@datagrok/sequence-translator 1.0.12 → 1.0.14

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

@@ -1,573 +1,30 @@
-const PHOSHATE = `
-Datagrok monomer library Nucleotides
-
-  0  0  0  0  0  0              0 V3000
-M  V30 BEGIN CTAB
-M  V30 COUNTS 5 4 0 0 0
-M  V30 BEGIN ATOM
-M  V30 1 O -1.5 0 0 0
-M  V30 2 P 0 0 0 0
-M  V30 3 O 0 1 0 0
-M  V30 4 O 0 -1 0 0
-M  V30 5 O 1.5 0 0 0
-M  V30 END ATOM
-M  V30 BEGIN BOND
-M  V30 1 1 1 2
-M  V30 2 2 2 3
-M  V30 3 1 2 4
-M  V30 4 1 2 5
-M  V30 END BOND
-M  V30 END CTAB
-M  V30 BEGIN COLLECTION
-M  V30 END COLLECTION
-M  END`;
-
-const THIOPHOSHATE = `
-Datagrok monomer library Nucleotides
-
-  0  0  0  0  0  0              0 V3000
-M  V30 BEGIN CTAB
-M  V30 COUNTS 5 4 0 0 0
-M  V30 BEGIN ATOM
-M  V30 1 O -1.5 0 0 0
-M  V30 2 P 0 0 0 0
-M  V30 3 O 0 1 0 0
-M  V30 4 S 0 -1 0 0
-M  V30 5 O 1.5 0 0 0
-M  V30 END ATOM
-M  V30 BEGIN BOND
-M  V30 1 1 1 2
-M  V30 2 2 2 3
-M  V30 3 1 2 4
-M  V30 4 1 2 5
-M  V30 END BOND
-M  V30 END CTAB
-M  V30 BEGIN COLLECTION
-M  V30 END COLLECTION
-M  END`;
-
-const INVABASIC = `
-Datagrok monomer library Nucleotides
-
-  0  0  0  0  0  0              0 V3000
-M  V30 BEGIN CTAB
-M  V30 COUNTS 8 8 0 0 0
-M  V30 BEGIN ATOM
-M  V30 1 O 1.0934 -2.1636 0 0
-M  V30 2 C 1.8365 -1.4945 0 0 CFG=2
-M  V30 3 C 2.8147 -1.7024 0 0
-M  V30 4 C 3.3147 -0.8364 0 0
-M  V30 5 O 2.6455 -0.0932 0 0
-M  V30 6 C 1.732 -0.5 0 0 CFG=1
-M  V30 7 C 0.866 0 0 0
-M  V30 8 O 0.866 1 0 0
-M  V30 END ATOM
-M  V30 BEGIN BOND
-M  V30 1 1 2 1 CFG=1
-M  V30 2 1 2 3
-M  V30 3 1 3 4
-M  V30 4 1 4 5
-M  V30 5 1 6 5
-M  V30 6 1 2 6
-M  V30 7 1 6 7 CFG=3
-M  V30 8 1 7 8
-M  V30 END BOND
-M  V30 BEGIN COLLECTION
-M  V30 MDLV30/STEABS ATOMS=(2 2 6)
-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[]) {
+export function getNucleotidesMol(codes: string[]) {
   const molBlocks: string[] = [];
 
-  for (let i = 0; i < smilesCodes.length - 1; i++) {
-    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]));
+  // for (let i = 0; i < smilesCodes.length - 1; i++) {
+  //   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]));
+  // }
+
+  for (let i = 0; i < codes.length - 1; i++) {
+    if(codes[i].includes('MODIFICATION')) {
+      if(i == 0)
+        molBlocks.push(reflect(codes[i]));
+      else
+        molBlocks.push(codes[i]);
+    }
+    else
+      molBlocks.push(rotateNucleotidesV3000(codes[i]));
   }
 
-  return linkV3000(molBlocks, false);
+  return linkV3000(molBlocks);
 }
 
-export function linkV3000(molBlocks: string[], twoChains: boolean = false, useChirality: boolean = true) {
+export function linkStrandsV3000(strands:{senseStrands: string[], antiStrands: string[]}, useChirality: boolean = true) {
   let macroMolBlock = '\nDatagrok macromolecule handler\n\n';
   macroMolBlock += '  0  0  0  0  0  0            999 V3000\n';
   macroMolBlock += 'M  V30 BEGIN CTAB\n';
@@ -579,18 +36,34 @@ export function linkV3000(molBlocks: string[], twoChains: boolean = false, useCh
   let nbond = 0;
   let xShift = 0;
 
-  if (twoChains && molBlocks.length > 1)
-    molBlocks[1] = invertNucleotidesV3000(molBlocks[1]);
+  // if (twoChains && molBlocks.length > 1)
+  //   molBlocks[1] = invertNucleotidesV3000(molBlocks[1]);
+
+  if (strands.antiStrands.length > 0) {
+    for(let i = 0; i < strands.antiStrands.length; i++) {
+      strands.antiStrands[i] = invertNucleotidesV3000(strands.antiStrands[i]);
+    }
+  }
+
+  let inverted = false;
+  let molBlocks = strands.senseStrands.concat(strands.antiStrands);
 
   for (let i = 0; i < molBlocks.length; i++) {
+
+    if (i >= strands.senseStrands.length && inverted == false) {
+      inverted = true;
+      xShift = 0;
+    }
+
+
     molBlocks[i] = molBlocks[i].replaceAll('(-\nM  V30 ', '(')
       .replaceAll('-\nM  V30 ', '').replaceAll(' )', ')');
     const numbers = extractAtomsBondsNumbersV3000(molBlocks[i]);
     const coordinates = extractAtomDataV3000(molBlocks[i]);
 
-    if (twoChains) {
-      const xShiftRight = Math.min(...coordinates.x);
-      const yShift = i == 0 ? Math.min(...coordinates.y) - 1 : Math.max(...coordinates.y) + 1;
+    if (inverted) {
+      const xShiftRight = Math.min(...coordinates.x) - xShift;
+      const yShift = !inverted ? Math.min(...coordinates.y) - 1 : Math.max(...coordinates.y) + 10;
       for (let j = 0; j < coordinates.x.length; j++)
         coordinates.x[j] -= xShiftRight;
       for (let j = 0; j < coordinates.y.length; j++)
@@ -603,11 +76,176 @@ export function linkV3000(molBlocks: string[], twoChains: boolean = false, useCh
     let indexEnd = indexAtoms;
 
     for (let j = 0; j < numbers.natom; j++) {
-      if (coordinates.atomIndex[j] != 1 || i == 0 || twoChains) {
+      // if (coordinates.atomIndex[j] != 1 || i == 0 || twoChains) {
+      //rewrite atom number
+      index = molBlocks[i].indexOf('V30', index) + 4;
+      indexEnd = molBlocks[i].indexOf(' ', index);
+      const atomNumber = parseInt(molBlocks[i].substring(index, indexEnd)) + natom;
+      molBlocks[i] = molBlocks[i].slice(0, index) + atomNumber + molBlocks[i].slice(indexEnd);
+
+      //rewrite coordinates
+      index = molBlocks[i].indexOf(' ', index) + 1;
+      index = molBlocks[i].indexOf(' ', index) + 1;
+      indexEnd = molBlocks[i].indexOf(' ', index);
+
+      const totalShift = true ? 0 : xShift - coordinates.x[0];
+      let coordinate = true ?
+        Math.round(10000*coordinates.x[j])/10000 :
+        Math.round(10000*(parseFloat(molBlocks[i].substring(index, indexEnd)) + totalShift))/10000;
+      molBlocks[i] = molBlocks[i].slice(0, index) + coordinate + molBlocks[i].slice(indexEnd);
+
+      index = molBlocks[i].indexOf(' ', index) + 1;
+      indexEnd = molBlocks[i].indexOf(' ', index);
+      coordinate = true ?
+        Math.round(10000*coordinates.y[j])/10000 :
+        Math.round(10000*(parseFloat(molBlocks[i].substring(index, indexEnd))))/10000;
+      molBlocks[i] = molBlocks[i].slice(0, index) + coordinate + molBlocks[i].slice(indexEnd);
+
+      index = molBlocks[i].indexOf('\n', index) + 1;
+    }
+
+    const indexAtomsEnd = molBlocks[i].indexOf('M  V30 END ATOM');
+    atomBlock += molBlocks[i].substring(indexAtoms + 1, indexAtomsEnd);
+
+    let indexBonds = molBlocks[i].indexOf('M  V30 BEGIN BOND'); // V3000 index for bonds
+    indexBonds = molBlocks[i].indexOf('\n', indexBonds);
+    index = indexBonds;
+    indexEnd = indexBonds;
+
+    for (let j = 0; j < numbers.nbond; j++) {
+      //rewrite bond number
+      index = molBlocks[i].indexOf('V30', index) + 4;
+      indexEnd = molBlocks[i].indexOf(' ', index);
+      const bondNumber = parseInt(molBlocks[i].substring(index, indexEnd)) + nbond;
+      molBlocks[i] = molBlocks[i].slice(0, index) + bondNumber + molBlocks[i].slice(indexEnd);
+
+      //rewrite atom pair in bond
+      index = molBlocks[i].indexOf(' ', index) + 1;
+      index = molBlocks[i].indexOf(' ', index) + 1;
+      indexEnd = molBlocks[i].indexOf(' ', index);
+      let atomNumber = parseInt(molBlocks[i].substring(index, indexEnd)) + natom;
+      molBlocks[i] = molBlocks[i].slice(0, index) + atomNumber + molBlocks[i].slice(indexEnd);
+      index = molBlocks[i].indexOf(' ', index) + 1;
+      indexEnd = Math.min(molBlocks[i].indexOf('\n', index), molBlocks[i].indexOf(' ', index));
+      atomNumber = parseInt(molBlocks[i].substring(index, indexEnd)) + natom;
+      molBlocks[i] = molBlocks[i].slice(0, index) + atomNumber + molBlocks[i].slice(indexEnd);
+
+      index = molBlocks[i].indexOf('\n', index) + 1;
+    }
+
+    const indexBondEnd = molBlocks[i].indexOf('M  V30 END BOND');
+    bondBlock += molBlocks[i].substring(indexBonds + 1, indexBondEnd);
+
+    let indexCollection = molBlocks[i].indexOf('M  V30 MDLV30/STEABS ATOMS=('); // V3000 index for collections
+
+    while (indexCollection != -1) {
+      indexCollection += 28;
+      const collectionEnd = molBlocks[i].indexOf(')', indexCollection);
+      const collectionEntries = molBlocks[i].substring(indexCollection, collectionEnd).split(' ').slice(1);
+      collectionEntries.forEach((e) => {
+        collection.push(parseInt(e) + natom);
+      });
+      indexCollection = collectionEnd;
+      indexCollection = molBlocks[i].indexOf('M  V30 MDLV30/STEABS ATOMS=(', indexCollection);
+    }
+
+    natom += true ? numbers.natom : numbers.natom - 1;
+    nbond += numbers.nbond;
+    xShift += Math.max(...coordinates.x) + 1;//twoChains ? 0 : coordinates.x[numbers.natom - 1] - coordinates.x[0];
+  }
+
+  const entries = 4;
+  const collNumber = Math.ceil(collection.length / entries);
+
+  //if (oclRender) {
+    // collectionBlock += 'M  V30 MDLV30/STEABS ATOMS=(' + collection.length;
+
+    // for (let j = 0; j < collection.length; j++)
+    //   collectionBlock += ' ' + collection[j];
+
+    // collectionBlock += ')\n';
+  //} else {
+    collectionBlock += 'M  V30 MDLV30/STEABS ATOMS=(' + collection.length + ' -\n';
+    for (let i = 0; i < collNumber; i++) {
+      collectionBlock += 'M  V30 ';
+      const entriesCurrent = i + 1 == collNumber ? collection.length - (collNumber - 1)*entries : entries;
+      for (let j = 0; j < entriesCurrent; j++) {
+        collectionBlock += (j + 1 == entriesCurrent) ?
+          (i == collNumber - 1 ? collection[entries*i + j] + ')\n' : collection[entries*i + j] + ' -\n') :
+          collection[entries*i + j] + ' ';
+      }
+    }
+  //}
+
+  //generate file
+  true? natom : natom++;
+  macroMolBlock += 'M  V30 COUNTS ' + natom + ' ' + nbond + ' 0 0 0\n';
+  macroMolBlock += 'M  V30 BEGIN ATOM\n';
+  macroMolBlock += atomBlock;
+  macroMolBlock += 'M  V30 END ATOM\n';
+  macroMolBlock += 'M  V30 BEGIN BOND\n';
+  macroMolBlock += bondBlock;
+  macroMolBlock += 'M  V30 END BOND\n';
+  if(useChirality){
+    macroMolBlock += 'M  V30 BEGIN COLLECTION\n';
+    macroMolBlock += collectionBlock;
+    macroMolBlock += 'M  V30 END COLLECTION\n';
+  } else
+    macroMolBlock = macroMolBlock.replace(/ CFG=\d/g, ' ');
+
+  macroMolBlock += 'M  V30 END CTAB\n';
+  macroMolBlock += 'M  END';
+
+  return macroMolBlock;
+}
+
+export function linkV3000(molBlocks: string[], useChirality: boolean = true) {
+  let macroMolBlock = '\nDatagrok macromolecule handler\n\n';
+  macroMolBlock += '  0  0  0  0  0  0            999 V3000\n';
+  macroMolBlock += 'M  V30 BEGIN CTAB\n';
+  let atomBlock = '';
+  let bondBlock = '';
+  let collectionBlock = '';
+  const collection: number [] = [];
+  let natom = 0;
+  let nbond = 0;
+  let xShift = 0;
+
+  for (let i = 0; i < molBlocks.length; i++) {
+    const isBoundary = molBlocks[i].includes('MODIFICATION') && i == 0;
+    let specLength = 0;
+    if (isBoundary) {
+      const coordinates = extractAtomDataV3000(molBlocks[i]);
+      specLength = coordinates.atomIndex.length;
+    }
+      
+
+    molBlocks[i] = molBlocks[i].replaceAll('(-\nM  V30 ', '(')
+      .replaceAll('-\nM  V30 ', '').replaceAll(' )', ')');
+    const numbers = extractAtomsBondsNumbersV3000(molBlocks[i]);
+    const coordinates = extractAtomDataV3000(molBlocks[i]);
+
+    let indexAtoms = molBlocks[i].indexOf('M  V30 BEGIN ATOM'); // V3000 index for atoms coordinates
+    indexAtoms = molBlocks[i].indexOf('\n', indexAtoms);
+    let index = indexAtoms;
+    let indexEnd = indexAtoms;
+
+    for (let j = 0; j < numbers.natom; j++) {
+      if (coordinates.atomIndex[j] != 1 || i == 0) {
         //rewrite atom number
         index = molBlocks[i].indexOf('V30', index) + 4;
         indexEnd = molBlocks[i].indexOf(' ', index);
-        const atomNumber = parseInt(molBlocks[i].substring(index, indexEnd)) + natom;
+        let atomNumber = 0;
+        if(isBoundary) {
+          atomNumber = parseInt(molBlocks[i].substring(index, indexEnd))
+          if(atomNumber == 1)
+            atomNumber = specLength;
+          else if(atomNumber == specLength)
+            atomNumber = 1;
+          atomNumber += natom;
+        } else {
+          atomNumber = parseInt(molBlocks[i].substring(index, indexEnd)) + natom;
+        }
         molBlocks[i] = molBlocks[i].slice(0, index) + atomNumber + molBlocks[i].slice(indexEnd);
 
         //rewrite coordinates
@@ -615,16 +253,14 @@ export function linkV3000(molBlocks: string[], twoChains: boolean = false, useCh
         index = molBlocks[i].indexOf(' ', index) + 1;
         indexEnd = molBlocks[i].indexOf(' ', index);
 
-        const totalShift = twoChains ? 0 : xShift - coordinates.x[0];
-        let coordinate = twoChains ?
-          Math.round(10000*coordinates.x[j])/10000 :
+        const totalShift = xShift - coordinates.x[0];
+        let coordinate = 
           Math.round(10000*(parseFloat(molBlocks[i].substring(index, indexEnd)) + totalShift))/10000;
         molBlocks[i] = molBlocks[i].slice(0, index) + coordinate + molBlocks[i].slice(indexEnd);
 
         index = molBlocks[i].indexOf(' ', index) + 1;
         indexEnd = molBlocks[i].indexOf(' ', index);
-        coordinate = twoChains ?
-          Math.round(10000*coordinates.y[j])/10000 :
+        coordinate = 
           Math.round(10000*(parseFloat(molBlocks[i].substring(index, indexEnd))))/10000;
         molBlocks[i] = molBlocks[i].slice(0, index) + coordinate + molBlocks[i].slice(indexEnd);
 
@@ -655,11 +291,32 @@ export function linkV3000(molBlocks: string[], twoChains: boolean = false, useCh
       index = molBlocks[i].indexOf(' ', index) + 1;
       index = molBlocks[i].indexOf(' ', index) + 1;
       indexEnd = molBlocks[i].indexOf(' ', index);
-      let atomNumber = parseInt(molBlocks[i].substring(index, indexEnd)) + natom;
+      let atomNumber = 0;
+      if(isBoundary) {
+        atomNumber = parseInt(molBlocks[i].substring(index, indexEnd))
+        if(atomNumber == 1)
+          atomNumber = specLength;
+        else if(atomNumber == specLength)
+          atomNumber = 1;
+        atomNumber += natom;
+      } else {
+        atomNumber = parseInt(molBlocks[i].substring(index, indexEnd)) + natom;
+      }
+
       molBlocks[i] = molBlocks[i].slice(0, index) + atomNumber + molBlocks[i].slice(indexEnd);
       index = molBlocks[i].indexOf(' ', index) + 1;
       indexEnd = Math.min(molBlocks[i].indexOf('\n', index), molBlocks[i].indexOf(' ', index));
-      atomNumber = parseInt(molBlocks[i].substring(index, indexEnd)) + natom;
+      atomNumber = 0;
+      if(isBoundary) {
+        atomNumber = parseInt(molBlocks[i].substring(index, indexEnd))
+        if(atomNumber == 1)
+          atomNumber = specLength;
+        else if(atomNumber == specLength)
+          atomNumber = 1;
+        atomNumber += natom;
+      } else {
+        atomNumber = parseInt(molBlocks[i].substring(index, indexEnd)) + natom;
+      }
       molBlocks[i] = molBlocks[i].slice(0, index) + atomNumber + molBlocks[i].slice(indexEnd);
 
       index = molBlocks[i].indexOf('\n', index) + 1;
@@ -681,9 +338,12 @@ export function linkV3000(molBlocks: string[], twoChains: boolean = false, useCh
       indexCollection = molBlocks[i].indexOf('M  V30 MDLV30/STEABS ATOMS=(', indexCollection);
     }
 
-    natom += twoChains ? numbers.natom : numbers.natom - 1;
+    natom += numbers.natom - 1;
     nbond += numbers.nbond;
-    xShift += twoChains ? 0 : coordinates.x[numbers.natom - 1] - coordinates.x[0];
+    if(isBoundary)
+      xShift += Math.max(...coordinates.x);
+    else
+      xShift += coordinates.x[numbers.natom - 1] - coordinates.x[0];
   }
 
   const entries = 4;
@@ -710,7 +370,7 @@ export function linkV3000(molBlocks: string[], twoChains: boolean = false, useCh
   //}
 
   //generate file
-  twoChains? natom : natom++;
+  natom++;
   macroMolBlock += 'M  V30 COUNTS ' + natom + ' ' + nbond + ' 0 0 0\n';
   macroMolBlock += 'M  V30 BEGIN ATOM\n';
   macroMolBlock += atomBlock;
@@ -760,7 +420,11 @@ function rotateNucleotidesV3000(molecule: string) {
     angle = coordinates.x[indexFivePrime] > coordinates.x[indexThreePrime] ? Math.PI : 0;
   else {
     const derivative = coordinates.y[indexFivePrime]/coordinates.x[indexFivePrime];
-    angle = derivative > 0 ? Math.PI - Math.atan(derivative) : Math.atan(derivative);
+    angle = derivative > 0 ? Math.PI - Math.atan(derivative) : 
+            (coordinates.x[indexFivePrime] < 0 ? 
+              Math.atan(derivative) : 
+              - Math.PI - Math.atan(derivative)
+            );
   }
 
   const cos = Math.cos(angle);
@@ -798,6 +462,55 @@ function rotateNucleotidesV3000(molecule: string) {
   return molBlock;
 }
 
+function reflect(molecule: string) {
+  // @ts-ignore
+  let molBlock = molecule.includes('M  END') ? molecule : OCL.Molecule.fromSmiles(molecule).toMolfileV3();
+  const coordinates = extractAtomDataV3000(molBlock);
+  const natom = coordinates.atomIndex.length;
+
+  const indexFivePrime = coordinates.atomIndex.indexOf(1);
+  const indexThreePrime = coordinates.atomIndex.indexOf(natom);
+
+  const xCenter = (coordinates.x[indexThreePrime] + coordinates.x[indexFivePrime])/2;
+  const yCenter = (coordinates.y[indexThreePrime] + coordinates.y[indexFivePrime])/2;
+
+  //place to center
+  for (let i = 0; i < natom; i++) {
+    coordinates.x[i] -= xCenter;
+    coordinates.y[i] -= yCenter;
+  }
+
+  //place to center
+  for (let i = 0; i < natom; i++)
+    coordinates.x[i] = -coordinates.x[i];
+
+  //place to right
+  const xShift = coordinates.x[indexFivePrime];
+  for (let i = 0; i < natom; i++)
+    coordinates.x[i] -= xShift;
+
+  //rewrite molBlock
+  let index = molBlock.indexOf('M  V30 BEGIN ATOM'); // V3000 index for atoms coordinates
+  index = molBlock.indexOf('\n', index);
+  let indexEnd = index;
+  for (let i = 0; i < natom; i++) {
+    index = molBlock.indexOf('V30', index) + 4;
+    index = molBlock.indexOf(' ', index) + 1;
+    index = molBlock.indexOf(' ', index) + 1;
+    indexEnd = molBlock.indexOf(' ', index) + 1;
+    indexEnd = molBlock.indexOf(' ', indexEnd);
+
+    molBlock = molBlock.slice(0, index) +
+      coordinates.x[i] + ' ' + coordinates.y[i] +
+      molBlock.slice(indexEnd);
+
+    index = molBlock.indexOf('\n', index) + 1;
+  }
+
+  return molBlock;
+}
+
+
 function invertNucleotidesV3000(molecule: string) {
   // @ts-ignore
   let molBlock = molecule.includes('M  END') ? molecule : OCL.Molecule.fromSmiles(molecule).toMolfileV3();