@datagrok/bio 2.22.10 → 2.22.11
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.
- package/dist/package-test.js +1 -1
- package/dist/package-test.js.map +1 -1
- package/dist/package.js.map +1 -1
- package/files/monomer-libraries/polytool-lib.json +227 -1
- package/package.json +2 -2
- package/src/package.g.ts +1 -1
- package/src/utils/monomer-lib/consts.ts +1 -1
- package/test-console-output-1.log +407 -406
- package/test-record-1.mp4 +0 -0
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@@ -96,5 +96,231 @@
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"id": "0",
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"polymerType": "PEPTIDE",
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"symbol": "azG"
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},
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{
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"symbol": "DRR1",
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"name": "Ethilenil Glycine",
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"molfile": "\n RDKit 2D\n\n 8 7 0 0 0 0 0 0 0 0999 V2000\n 2.5981 0.5625 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 1.2990 1.3125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -0.0000 0.5625 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -1.2990 1.3125 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n -2.5981 0.5625 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0\n 0.0000 -0.9375 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -1.2990 -1.6875 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 1.2990 -1.6875 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0\n 1 2 2 0\n 2 3 1 0\n 3 4 1 0\n 4 5 1 0\n 3 6 1 0\n 6 7 2 0\n 6 8 1 0\nM RGP 2 5 1 8 2\nM END\n",
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"smiles": "C=CC(N[*:1])C(=O)[*:2]",
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"polymerType": "PEPTIDE",
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"monomerType": "Backbone",
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"naturalAnalog": "A",
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"id": 0,
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"rgroups": [
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{
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"alternateId": "R1-H",
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"capGroupName": "H",
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"capGroupSMILES": "[*:1][H]",
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"label": "R1"
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},
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{
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"alternateId": "R2-OH",
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"capGroupName": "OH",
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"capGroupSMILES": "O[*:2]",
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"label": "R2"
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}
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],
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"author": "Admin",
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"createDate": "2025-09-02T19:03:15.744Z",
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"meta": {}
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},
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{
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"symbol": "DRR2",
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"name": "Alino Glycine",
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"molfile": "\n RDKit 2D\n\n 11 10 0 0 0 0 0 0 0 0999 V2000\n 5.0781 1.0227 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 3.7790 0.2727 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 2.4800 1.0227 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 1.1809 0.2727 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -0.1181 1.0227 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -1.4171 0.2727 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -2.7162 1.0227 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n -4.0152 0.2727 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0\n -1.4171 -1.2273 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -2.7162 -1.9773 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n -0.1181 -1.9773 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0\n 1 2 2 0\n 2 3 1 0\n 3 4 2 3\n 4 5 1 0\n 5 6 1 0\n 6 7 1 0\n 7 8 1 0\n 6 9 1 0\n 9 10 2 0\n 9 11 1 0\nM RGP 2 8 1 11 2\nM END\n",
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"smiles": "C=CC=CCC(N[*:1])C(=O)[*:2]",
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"polymerType": "PEPTIDE",
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"monomerType": "Backbone",
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"naturalAnalog": "S",
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"id": 0,
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"rgroups": [
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{
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"alternateId": "R1-H",
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"capGroupName": "H",
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"capGroupSMILES": "[*:1][H]",
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"label": "R1"
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{
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"alternateId": "R2-OH",
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"capGroupName": "OH",
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"capGroupSMILES": "O[*:2]",
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"label": "R2"
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}
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],
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"author": "Admin",
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"createDate": "2025-09-02T19:06:18.398Z",
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"meta": {}
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},
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{
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"symbol": "ODAR1",
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"name": "Oxiethilenil Glycine",
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"molfile": "\n RDKit 2D\n\n 11 10 0 0 0 0 0 0 0 0999 V2000\n 4.1333 0.4773 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 2.8343 1.2273 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 1.5352 0.4773 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 1.5352 -1.0227 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 0.2362 1.2273 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -1.0628 0.4773 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -2.3619 1.2273 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n -3.6609 0.4773 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0\n -1.0628 -1.0227 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -2.3619 -1.7727 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 0.2362 -1.7727 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0\n 1 2 2 0\n 2 3 1 0\n 3 4 2 0\n 3 5 1 0\n 5 6 1 0\n 6 7 1 0\n 7 8 1 0\n 6 9 1 0\n 9 10 2 0\n 9 11 1 0\nM RGP 2 8 1 11 2\nM END\n",
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"smiles": "C=CC(=O)CC(N[*:1])C(=O)[*:2]",
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"polymerType": "PEPTIDE",
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"monomerType": "Backbone",
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"naturalAnalog": "D",
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"id": 0,
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"rgroups": [
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{
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"alternateId": "R1-H",
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"capGroupName": "H",
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"capGroupSMILES": "[*:1][H]",
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"label": "R1"
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{
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"alternateId": "R2-OH",
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"capGroupName": "OH",
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"capGroupSMILES": "O[*:2]",
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"label": "R2"
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}
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],
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"author": "Admin",
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"createDate": "2025-09-02T22:46:35.012Z",
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"meta": {}
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},
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{
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"symbol": "ODAR2",
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"name": "Ethilenil Glycine",
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"molfile": "\n RDKit 2D\n\n 8 7 0 0 0 0 0 0 0 0999 V2000\n 2.5981 0.5625 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 1.2990 1.3125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -0.0000 0.5625 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -1.2990 1.3125 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n -2.5981 0.5625 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0\n 0.0000 -0.9375 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -1.2990 -1.6875 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 1.2990 -1.6875 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0\n 1 2 2 0\n 2 3 1 0\n 3 4 1 0\n 4 5 1 0\n 3 6 1 0\n 6 7 2 0\n 6 8 1 0\nM RGP 2 5 1 8 2\nM END\n",
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"smiles": "C=CC(N[*:1])C(=O)[*:2]",
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"polymerType": "PEPTIDE",
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"monomerType": "Backbone",
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"naturalAnalog": "A",
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"id": 0,
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"rgroups": [
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{
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"alternateId": "R1-H",
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"capGroupName": "H",
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"capGroupSMILES": "[*:1][H]",
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"label": "R1"
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},
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{
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"alternateId": "R2-OH",
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"capGroupName": "OH",
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"capGroupSMILES": "O[*:2]",
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"label": "R2"
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}
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],
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"author": "Admin",
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"createDate": "2025-09-02T22:47:19.803Z",
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"meta": {}
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},
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{
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"symbol": "PHAR1",
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"name": "Propylenil Glycine",
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"molfile": "\n RDKit 2D\n\n 9 8 0 0 0 0 0 0 0 0999 V2000\n 3.4641 1.1667 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 2.1651 0.4167 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 0.8660 1.1667 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -0.4330 0.4167 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -1.7321 1.1667 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n -3.0311 0.4167 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0\n -0.4330 -1.0833 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -1.7321 -1.8333 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 0.8660 -1.8333 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0\n 1 2 2 0\n 2 3 1 0\n 3 4 1 0\n 4 5 1 0\n 5 6 1 0\n 4 7 1 0\n 7 8 2 0\n 7 9 1 0\nM RGP 2 6 1 9 2\nM END\n",
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"smiles": "C=CCC(N[*:1])C(=O)[*:2]",
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"polymerType": "PEPTIDE",
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"monomerType": "Backbone",
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"naturalAnalog": "S",
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"id": 0,
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"rgroups": [
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{
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"alternateId": "R1-H",
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"capGroupName": "H",
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"capGroupSMILES": "[*:1][H]",
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"label": "R1"
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},
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{
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"alternateId": "R2-OH",
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"capGroupName": "OH",
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"capGroupSMILES": "O[*:2]",
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"label": "R2"
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}
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],
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"author": "Admin",
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"createDate": "2025-09-02T22:49:15.303Z",
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"meta": {}
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},
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{
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"symbol": "PHAR2",
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"name": "PHAR2",
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"molfile": "\n RDKit 2D\n\n 11 10 0 0 0 0 0 0 0 0999 V2000\n 2.1257 -2.4545 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 0.8267 -1.7045 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 0.8267 -0.2045 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 2.1257 0.5455 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 3.4247 -0.2045 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0\n -0.4724 0.5455 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -0.4724 2.0455 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n -1.7714 2.7955 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0\n -1.7714 -0.2045 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -3.0705 0.5455 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n -1.7714 -1.7045 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0\n 1 2 2 0\n 2 3 1 0\n 3 4 1 0\n 4 5 1 0\n 3 6 1 0\n 6 7 1 0\n 7 8 1 0\n 6 9 1 0\n 9 10 2 0\n 9 11 1 0\nM RGP 2 8 1 11 2\nM END\n",
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"smiles": "C=CC(CS)C(N[*:1])C(=O)[*:2]",
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"polymerType": "PEPTIDE",
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"monomerType": "Backbone",
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"naturalAnalog": "C",
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"id": 0,
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"rgroups": [
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{
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"alternateId": "R1-H",
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"capGroupName": "H",
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"capGroupSMILES": "[*:1][H]",
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"label": "R1"
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},
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{
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"alternateId": "R2-OH",
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"capGroupName": "OH",
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"capGroupSMILES": "O[*:2]",
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"label": "R2"
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}
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],
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"author": "Admin",
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"createDate": "2025-09-02T22:50:11.922Z",
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"meta": {}
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},
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{
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"symbol": "THA",
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"name": "Trihexilamine",
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"molfile": "\n RDKit 2D\n\n 22 21 0 0 0 0 0 0 0 0999 V2000\n -4.6057 -1.9773 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -5.9047 -1.2273 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -7.2038 -1.9773 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -8.5028 -1.2273 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -9.8018 -1.9773 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0\n -3.3066 -1.2273 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -2.0076 -1.9773 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -0.7086 -1.2273 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n 0.5905 -1.9773 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 1.8895 -1.2273 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 3.1885 -1.9773 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 4.4876 -1.2273 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 5.7866 -1.9773 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 7.0857 -1.2273 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 8.3847 -1.9773 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0\n -0.7086 0.2727 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 0.5905 1.0227 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 0.5905 2.5227 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 1.8895 3.2727 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 1.8895 4.7727 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 3.1885 5.5227 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 3.1885 7.0227 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0\n 1 2 1 0\n 2 3 1 0\n 3 4 1 0\n 4 5 1 0\n 1 6 1 0\n 6 7 1 0\n 7 8 1 0\n 8 9 1 0\n 9 10 1 0\n 10 11 1 0\n 11 12 1 0\n 12 13 1 0\n 13 14 1 0\n 14 15 1 0\n 8 16 1 0\n 16 17 1 0\n 17 18 1 0\n 18 19 1 0\n 19 20 1 0\n 20 21 1 0\n 21 22 1 0\nM RGP 3 5 1 15 2 22 3\nM END\n",
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"smiles": "C(CCC[*:1])CCN(CCCCCC[*:2])CCCCCC[*:3]",
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"polymerType": "PEPTIDE",
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"monomerType": "Backbone",
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"id": 0,
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"rgroups": [
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"capGroupSMILES": "[*:1][H]",
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"alternateId": "R1-H",
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"capGroupName": "H",
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"label": "R1"
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},
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{
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"capGroupSMILES": "[*:2][H]",
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"alternateId": "R2-H",
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"capGroupName": "H",
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"label": "R2"
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},
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{
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"capGroupSMILES": "[*:3][H]",
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"alternateId": "R3-H",
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"capGroupName": "H",
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"label": "R3"
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}
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],
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"author": "Admin",
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"createDate": "2025-09-02T23:15:21.760Z",
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"meta": {}
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},
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{
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"symbol": "MG3",
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"name": "MG3",
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"molfile": "\n RDKit 2D\n\n 22 21 0 0 0 0 0 0 0 0999 V2000\n 4.4876 -1.2273 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 3.1885 -1.9773 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 1.8895 -1.2273 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 0.5905 -1.9773 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n -0.7086 -1.2273 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -2.0076 -1.9773 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n -3.3066 -1.2273 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -4.6057 -1.9773 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n -5.9047 -1.2273 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -7.2038 -1.9773 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n -8.5028 -1.2273 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -9.8018 -1.9773 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0\n -0.7086 0.2727 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 0.5905 1.0227 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 0.5905 2.5227 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 1.8895 3.2727 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 1.8895 4.7727 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 3.1885 5.5227 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 3.1885 7.0227 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0\n 5.7866 -1.9773 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 7.0857 -1.2273 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 8.3847 -1.9773 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0\n 1 2 1 0\n 2 3 1 0\n 3 4 1 0\n 4 5 1 0\n 5 6 1 0\n 6 7 1 0\n 7 8 1 0\n 8 9 1 0\n 9 10 1 0\n 10 11 1 0\n 11 12 1 0\n 5 13 1 0\n 13 14 1 0\n 14 15 1 0\n 15 16 1 0\n 16 17 1 0\n 17 18 1 0\n 18 19 1 0\n 1 20 1 0\n 20 21 1 0\n 21 22 1 0\nM RGP 3 12 2 19 3 22 1\nM END\n",
|
|
298
|
+
"smiles": "C(OCOC(OCOCOC[*:2])OCOCOC[*:3])OC[*:1]",
|
|
299
|
+
"polymerType": "PEPTIDE",
|
|
300
|
+
"monomerType": "Backbone",
|
|
301
|
+
"id": 0,
|
|
302
|
+
"rgroups": [
|
|
303
|
+
{
|
|
304
|
+
"capGroupSMILES": "[*:1][H]",
|
|
305
|
+
"alternateId": "R1-H",
|
|
306
|
+
"capGroupName": "H",
|
|
307
|
+
"label": "R1"
|
|
308
|
+
},
|
|
309
|
+
{
|
|
310
|
+
"capGroupSMILES": "[*:2][H]",
|
|
311
|
+
"alternateId": "R2-H",
|
|
312
|
+
"capGroupName": "H",
|
|
313
|
+
"label": "R2"
|
|
314
|
+
},
|
|
315
|
+
{
|
|
316
|
+
"capGroupSMILES": "[*:3][H]",
|
|
317
|
+
"alternateId": "R3-H",
|
|
318
|
+
"capGroupName": "H",
|
|
319
|
+
"label": "R3"
|
|
320
|
+
}
|
|
321
|
+
],
|
|
322
|
+
"author": "Admin",
|
|
323
|
+
"createDate": "2025-09-02T23:18:56.405Z",
|
|
324
|
+
"meta": {}
|
|
99
325
|
}
|
|
100
|
-
]
|
|
326
|
+
]
|
package/package.json
CHANGED
|
@@ -5,7 +5,7 @@
|
|
|
5
5
|
"name": "Davit Rizhinashvili",
|
|
6
6
|
"email": "drizhinashvili@datagrok.ai"
|
|
7
7
|
},
|
|
8
|
-
"version": "2.22.
|
|
8
|
+
"version": "2.22.11",
|
|
9
9
|
"description": "Bioinformatics support (import/export of sequences, conversion, visualization, analysis). [See more](https://github.com/datagrok-ai/public/blob/master/packages/Bio/README.md) for details.",
|
|
10
10
|
"repository": {
|
|
11
11
|
"type": "git",
|
|
@@ -73,7 +73,7 @@
|
|
|
73
73
|
"@types/wu": "^2.1.44",
|
|
74
74
|
"@typescript-eslint/eslint-plugin": "^8.8.1",
|
|
75
75
|
"@typescript-eslint/parser": "^8.8.1",
|
|
76
|
-
"datagrok-tools": "^4.14.
|
|
76
|
+
"datagrok-tools": "^4.14.48",
|
|
77
77
|
"eslint": "^8.57.1",
|
|
78
78
|
"eslint-config-google": "^0.14.0",
|
|
79
79
|
"eslint-plugin-rxjs": "^5.0.3",
|
package/src/package.g.ts
CHANGED
|
@@ -561,7 +561,7 @@ export async function sdfToJsonLib(table: DG.DataFrame) : Promise<void> {
|
|
|
561
561
|
//description: Converts a `Macromolecule` sequence to its atomic level `Molecule` representation
|
|
562
562
|
//input: string seq { semType: Macromolecule }
|
|
563
563
|
//input: bool nonlinear
|
|
564
|
-
//output: string molfile {
|
|
564
|
+
//output: string molfile { semType: Molecule }
|
|
565
565
|
//friendlyName: seq2atomic
|
|
566
566
|
export async function seq2atomic(seq: string, nonlinear: boolean) : Promise<any> {
|
|
567
567
|
return await PackageFunctions.seq2atomic(seq, nonlinear);
|
|
@@ -14,5 +14,5 @@ export const LIB_SETTINGS_FOR_TESTS: UserLibSettings =
|
|
|
14
14
|
{explicit: ['HELMCoreLibrary.json', 'polytool-lib.json'], exclude: [], duplicateMonomerPreferences: {}};
|
|
15
15
|
|
|
16
16
|
/** Summary for settings {@link LIB_SETTINGS_FOR_TESTS} */
|
|
17
|
-
export const monomerLibForTestsSummary: MonomerLibSummaryType = {'PEPTIDE':
|
|
17
|
+
export const monomerLibForTestsSummary: MonomerLibSummaryType = {'PEPTIDE': 334, 'RNA': 383, 'CHEM': 0};
|
|
18
18
|
|