0
+M  V30 88 N 5.1978 5.3804 0 0
+M  V30 89 C 6.2282 6.5248 0 0
+M  V30 90 C 7.7346 6.2045 0 0
+M  V30 91 C 8.765 7.349 0 0
+M  V30 92 C 10.2714 7.0288 0 0
+M  V30 93 C 11.3018 8.1733 0 0
+M  V30 94 O 12.8082 7.8532 0 0
+M  V30 95 O -1.858 5.5167 0 0
+M  V30 96 O 5.7524 7.9894 0 0
+M  V30 97 C 13.8386 8.9976 0 0
+M  V30 98 C 15.345 8.6773 0 0
+M  V30 99 C 16.3756 9.8219 0 0
+M  V30 100 C 15.8996 11.2863 0 0
+M  V30 101 C 14.3934 11.6068 0 0
+M  V30 102 O 13.3628 10.4622 0 0
+M  V30 103 C 13.9176 13.0714 0 0
+M  V30 104 O 16.93 12.4308 0 0
+M  V30 105 O 17.882 9.5018 0 0
+M  V30 106 N 15.8208 7.2127 0 0
+M  V30 107 C 17.2856 6.7367 0 0
+M  V30 108 C 17.7614 5.2721 0 0
+M  V30 109 O 18.3744 7.8257 0 0
+M  V30 110 O 15.062 14.1018 0 0
+M  V30 111 O -4.8241 1.9817 0 0
+M  V30 END ATOM
+M  V30 BEGIN BOND
+M  V30 1 1 2 3
+M  V30 2 1 3 4
+M  V30 3 1 6 7
+M  V30 4 1 7 8
+M  V30 5 1 8 9
+M  V30 6 1 9 10
+M  V30 7 1 1 2
+M  V30 8 1 3 12
+M  V30 9 1 4 5
+M  V30 10 1 5 6
+M  V30 11 2 6 13
+M  V30 12 1 10 11
+M  V30 13 1 11 15
+M  V30 14 1 15 16
+M  V30 15 1 15 17
+M  V30 16 2 10 14
+M  V30 17 1 18 19
+M  V30 18 1 19 20
+M  V30 19 1 22 23
+M  V30 20 1 23 24
+M  V30 21 1 26 27
+M  V30 22 1 27 28
+M  V30 23 1 28 29
+M  V30 24 1 29 30
+M  V30 25 2 26 33
+M  V30 26 2 20 32
+M  V30 27 1 20 21
+M  V30 28 1 21 22
+M  V30 29 1 24 25
+M  V30 30 1 25 26
+M  V30 31 1 30 31
+M  V30 32 1 31 34
+M  V30 33 1 35 36
+M  V30 34 1 36 37
+M  V30 35 1 37 38
+M  V30 36 1 34 35
+M  V30 37 1 38 39
+M  V30 38 1 34 39
+M  V30 39 1 38 40
+M  V30 40 1 35 43
+M  V30 41 1 43 44
+M  V30 42 1 44 45
+M  V30 43 2 44 46
+M  V30 44 1 36 42
+M  V30 45 1 37 41
+M  V30 46 1 40 47
+M  V30 47 1 18 48
+M  V30 48 1 15 49
+M  V30 49 1 50 51
+M  V30 50 1 51 52
+M  V30 51 1 54 55
+M  V30 52 1 55 56
+M  V30 53 1 58 59
+M  V30 54 1 59 60
+M  V30 55 2 58 64
+M  V30 56 2 52 63
+M  V30 57 1 52 53
+M  V30 58 1 53 54
+M  V30 59 1 56 57
+M  V30 60 1 57 58
+M  V30 61 1 61 62
+M  V30 62 1 62 65
+M  V30 63 1 66 67
+M  V30 64 1 67 68
+M  V30 65 1 68 69
+M  V30 66 1 65 66
+M  V30 67 1 69 70
+M  V30 68 1 65 70
+M  V30 69 1 69 71
+M  V30 70 1 66 74
+M  V30 71 1 74 75
+M  V30 72 1 75 76
+M  V30 73 2 75 77
+M  V30 74 1 67 73
+M  V30 75 1 68 72
+M  V30 76 1 71 78
+M  V30 77 1 50 79
+M  V30 78 1 49 79
+M  V30 79 1 60 80
+M  V30 80 1 80 61
+M  V30 81 1 81 82
+M  V30 82 1 82 83
+M  V30 83 1 85 86
+M  V30 84 1 86 87
+M  V30 85 1 89 90
+M  V30 86 1 90 91
+M  V30 87 1 91 92
+M  V30 88 1 92 93
+M  V30 89 2 89 96
+M  V30 90 2 83 95
+M  V30 91 1 83 84
+M  V30 92 1 84 85
+M  V30 93 1 87 88
+M  V30 94 1 88 89
+M  V30 95 1 93 94
+M  V30 96 1 94 97
+M  V30 97 1 98 99
+M  V30 98 1 99 100
+M  V30 99 1 100 101
+M  V30 100 1 97 98
+M  V30 101 1 101 102
+M  V30 102 1 97 102
+M  V30 103 1 101 103
+M  V30 104 1 98 106
+M  V30 105 1 106 107
+M  V30 106 1 107 108
+M  V30 107 2 107 109
+M  V30 108 1 99 105
+M  V30 109 1 100 104
+M  V30 110 1 103 110
+M  V30 111 1 81 111
+M  V30 112 1 16 111
+M  V30 113 1 17 48
+M  V30 END BOND
+M  V30 END CTAB
+M  END`;
+
+const GALNACPRIME = `
+Datagrok monomer library Nucleotides          
+
+0  0  0     0  0            999 V3000
+M  V30 BEGIN CTAB
+M  V30 COUNTS 111 113 0 0 0
+M  V30 BEGIN ATOM
+M  V30 1 O 20.7313 0.7027 0 0
+M  V30 2 C 19.3976 -0.0673 0 0
+M  V30 3 C 18.0638 0.7027 0 0
+M  V30 4 C 16.7303 -0.0673 0 0
+M  V30 5 N 15.3965 0.7027 0 0
+M  V30 6 C 14.0628 -0.0673 0 0
+M  V30 7 C 12.7293 0.7027 0 0
+M  V30 8 C 11.3955 -0.0673 0 0
+M  V30 9 C 10.062 0.7027 0 0
+M  V30 10 C 8.7283 -0.0673 0 0
+M  V30 11 N 7.3947 0.7027 0 0
+M  V30 12 O 18.0638 2.2427 0 0
+M  V30 13 O 14.0628 -1.6073 0 0
+M  V30 14 O 8.7283 -1.6073 0 0
+M  V30 15 C 5.8547 0.7027 0 0
+M  V30 16 C 5.8547 -0.8373 0 0
+M  V30 17 C 5.8547 2.2427 0 0
+M  V30 18 C 3.4848 3.0127 0 0
+M  V30 19 C 2.4544 4.157 0 0
+M  V30 20 C 0.948 3.8368 0 0
+M  V30 21 N -0.0824 4.9813 0 0
+M  V30 22 C -1.5888 4.6612 0 0
+M  V30 23 C -2.6192 5.8056 0 0
+M  V30 24 C -4.1256 5.4855 0 0
+M  V30 25 N -5.156 6.6297 0 0
+M  V30 26 C -6.6624 6.3096 0 0
+M  V30 27 C -7.6928 7.4541 0 0
+M  V30 28 C -9.1992 7.1339 0 0
+M  V30 29 C -10.2296 8.2784 0 0
+M  V30 30 C -11.736 7.9583 0 0
+M  V30 31 O -12.7664 9.1027 0 0
+M  V30 32 O 0.4722 2.3723 0 0
+M  V30 33 O -7.1382 4.845 0 0
+M  V30 34 C -14.2728 8.7824 0 0
+M  V30 35 C -15.3032 9.9267 0 0
+M  V30 36 C -16.8098 9.6065 0 0
+M  V30 37 C -17.2856 8.1421 0 0
+M  V30 38 C -16.2552 6.9975 0 0
+M  V30 39 O -14.7486 7.3178 0 0
+M  V30 40 C -16.7312 5.5329 0 0
+M  V30 41 O -18.7918 7.8218 0 0
+M  V30 42 O -17.8404 10.751 0 0
+M  V30 43 N -14.8274 11.3914 0 0
+M  V30 44 C -15.7325 12.6372 0 0
+M  V30 45 C -15.2567 14.1018 0 0
+M  V30 46 O -17.2537 12.3963 0 0
+M  V30 47 O -18.2628 5.372 0 0
+M  V30 48 O 4.9494 3.4885 0 0
+M  V30 49 C 4.521 -0.0673 0 0
+M  V30 50 C 1.9414 -0.2026 0 0
+M  V30 51 C 0.6077 0.5674 0 0
+M  V30 52 C -0.726 -0.2026 0 0
+M  V30 53 N -2.0596 0.5674 0 0
+M  V30 54 C -3.3933 -0.2026 0 0
+M  V30 55 C -4.7271 0.5674 0 0
+M  V30 56 C -6.0606 -0.2026 0 0
+M  V30 57 N -7.3943 0.5674 0 0
+M  V30 58 C -8.7281 -0.2026 0 0
+M  V30 59 C -10.0618 0.5674 0 0
+M  V30 60 C -11.3953 -0.2026 0 0
+M  V30 61 C -14.0628 -0.2026 0 0
+M  V30 62 O -15.3964 0.5674 0 0
+M  V30 63 O -0.726 -1.7426 0 0
+M  V30 64 O -8.7281 -1.7426 0 0
+M  V30 65 C -16.7301 -0.2026 0 0
+M  V30 66 C -18.0638 0.5676 0 0
+M  V30 67 C -19.3976 -0.2026 0 0
+M  V30 68 C -19.3974 -1.7426 0 0
+M  V30 69 C -18.0638 -2.5126 0 0
+M  V30 70 O -16.7301 -1.7426 0 0
+M  V30 71 C -18.064 -4.0526 0 0
+M  V30 72 O -20.7311 -2.5126 0 0
+M  V30 73 O -20.7313 0.5674 0 0
+M  V30 74 N -18.0638 2.1076 0 0
+M  V30 75 C -19.3096 3.0127 0 0
+M  V30 76 C -19.3096 4.5527 0 0
+M  V30 77 O -20.6818 2.3135 0 0
+M  V30 78 O -19.4709 -4.6791 0 0
+M  V30 79 O 3.1872 0.7027 0 0
+M  V30 80 C -12.7291 0.5674 0 0
+M  V30 81 C 3.919 -3.2277 0 0
+M  V30 82 C 2.4126 -2.9076 0 0
+M  V30 83 C 1.3822 -4.0519 0 0
+M  V30 84 N -0.1242 -3.7317 0 0
+M  V30 85 C -1.1546 -4.8762 0 0
+M  V30 86 C -2.661 -4.5561 0 0
+M  V30 87 C -3.6914 -5.7005 0 0
+M  V30 88 N -5.1978 -5.3804 0 0
+M  V30 89 C -6.2282 -6.5248 0 0
+M  V30 90 C -7.7346 -6.2045 0 0
+M  V30 91 C -8.765 -7.349 0 0
+M  V30 92 C -10.2714 -7.0288 0 0
+M  V30 93 C -11.3018 -8.1733 0 0
+M  V30 94 O -12.8082 -7.8532 0 0
+M  V30 95 O 1.858 -5.5167 0 0
+M  V30 96 O -5.7524 -7.9894 0 0
+M  V30 97 C -13.8386 -8.9976 0 0
+M  V30 98 C -15.345 -8.6773 0 0
+M  V30 99 C -16.3756 -9.8219 0 0
+M  V30 100 C -15.8996 -11.2863 0 0
+M  V30 101 C -14.3934 -11.6068 0 0
+M  V30 102 O -13.3628 -10.4622 0 0
+M  V30 103 C -13.9176 -13.0714 0 0
+M  V30 104 O -16.93 -12.4308 0 0
+M  V30 105 O -17.882 -9.5018 0 0
+M  V30 106 N -15.8208 -7.2127 0 0
+M  V30 107 C -17.2856 -6.7367 0 0
+M  V30 108 C -17.7614 -5.2721 0 0
+M  V30 109 O -18.3744 -7.8257 0 0
+M  V30 110 O -15.062 -14.1018 0 0
+M  V30 111 O 4.8241 -1.9817 0 0
+M  V30 END ATOM
+M  V30 BEGIN BOND
+M  V30 1 1 2 3
+M  V30 2 1 3 4
+M  V30 3 1 6 7
+M  V30 4 1 7 8
+M  V30 5 1 8 9
+M  V30 6 1 9 10
+M  V30 7 1 1 2
+M  V30 8 1 3 12
+M  V30 9 1 4 5
+M  V30 10 1 5 6
+M  V30 11 2 6 13
+M  V30 12 1 10 11
+M  V30 13 1 11 15
+M  V30 14 1 15 16
+M  V30 15 1 15 17
+M  V30 16 2 10 14
+M  V30 17 1 18 19
+M  V30 18 1 19 20
+M  V30 19 1 22 23
+M  V30 20 1 23 24
+M  V30 21 1 26 27
+M  V30 22 1 27 28
+M  V30 23 1 28 29
+M  V30 24 1 29 30
+M  V30 25 2 26 33
+M  V30 26 2 20 32
+M  V30 27 1 20 21
+M  V30 28 1 21 22
+M  V30 29 1 24 25
+M  V30 30 1 25 26
+M  V30 31 1 30 31
+M  V30 32 1 31 34
+M  V30 33 1 35 36
+M  V30 34 1 36 37
+M  V30 35 1 37 38
+M  V30 36 1 34 35
+M  V30 37 1 38 39
+M  V30 38 1 34 39
+M  V30 39 1 38 40
+M  V30 40 1 35 43
+M  V30 41 1 43 44
+M  V30 42 1 44 45
+M  V30 43 2 44 46
+M  V30 44 1 36 42
+M  V30 45 1 37 41
+M  V30 46 1 40 47
+M  V30 47 1 18 48
+M  V30 48 1 15 49
+M  V30 49 1 50 51
+M  V30 50 1 51 52
+M  V30 51 1 54 55
+M  V30 52 1 55 56
+M  V30 53 1 58 59
+M  V30 54 1 59 60
+M  V30 55 2 58 64
+M  V30 56 2 52 63
+M  V30 57 1 52 53
+M  V30 58 1 53 54
+M  V30 59 1 56 57
+M  V30 60 1 57 58
+M  V30 61 1 61 62
+M  V30 62 1 62 65
+M  V30 63 1 66 67
+M  V30 64 1 67 68
+M  V30 65 1 68 69
+M  V30 66 1 65 66
+M  V30 67 1 69 70
+M  V30 68 1 65 70
+M  V30 69 1 69 71
+M  V30 70 1 66 74
+M  V30 71 1 74 75
+M  V30 72 1 75 76
+M  V30 73 2 75 77
+M  V30 74 1 67 73
+M  V30 75 1 68 72
+M  V30 76 1 71 78
+M  V30 77 1 50 79
+M  V30 78 1 49 79
+M  V30 79 1 60 80
+M  V30 80 1 80 61
+M  V30 81 1 81 82
+M  V30 82 1 82 83
+M  V30 83 1 85 86
+M  V30 84 1 86 87
+M  V30 85 1 89 90
+M  V30 86 1 90 91
+M  V30 87 1 91 92
+M  V30 88 1 92 93
+M  V30 89 2 89 96
+M  V30 90 2 83 95
+M  V30 91 1 83 84
+M  V30 92 1 84 85
+M  V30 93 1 87 88
+M  V30 94 1 88 89
+M  V30 95 1 93 94
+M  V30 96 1 94 97
+M  V30 97 1 98 99
+M  V30 98 1 99 100
+M  V30 99 1 100 101
+M  V30 100 1 97 98
+M  V30 101 1 101 102
+M  V30 102 1 97 102
+M  V30 103 1 101 103
+M  V30 104 1 98 106
+M  V30 105 1 106 107
+M  V30 106 1 107 108
+M  V30 107 2 107 109
+M  V30 108 1 99 105
+M  V30 109 1 100 104
+M  V30 110 1 103 110
+M  V30 111 1 81 111
+M  V30 112 1 16 111
+M  V30 113 1 17 48
+M  V30 END BOND
+M  V30 END CTAB
+M  END`;
+
 export function getNucleotidesMol(smilesCodes: string[]) {
   const molBlocks: string[] = [];
 
@@ -85,6 +559,8 @@ export function getNucleotidesMol(smilesCodes: string[]) {
     smilesCodes[i] == 'OP(=O)(O)O' ? molBlocks.push(PHOSHATE) :
       smilesCodes[i] == 'OP(=O)(S)O' ? molBlocks.push(THIOPHOSHATE) :
         smilesCodes[i] == 'O[C@@H]1C[C@@H]O[C@H]1CO' ? molBlocks.push(rotateNucleotidesV3000(INVABASIC)) :
+          smilesCodes[i] == 'OCC(O)CNC(=O)CCCC(=O)NC(COCCC(=O)NCCCNC(=O)CCCCOC2OC(CO)C(O)C(O)C2NC(=O)C)(COCCC(=O)NCCCNC(=O)CCCCOC2OC(CO)C(O)C(O)C2NC(=O)C)(COCCC(=O)NCCCNC(=O)CCCCOC2OC(CO)C(O)C(O)C2NC(=O)C)' ? molBlocks.push(GALNAC) :
+            smilesCodes[i] == 'C(COCCC(=O)NCCCNC(=O)CCCCOC2OC(CO)C(O)C(O)C2NC(=O)C)(COCCC(=O)NCCCNC(=O)CCCCOC2OC(CO)C(O)C(O)C2NC(=O)C)(COCCC(=O)NCCCNC(=O)CCCCOC2OC(CO)C(O)C(O)C2NC(=O)C)NC(=O)CCCC(=O)NCC(O)CO' ? molBlocks.push(GALNACPRIME) :
           molBlocks.push(rotateNucleotidesV3000(smilesCodes[i]));
   }
 

package/src/structures-works/sequence-codes-tools.ts

@@ -1,8 +1,7 @@
 
 import {map, SYNTHESIZERS, TECHNOLOGIES, MODIFICATIONS, delimiter, gcrsCodesWithoutSmiles} from './map';
 import {asoGapmersNucleotidesToBioSpring, asoGapmersNucleotidesToGcrs,
-  asoGapmersBioSpringToNucleotides, asoGapmersBioSpringToGcrs, asoGapmersGcrsToNucleotides,
-  asoGapmersGcrsToBioSpring, gcrsToMermade12, siRnaNucleotideToBioSpringSenseStrand,
+  asoGapmersBioSpringToNucleotides, asoGapmersBioSpringToGcrs, gcrsToMermade12, siRnaNucleotideToBioSpringSenseStrand,
   siRnaNucleotideToAxolabsSenseStrand, siRnaNucleotidesToGcrs, siRnaBioSpringToNucleotides,
   siRnaBioSpringToAxolabs, siRnaBioSpringToGcrs, siRnaAxolabsToNucleotides,
   siRnaAxolabsToBioSpring, siRnaAxolabsToGcrs, siRnaGcrsToNucleotides,
@@ -95,7 +94,7 @@ function sortByStringLengthInDescendingOrder(array: string[]): string[] {
 export function isValidSequence(sequence: string, format: string | null): {
   indexOfFirstNotValidChar: number,
   synthesizer: string[] | null,
-  technology: string[] | null
+  // technology: string[] | null
 } {
   const possibleSynthesizers = format == null ?
     getListOfPossibleSynthesizersByFirstMatchedCode(sequence) :
@@ -114,49 +113,51 @@ export function isValidSequence(sequence: string, format: string | null): {
   //     .show();
   // } else if (possibleSynthesizers.length == 0)
   if (possibleSynthesizers.length == 0)
-    return {indexOfFirstNotValidChar: 0, synthesizer: null, technology: null};
+    return {indexOfFirstNotValidChar: 0, synthesizer: null};//, technology: null};
 
-  let outputIndex = 0;
+  const outputIndices = Array(possibleSynthesizers.length).fill(0);
 
   const firstUniqueCharacters = ['r', 'd'];
   const nucleotides = ['A', 'U', 'T', 'C', 'G'];
-
-  possibleSynthesizers.forEach((synthesizer) => {
+  possibleSynthesizers.forEach(function(synthesizer, i) {
     const codes = sortByStringLengthInDescendingOrder(getAllCodesOfSynthesizer(synthesizer));
-    while (outputIndex < sequence.length) {
-      const matchedCode = codes.find((c) => c == sequence.slice(outputIndex, outputIndex + c.length));
+    while (outputIndices[i] < sequence.length) {
+      const matchedCode = codes.find((c) => c == sequence.slice(outputIndices[i], outputIndices[i] + c.length));
 
       if (matchedCode == null)
         break;
 
       if ( // for mistake pattern 'rAA'
-        outputIndex > 1 &&
-        nucleotides.includes(sequence[outputIndex]) &&
-        firstUniqueCharacters.includes(sequence[outputIndex - 2])
+        outputIndices[i] > 1 &&
+        nucleotides.includes(sequence[outputIndices[i]]) &&
+        firstUniqueCharacters.includes(sequence[outputIndices[i] - 2])
       ) break;
 
       if ( // for mistake pattern 'ArA'
-        firstUniqueCharacters.includes(sequence[outputIndex + 1]) &&
-        nucleotides.includes(sequence[outputIndex])
+        firstUniqueCharacters.includes(sequence[outputIndices[i] + 1]) &&
+        nucleotides.includes(sequence[outputIndices[i]])
       ) {
-        outputIndex++;
+        outputIndices[i]++;
         break;
       }
 
-      outputIndex += matchedCode.length;
+      outputIndices[i] += matchedCode.length;
     }
   });
 
+  const outputIndex = Math.max(...outputIndices);
+  const synthesizer = possibleSynthesizers[outputIndices.indexOf(outputIndex)];
   const indexOfFirstNotValidChar = (outputIndex == sequence.length) ? -1 : outputIndex;
   if (indexOfFirstNotValidChar != -1) {
     return {
       indexOfFirstNotValidChar: indexOfFirstNotValidChar,
-      synthesizer: possibleSynthesizers,
-      technology: null,
+      synthesizer: [synthesizer],
+      // technology: null,
     };
   }
 
-  const possibleTechnologies = getListOfPossibleTechnologiesByFirstMatchedCode(sequence, possibleSynthesizers[0]);
+  // const possibleTechnologies =
+  //   getListOfPossibleTechnologiesByFirstMatchedCode(sequence, possibleSynthesizers[outputIndex]);
 
   // if (possibleTechnologies.length > 1) {
   //   const technology = ui.choiceInput('Choose technology from list: ', possibleTechnologies[0],
@@ -173,7 +174,7 @@ export function isValidSequence(sequence: string, format: string | null): {
   // if (possibleTechnologies.length == 0)
   //   return {indexOfFirstNotValidChar: 0, synthesizer: [possibleSynthesizers[3]], technology: null};
 
-  outputIndex = 0;
+  // outputIndex = 0;
 
   // possibleTechnologies.forEach((technology: string) => {
   //   const codes = Object.keys(map[possibleSynthesizers[0]][technology]);
@@ -203,8 +204,8 @@ export function isValidSequence(sequence: string, format: string | null): {
 
   return {
     indexOfFirstNotValidChar: indexOfFirstNotValidChar,
-    synthesizer: possibleSynthesizers,
-    technology: [possibleTechnologies[outputIndex]],
+    synthesizer: [synthesizer],
+    // technology: [possibleTechnologies[0]],
   };
 }
 
@@ -248,7 +249,7 @@ function getListOfPossibleTechnologiesByFirstMatchedCode(sequence: string, synth
 }
 
 export function convertSequence(sequence: string, output: {
-  indexOfFirstNotValidChar: number, synthesizer: string[] | null, technology: string[] | null}) {
+  indexOfFirstNotValidChar: number, synthesizer: string[] | null}) {//, technology: string[] | null}) {
   if (output.indexOfFirstNotValidChar != -1) {
     return {
       // type: '',
@@ -264,7 +265,8 @@ export function convertSequence(sequence: string, output: {
       GCRS: asoGapmersNucleotidesToGcrs(sequence),
     };
   }
-  if (output.synthesizer!.includes(SYNTHESIZERS.BIOSPRING) && output.technology!.includes(TECHNOLOGIES.ASO_GAPMERS)) {
+  if (output.synthesizer!.includes(SYNTHESIZERS.BIOSPRING)) {
+    // && output.technology!.includes(TECHNOLOGIES.ASO_GAPMERS)) {
     return {
       type: SYNTHESIZERS.BIOSPRING + ' ' + TECHNOLOGIES.ASO_GAPMERS,
       Nucleotides: asoGapmersBioSpringToNucleotides(sequence),
@@ -272,17 +274,19 @@ export function convertSequence(sequence: string, output: {
       GCRS: asoGapmersBioSpringToGcrs(sequence),
     };
   }
-  if (output.synthesizer!.includes(SYNTHESIZERS.GCRS) && output.technology!.includes(TECHNOLOGIES.ASO_GAPMERS)) {
+  if (output.synthesizer!.includes(SYNTHESIZERS.GCRS)) { // && output.technology!.includes(TECHNOLOGIES.ASO_GAPMERS)) {
     return {
       type: SYNTHESIZERS.GCRS + ' ' + TECHNOLOGIES.ASO_GAPMERS,
-      Nucleotides: asoGapmersGcrsToNucleotides(sequence),
-      BioSpring: asoGapmersGcrsToBioSpring(sequence),
+      Nucleotides: gcrsToNucleotides(sequence),
+      BioSpring: siRnaGcrsToBioSpring(sequence),
+      Axolabs: siRnaGcrsToAxolabs(sequence),
       Mermade12: gcrsToMermade12(sequence),
       GCRS: sequence,
       LCMS: gcrsToLcms(sequence),
     };
   }
-  if (output.synthesizer!.includes(SYNTHESIZERS.RAW_NUCLEOTIDES) && output.technology!.includes(TECHNOLOGIES.RNA)) {
+  if (output.synthesizer!.includes(SYNTHESIZERS.RAW_NUCLEOTIDES)) {
+    // && output.technology!.includes(TECHNOLOGIES.RNA)) {
     return {
       type: SYNTHESIZERS.RAW_NUCLEOTIDES + ' ' + TECHNOLOGIES.RNA,
       Nucleotides: sequence,
@@ -291,7 +295,7 @@ export function convertSequence(sequence: string, output: {
       GCRS: siRnaNucleotidesToGcrs(sequence),
     };
   }
-  if (output.synthesizer!.includes(SYNTHESIZERS.BIOSPRING) && output.technology!.includes(TECHNOLOGIES.SI_RNA)) {
+  if (output.synthesizer!.includes(SYNTHESIZERS.BIOSPRING)) { // && output.technology!.includes(TECHNOLOGIES.SI_RNA)) {
     return {
       type: SYNTHESIZERS.BIOSPRING + ' ' + TECHNOLOGIES.SI_RNA,
       Nucleotides: siRnaBioSpringToNucleotides(sequence),
@@ -309,7 +313,7 @@ export function convertSequence(sequence: string, output: {
       GCRS: siRnaAxolabsToGcrs(sequence),
     };
   }
-  if (output.synthesizer!.includes(SYNTHESIZERS.GCRS) && output.technology!.includes(TECHNOLOGIES.SI_RNA)) {
+  if (output.synthesizer!.includes(SYNTHESIZERS.GCRS)) { // && output.technology!.includes(TECHNOLOGIES.SI_RNA)) {
     return {
       type: SYNTHESIZERS.GCRS + ' ' + TECHNOLOGIES.SI_RNA,
       Nucleotides: siRnaGcrsToNucleotides(sequence),

package/{test-SequenceTranslator-7770371320b2-1d307ddc.html → test-SequenceTranslator-916a90d7d48b-7afd2a61.html}

@@ -1,4 +1,4 @@
-<html><head><meta charset="utf-8"/><title>SequenceTranslator Test Report. Datagrok version datagrok/datagrok:latest SHA=7770371320b2. Commit 1d307ddc.</title><style type="text/css">html,
+<html><head><meta charset="utf-8"/><title>SequenceTranslator Test Report. Datagrok version datagrok/datagrok:latest SHA=916a90d7d48b. Commit 7afd2a61.</title><style type="text/css">html,
 body {
   font-family: Arial, Helvetica, sans-serif;
   font-size: 1rem;
@@ -229,7 +229,7 @@ header {
   font-size: 1rem;
   padding: 0 0.5rem;
 }
-</style></head><body><div id="jesthtml-content"><header><h1 id="title">SequenceTranslator Test Report. Datagrok version datagrok/datagrok:latest SHA=7770371320b2. Commit 1d307ddc.</h1></header><div id="metadata-container"><div id="timestamp">Started: 2022-09-29 08:43:13</div><div id="summary"><div id="suite-summary"><div class="summary-total">Suites (1)</div><div class="summary-passed">1 passed</div><div class="summary-failed summary-empty">0 failed</div><div class="summary-pending summary-empty">0 pending</div></div><div id="test-summary"><div class="summary-total">Tests (1)</div><div class="summary-passed">1 passed</div><div class="summary-failed summary-empty">0 failed</div><div class="summary-pending summary-empty">0 pending</div></div></div></div><div id="suite-1" class="suite-container"><div class="suite-info"><div class="suite-path">/home/runner/work/public/public/packages/SequenceTranslator/src/__jest__/remote.test.ts</div><div class="suite-time warn">17.787s</div></div><div class="suite-tests"><div class="test-result passed"><div class="test-info"><div class="test-suitename"> </div><div class="test-title">TEST</div><div class="test-status">passed</div><div class="test-duration">2.717s</div></div></div></div><div class="suite-consolelog"><div class="suite-consolelog-header">Console Log</div><div class="suite-consolelog-item"><pre class="suite-consolelog-item-origin">    at Object.&lt;anonymous&gt; (/home/runner/work/public/public/packages/SequenceTranslator/src/__jest__/test-node.ts:62:11)
+</style></head><body><div id="jesthtml-content"><header><h1 id="title">SequenceTranslator Test Report. Datagrok version datagrok/datagrok:latest SHA=916a90d7d48b. Commit 7afd2a61.</h1></header><div id="metadata-container"><div id="timestamp">Started: 2022-10-19 12:32:26</div><div id="summary"><div id="suite-summary"><div class="summary-total">Suites (1)</div><div class="summary-passed">1 passed</div><div class="summary-failed summary-empty">0 failed</div><div class="summary-pending summary-empty">0 pending</div></div><div id="test-summary"><div class="summary-total">Tests (1)</div><div class="summary-passed">1 passed</div><div class="summary-failed summary-empty">0 failed</div><div class="summary-pending summary-empty">0 pending</div></div></div></div><div id="suite-1" class="suite-container"><div class="suite-info"><div class="suite-path">/home/runner/work/public/public/packages/SequenceTranslator/src/__jest__/remote.test.ts</div><div class="suite-time warn">17.557s</div></div><div class="suite-tests"><div class="test-result passed"><div class="test-info"><div class="test-suitename"> </div><div class="test-title">TEST</div><div class="test-status">passed</div><div class="test-duration">2.994s</div></div></div></div><div class="suite-consolelog"><div class="suite-consolelog-header">Console Log</div><div class="suite-consolelog-item"><pre class="suite-consolelog-item-origin">    at Object.&lt;anonymous&gt; (/home/runner/work/public/public/packages/SequenceTranslator/src/__jest__/test-node.ts:62:11)
     at Generator.next (&lt;anonymous&gt;)
     at fulfilled (/home/runner/work/public/public/packages/SequenceTranslator/src/__jest__/test-node.ts:28:58)
     at processTicksAndRejections (internal/process/task_queues.js:97:5)</pre><pre class="suite-consolelog-item-message">Using web root: http://localhost:8080</pre></div><div class="suite-consolelog-item"><pre class="suite-consolelog-item-origin">    at /home/runner/work/public/public/packages/SequenceTranslator/src/__jest__/remote.test.ts:40:11
@@ -242,15 +242,15 @@ header {
     at new Promise (&lt;anonymous&gt;)</pre><pre class="suite-consolelog-item-message">Testing SequenceTranslator package</pre></div><div class="suite-consolelog-item"><pre class="suite-consolelog-item-origin">    at /home/runner/work/public/public/packages/SequenceTranslator/src/__jest__/remote.test.ts:66:11
     at Generator.next (&lt;anonymous&gt;)
     at fulfilled (/home/runner/work/public/public/packages/SequenceTranslator/src/__jest__/remote.test.ts:28:58)
-    at processTicksAndRejections (internal/process/task_queues.js:97:5)</pre><pre class="suite-consolelog-item-message">Test result : Success : 2 : SequenceTranslator.sequence-translator.usCfCfUfGfAf : OK
-Test result : Success : 1 : SequenceTranslator.sequence-translator.usAfsusgsgsg : OK
+    at processTicksAndRejections (internal/process/task_queues.js:97:5)</pre><pre class="suite-consolelog-item-message">Test result : Success : 1 : SequenceTranslator.sequence-translator.usCfCfUfGfAf : OK
+Test result : Success : 0 : SequenceTranslator.sequence-translator.usAfsusgsgsg : OK
 Test result : Success : 0 : SequenceTranslator.sequence-translator.UfUfUfsCfsuacg : OK
 Test result : Success : 0 : SequenceTranslator.sequence-translator.susususauasu : OK
 Test result : Success : 0 : SequenceTranslator.sequence-translator.CfGfCfsGfsCf : OK
 Test result : Success : 1 : SequenceTranslator.sequence-translator.acacacsacsac : OK
 Test result : Success : 0 : SequenceTranslator.sequence-translator.cccgggusug : OK
 Test result : Success : 0 : SequenceTranslator.sequence-translator.UfAfCfGfGfCfAfUf : OK
-Test result : Success : 0 : SequenceTranslator.sequence-translator.(invabasic)cuCfuUfsc : OK
+Test result : Success : 1 : SequenceTranslator.sequence-translator.(invabasic)cuCfuUfsc : OK
 Test result : Success : 0 : SequenceTranslator.sequence-translator.(invabasic)usAfsucuCfuUfAfgcugUfgCfacususu : OK
-Test result : Success : 0 : SequenceTranslator.sequence-translator.(invabasic)asacgGfuGfCfAfacucuauuca : OK
+Test result : Success : 1 : SequenceTranslator.sequence-translator.(invabasic)asacgGfuGfCfAfacucuauuca : OK
 </pre></div></div></div></div></body></html>