@datagrok-libraries/bio 5.38.2 → 5.38.3
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/cleanup +0 -0
- package/package.json +3 -3
- package/src/monomer-works/monomer-utils.d.ts +3 -0
- package/src/monomer-works/monomer-utils.d.ts.map +1 -1
- package/src/monomer-works/monomer-utils.js +52 -1
- package/src/monomer-works/monomer-utils.js.map +1 -1
- package/src/types/index.d.ts +1 -0
- package/src/types/index.d.ts.map +1 -1
- package/src/utils/const.d.ts +26 -0
- package/src/utils/const.d.ts.map +1 -1
- package/src/utils/const.js +34 -0
- package/src/utils/const.js.map +1 -1
- package/src/utils/types.d.ts +7 -0
- package/src/utils/types.d.ts.map +1 -0
- package/src/utils/types.js +2 -0
- package/src/utils/types.js.map +1 -0
package/cleanup
CHANGED
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File without changes
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package/package.json
CHANGED
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@@ -8,15 +8,15 @@
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"access": "public"
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},
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"friendlyName": "Datagrok bio library",
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-
"version": "5.38.
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"version": "5.38.3",
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"description": "",
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"dependencies": {
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"@datagrok-libraries/gridext": "^1.3.64",
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"@datagrok-libraries/utils": "^
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"@datagrok-libraries/utils": "^4.1.0",
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"@datagrok-libraries/ml": "^6.3.28",
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"@deck.gl/core": "8.8.12",
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"cash-dom": "latest",
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-
"datagrok-api": "^1.
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"datagrok-api": "^1.13.3",
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"dayjs": "latest",
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"fastest-levenshtein": "^1.0.16",
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"mjolnir.js": "^2.7.0",
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@@ -7,6 +7,9 @@ export declare function getMolfilesFromSingleSeq(cell: DG.Cell, monomersLibObjec
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export declare function createMomomersMolDict(lib: any[]): {
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[key: string]: string | any;
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};
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export declare function isValidEnumeratorLib(json: any[]): boolean;
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/** Specific to Enumerator for peptides */
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export declare function getJsonMonomerLibForEnumerator(rawLib: any[]): any;
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export declare function createJsonMonomerLibFromSdf(table: DG.DataFrame): any;
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export interface IMonomerLibHelper {
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/** Singleton monomer library */
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@@ -1 +1 @@
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-
{"version":3,"file":"monomer-utils.d.ts","sourceRoot":"","sources":["monomer-utils.ts"],"names":[],"mappings":"AACA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;
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{"version":3,"file":"monomer-utils.d.ts","sourceRoot":"","sources":["monomer-utils.ts"],"names":[],"mappings":"AACA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAQtC,OAAO,EAAC,WAAW,EAAU,MAAM,gBAAgB,CAAC;AACpD,OAAO,EAAC,YAAY,EAAe,MAAM,8BAA8B,CAAC;AAIxE,wBAAgB,cAAc,CAAC,GAAG,EAAE,EAAE,CAAC,MAAM,GAAG,EAAE,CAAC,MAAM,GAAG,IAAI,CAuB/D;AAED,wBAAgB,kBAAkB,CAAC,GAAG,EAAE,EAAE,CAAC,MAAM,EAAE,iBAAiB,EAAE,GAAG,EAAE,GAAG,GAAG,EAAE,EAAE,GAAG,IAAI,CAsB3F;AAED,wBAAgB,wBAAwB,CAAC,IAAI,EAAE,EAAE,CAAC,IAAI,EAAE,iBAAiB,EAAE,GAAG,EAAE,GAAG,GAAG,EAAE,EAAE,GAAG,IAAI,CAmBhG;AAED,wBAAgB,qBAAqB,CAAC,GAAG,EAAE,GAAG,EAAE,GAAG;IAAE,CAAC,GAAG,EAAE,MAAM,GAAG,MAAM,GAAG,GAAG,CAAA;CAAE,CAYjF;AAED,wBAAgB,oBAAoB,CAAC,IAAI,EAAE,GAAG,EAAE,GAAG,OAAO,CAQzD;AAED,0CAA0C;AAC1C,wBAAgB,8BAA8B,CAAC,MAAM,EAAE,GAAG,EAAE,GAAG,GAAG,CAkDjE;AAGD,wBAAgB,2BAA2B,CAAC,KAAK,EAAE,EAAE,CAAC,SAAS,GAAG,GAAG,CA8BpE;AAED,MAAM,WAAW,iBAAiB;IAChC,gCAAgC;IAChC,SAAS,IAAI,WAAW,CAAC;IAEzB;;OAEG;IACH,aAAa,CAAC,MAAM,CAAC,EAAE,OAAO,GAAG,OAAO,CAAC,IAAI,CAAC,CAAC;IAE/C,6DAA6D;IAC7D,WAAW,CAAC,IAAI,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,GAAG,OAAO,CAAC,WAAW,CAAC,CAAC;CACnE;AAED,wBAAsB,mBAAmB,IAAI,OAAO,CAAC,iBAAiB,CAAC,CAOtE;AAED;;;;;0EAK0E;AAC1E,wBAAsB,sBAAsB,CAAC,WAAW,EAAE,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,EAAE,iBAAiB,EAAE,YAAY,GAAG,OAAO,CAAC,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC;AAC1I,wBAAsB,sBAAsB,CAAC,eAAe,EAAE,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,EAAE,EAAE,iBAAiB,EAAE,YAAY,GAAG,OAAO,CAAC,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC"}
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@@ -1,7 +1,7 @@
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// import * as ui from 'datagrok-api/ui';
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import * as DG from 'datagrok-api/dg';
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import * as grok from 'datagrok-api/grok';
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import { HELM_CORE_FIELDS, jsonSdfMonomerLibDict, MONOMER_ENCODE_MAX, MONOMER_ENCODE_MIN, SDF_MONOMER_NAME } from '../utils/const';
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import { HELM_CORE_FIELDS, jsonSdfMonomerLibDict, MONOMER_ENCODE_MAX, MONOMER_ENCODE_MIN, SDF_MONOMER_NAME, helmFieldsToEnumeratorInputFields, rGroupsDummy, dummyMonomer } from '../utils/const';
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import { UnitsHandler } from '../utils/units-handler';
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import { splitAlignedSequences } from '../utils/splitter';
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export function encodeMonomers(col) {
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@@ -84,6 +84,57 @@ export function createMomomersMolDict(lib) {
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});
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return dict;
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}
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export function isValidEnumeratorLib(json) {
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return json.every((entry) => {
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return typeof entry === 'object' &&
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Object.values(helmFieldsToEnumeratorInputFields).every((field) => {
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return field in entry &&
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typeof entry[field] === 'string';
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});
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});
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}
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/** Specific to Enumerator for peptides */
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export function getJsonMonomerLibForEnumerator(rawLib) {
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// todo
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function validateMonomerLibWithSmiles() {
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}
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function restoreRgroupsInSmiles(rawSmiles) {
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const regex = new RegExp('\\[r\\]', 'g');
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let i = 0;
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return rawSmiles.replace(regex, (match) => { ++i; return `[${i}*]`; });
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}
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function prepareOutputSmilesColValue(smilesWithRestoredRgroups) {
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const result = smilesWithRestoredRgroups.replace('[1*]', '[H:1]');
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return result.replace('[2*]', '[OH:2]');
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}
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function prepareMolblock(rawMolblock) {
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return rawMolblock.replace('M ISO', 'M RGP');
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}
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const resultLib = [];
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validateMonomerLibWithSmiles();
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rawLib.forEach((rawMonomer) => {
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const monomer = { ...dummyMonomer };
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Object.entries(helmFieldsToEnumeratorInputFields).forEach(([key, value]) => {
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const monomerSymbol = rawMonomer[value];
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//@ts-ignore
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monomer[key] = monomerSymbol;
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});
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let key = "smiles" /* HELM_FIELDS.SMILES */;
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const rawSmiles = rawMonomer[helmFieldsToEnumeratorInputFields[key]];
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const smilesWithRestoredRgroups = restoreRgroupsInSmiles(rawSmiles);
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const smiles = prepareOutputSmilesColValue(smilesWithRestoredRgroups);
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monomer[key] = smiles;
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key = "rgroups" /* HELM_FIELDS.RGROUPS */;
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monomer[key] = rGroupsDummy;
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key = "molfile" /* HELM_FIELDS.MOLFILE */;
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const smilesWithRgroups = restoreRgroupsInSmiles(rawSmiles);
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const rawMolfile = DG.chem.convert(smilesWithRgroups, DG.chem.Notation.Smiles, DG.chem.Notation.MolBlock);
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monomer[key] = prepareMolblock(rawMolfile);
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resultLib.push(monomer);
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});
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console.log('resultLib:', resultLib);
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return resultLib;
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}
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export function createJsonMonomerLibFromSdf(table) {
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const resultLib = [];
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for (let i = 0; i < table.rowCount; i++) {
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"monomer-utils.js","sourceRoot":"","sources":["monomer-utils.ts"],"names":[],"mappings":"AAAA,yCAAyC;AACzC,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AACtC,OAAO,KAAK,IAAI,MAAM,mBAAmB,CAAC;AAE1C,OAAO,EACQ,gBAAgB,EAAsB,qBAAqB,EACxE,kBAAkB,EAAE,kBAAkB,EAAE,gBAAgB,
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+
{"version":3,"file":"monomer-utils.js","sourceRoot":"","sources":["monomer-utils.ts"],"names":[],"mappings":"AAAA,yCAAyC;AACzC,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AACtC,OAAO,KAAK,IAAI,MAAM,mBAAmB,CAAC;AAE1C,OAAO,EACQ,gBAAgB,EAAsB,qBAAqB,EACxE,kBAAkB,EAAE,kBAAkB,EAAE,gBAAgB,EACxD,iCAAiC,EAAE,YAAY,EAAE,YAAY,EAC9D,MAAM,gBAAgB,CAAC;AAGxB,OAAO,EAAC,YAAY,EAAC,MAAM,wBAAwB,CAAC;AACpD,OAAO,EAAC,qBAAqB,EAAC,MAAM,mBAAmB,CAAC;AAExD,MAAM,UAAU,cAAc,CAAC,GAAc;IAC3C,IAAI,YAAY,GAAG,kBAAkB,CAAC;IACtC,MAAM,iBAAiB,GAA8B,EAAE,CAAC;IACxD,MAAM,EAAE,GAAG,YAAY,CAAC,WAAW,CAAC,GAAG,CAAC,CAAC;IACzC,MAAM,YAAY,GAAiB,EAAE,CAAC,WAAW,EAAE,CAAC;IACpD,MAAM,kBAAkB,GAAG,EAAE,CAAC;IAC9B,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,GAAG,CAAC,MAAM,EAAE,EAAE,CAAC,EAAE;QACnC,IAAI,iBAAiB,GAAG,EAAE,CAAC;QAC3B,MAAM,QAAQ,GAAG,YAAY,CAAC,GAAG,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC;QAC1C,KAAK,MAAM,CAAC,IAAI,QAAQ,EAAE;YACxB,IAAI,CAAC,iBAAiB,CAAC,CAAC,CAAC,EAAE;gBACzB,IAAI,YAAY,GAAG,kBAAkB,EAAE;oBACrC,IAAI,CAAC,KAAK,CAAC,KAAK,CAAC,uCAAuC,CAAC,CAAC;oBAC1D,OAAO,IAAI,CAAC;iBACb;gBACD,iBAAiB,CAAC,CAAC,CAAC,GAAG,YAAY,CAAC;gBACpC,YAAY,EAAE,CAAC;aAChB;YACD,iBAAiB,IAAI,MAAM,CAAC,aAAa,CAAC,iBAAiB,CAAC,CAAC,CAAC,CAAC,CAAC;SACjE;QACD,kBAAkB,CAAC,IAAI,CAAC,iBAAiB,CAAC,CAAC;KAC5C;IACD,OAAO,EAAE,CAAC,MAAM,CAAC,WAAW,CAAC,kBAAkB,EAAE,kBAAkB,CAAC,CAAC;AACvE,CAAC;AAED,MAAM,UAAU,kBAAkB,CAAC,GAAc,EAAE,iBAAwB;IACzE,MAAM,EAAE,GAAG,YAAY,CAAC,WAAW,CAAC,GAAG,CAAC,CAAC;IACzC,MAAM,QAAQ,GAAiB,EAAE,CAAC,WAAW,EAAE,CAAC;IAChD,MAAM,YAAY,GAAG,qBAAqB,CAAC,iBAAiB,CAAC,CAAC;IAC9D,MAAM,QAAQ,GAAG,EAAE,CAAC;IACpB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,GAAG,CAAC,MAAM,EAAE,EAAE,CAAC,EAAE;QACnC,MAAM,aAAa,GAAG,GAAG,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC;QACjC,MAAM,QAAQ,GAAG,QAAQ,CAAC,aAAa,CAAC,CAAC;QACzC,MAAM,cAAc,GAAG,EAAE,CAAC;QAC1B,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,CAAC,MAAM,EAAE,EAAE,CAAC,EAAE;YACxC,IAAI,QAAQ,CAAC,CAAC,CAAC,EAAE;gBACf,IAAI,CAAC,YAAY,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,EAAE;oBAC9B,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,WAAW,QAAQ,CAAC,CAAC,CAAC,0DAA0D,CAAC,CAAC;oBACrG,OAAO,IAAI,CAAC;iBACb;gBACD,2CAA2C;gBAC3C,cAAc,CAAC,IAAI,CAAC,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,YAAY,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;aAC5E;SACF;QACD,QAAQ,CAAC,IAAI,CAAC,cAAc,CAAC,CAAC;KAC/B;IACD,OAAO,QAAQ,CAAC;AAClB,CAAC;AAED,MAAM,UAAU,wBAAwB,CAAC,IAAa,EAAE,iBAAwB;IAC9E,MAAM,EAAE,GAAG,YAAY,CAAC,WAAW,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC;IACjD,MAAM,YAAY,GAAiB,EAAE,CAAC,WAAW,EAAE,CAAC;IACpD,MAAM,YAAY,GAAG,qBAAqB,CAAC,iBAAiB,CAAC,CAAC;IAC9D,MAAM,QAAQ,GAAG,EAAE,CAAC;IACpB,MAAM,aAAa,GAAG,IAAI,CAAC,KAAK,CAAC;IACjC,MAAM,QAAQ,GAAG,YAAY,CAAC,aAAa,CAAC,CAAC;IAC7C,MAAM,cAAc,GAAG,EAAE,CAAC;IAC1B,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,CAAC,MAAM,EAAE,EAAE,CAAC,EAAE;QACxC,IAAI,QAAQ,CAAC,CAAC,CAAC,EAAE;YACf,IAAI,CAAC,YAAY,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,EAAE;gBAC9B,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,WAAW,QAAQ,CAAC,CAAC,CAAC,0DAA0D,CAAC,CAAC;gBACrG,OAAO,IAAI,CAAC;aACb;YACD,cAAc,CAAC,IAAI,CAAC,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,YAAY,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;SAC5E;KACF;IACD,QAAQ,CAAC,IAAI,CAAC,cAAc,CAAC,CAAC;IAC9B,OAAO,QAAQ,CAAC;AAClB,CAAC;AAED,MAAM,UAAU,qBAAqB,CAAC,GAAU;IAC9C,MAAM,IAAI,GAAoC,EAAE,CAAC;IACjD,GAAG,CAAC,OAAO,CAAC,CAAC,EAAE,EAAE,EAAE;QACjB,IAAI,EAAE,CAAC,aAAa,CAAC,KAAK,SAAS,EAAE;YACnC,MAAM,aAAa,GAA2B,EAAE,CAAC;YACjD,gBAAgB,CAAC,OAAO,CAAC,CAAC,KAAK,EAAE,EAAE;gBACjC,aAAa,CAAC,KAAK,CAAC,GAAG,EAAE,CAAC,KAAK,CAAC,CAAC;YACnC,CAAC,CAAC,CAAC;YACH,IAAI,CAAC,EAAE,mCAAoB,CAAC,GAAG,aAAa,CAAC;SAC9C;IACH,CAAC,CAAC,CAAC;IACH,OAAO,IAAI,CAAC;AACd,CAAC;AAED,MAAM,UAAU,oBAAoB,CAAC,IAAW;IAC9C,OAAO,IAAI,CAAC,KAAK,CAAC,CAAC,KAAK,EAAE,EAAE;QAC1B,OAAO,OAAO,KAAK,KAAK,QAAQ;YAC9B,MAAM,CAAC,MAAM,CAAC,iCAAiC,CAAC,CAAC,KAAK,CAAC,CAAC,KAAK,EAAE,EAAE;gBAC/D,OAAO,KAAK,IAAI,KAAK;oBACnB,OAAO,KAAK,CAAC,KAAK,CAAC,KAAK,QAAQ,CAAC;YACrC,CAAC,CAAC,CAAC;IACP,CAAC,CAAC,CAAC;AACL,CAAC;AAED,0CAA0C;AAC1C,MAAM,UAAU,8BAA8B,CAAC,MAAa;IAC1D,OAAO;IACP,SAAS,4BAA4B;IACrC,CAAC;IAED,SAAS,sBAAsB,CAAC,SAAiB;QAC/C,MAAM,KAAK,GAAG,IAAI,MAAM,CAAC,SAAS,EAAE,GAAG,CAAC,CAAC;QACzC,IAAI,CAAC,GAAG,CAAC,CAAC;QACV,OAAO,SAAS,CAAC,OAAO,CAAC,KAAK,EAAE,CAAC,KAAK,EAAE,EAAE,GAAG,EAAE,CAAC,CAAC,CAAC,OAAO,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC;IACzE,CAAC;IAED,SAAS,2BAA2B,CAAC,yBAAiC;QACpE,MAAM,MAAM,GAAG,yBAAyB,CAAC,OAAO,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC;QAClE,OAAO,MAAM,CAAC,OAAO,CAAC,MAAM,EAAE,QAAQ,CAAC,CAAC;IAC1C,CAAC;IAED,SAAS,eAAe,CAAC,WAAmB;QAC1C,OAAO,WAAW,CAAC,OAAO,CAAC,QAAQ,EAAE,QAAQ,CAAC,CAAC;IACjD,CAAC;IAED,MAAM,SAAS,GAAU,EAAE,CAAC;IAC5B,4BAA4B,EAAE,CAAC;IAE/B,MAAM,CAAC,OAAO,CAAC,CAAC,UAAU,EAAE,EAAE;QAC5B,MAAM,OAAO,GAAY,EAAC,GAAG,YAAY,EAAC,CAAC;QAE3C,MAAM,CAAC,OAAO,CAAC,iCAAiC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,GAAG,EAAE,KAAK,CAAC,EAAE,EAAE;YACzE,MAAM,aAAa,GAAG,UAAU,CAAC,KAAK,CAAW,CAAC;YAClD,YAAY;YACZ,OAAO,CAAC,GAAG,CAAC,GAAG,aAAa,CAAC;QAC/B,CAAC,CAAC,CAAC;QAEH,IAAI,GAAG,oCAAqB,CAAC;QAC7B,MAAM,SAAS,GAAG,UAAU,CAAC,iCAAiC,CAAC,GAAG,CAAC,CAAC,CAAC;QACrE,MAAM,yBAAyB,GAAG,sBAAsB,CAAC,SAAS,CAAC,CAAC;QACpE,MAAM,MAAM,GAAG,2BAA2B,CAAC,yBAAyB,CAAC,CAAC;QACtE,OAAO,CAAC,GAAG,CAAC,GAAG,MAAM,C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|
package/src/types/index.d.ts
CHANGED
|
@@ -28,6 +28,7 @@ export interface IMonomerLib {
|
|
|
28
28
|
getMonomerMolsByPolymerType(polymerType: string): {
|
|
29
29
|
[monomerSymbol: string]: string;
|
|
30
30
|
} | null;
|
|
31
|
+
getMonomerSymbolsByRGroup(rGroupNumber: number, polymerType: string, element?: string): string[];
|
|
31
32
|
getMonomerSymbolsByType(polymerType: string): string[];
|
|
32
33
|
getPolymerTypes(): string[];
|
|
33
34
|
update(lib: IMonomerLib): void;
|
package/src/types/index.d.ts.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["index.ts"],"names":[],"mappings":"AAIA,OAAO,EAAC,UAAU,EAAC,MAAM,MAAM,CAAC;AAChC,OAAO,EACL,oBAAoB,IAAI,GAAG,EAC3B,kBAAkB,IAAI,GAAG,EAAE,oBAAoB,IAAI,GAAG,EACvD,MAAM,gBAAgB,CAAC;AAExB,KAAK,MAAM,GAAG;IACZ,CAAC,GAAG,CAAC,gBAAgB,CAAC,EAAE,MAAM,CAAC;IAC/B,CAAC,GAAG,CAAC,YAAY,CAAC,EAAE,MAAM,CAAC;IAC3B,CAAC,GAAG,CAAC,cAAc,CAAC,EAAE,MAAM,CAAC;IAC7B,CAAC,GAAG,CAAC,KAAK,CAAC,EAAE,MAAM,CAAC;CACrB,CAAA;AACD,MAAM,MAAM,OAAO,GAAG;IACpB,CAAC,GAAG,CAAC,MAAM,CAAC,EAAE,MAAM,CAAC;IACrB,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE,MAAM,CAAC;IACnB,CAAC,GAAG,CAAC,OAAO,CAAC,EAAE,MAAM,CAAC;IACtB,CAAC,GAAG,CAAC,MAAM,CAAC,EAAE,MAAM,CAAC;IACrB,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,MAAM,CAAC;IACjB,CAAC,GAAG,CAAC,OAAO,CAAC,EAAE,MAAM,EAAE,CAAC;IACxB,CAAC,GAAG,CAAC,MAAM,CAAC,EAAE,MAAM,CAAC;IACrB,CAAC,GAAG,CAAC,YAAY,CAAC,EAAE,MAAM,CAAC;IAC3B,CAAC,GAAG,CAAC,YAAY,CAAC,EAAE,MAAM,CAAC;IAC3B,CAAC,GAAG,CAAC,WAAW,CAAC,EAAE,MAAM,GAAG,IAAI,CAAC;IACjC,CAAC,GAAG,CAAC,cAAc,CAAC,CAAC,EAAE,MAAM,CAAC;IAC9B,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC,EAAE;QAAE,CAAC,QAAQ,EAAE,MAAM,GAAG,GAAG,CAAA;KAAE,CAAA;CACzC,CAAC;AAEF,MAAM,WAAW,WAAW;IAC1B,IAAI,KAAK,IAAI,MAAM,GAAG,SAAS,CAAC;IAChC,UAAU,CAAC,WAAW,EAAE,MAAM,EAAE,aAAa,EAAE,MAAM,GAAG,OAAO,GAAG,IAAI,CAAC;IACvE,2BAA2B,CAAC,WAAW,EAAE,MAAM,GAAG;QAAE,CAAC,aAAa,EAAE,MAAM,GAAG,MAAM,CAAA;KAAE,GAAG,IAAI,CAAC;IAC7F,uBAAuB,CAAC,WAAW,EAAE,MAAM,GAAG,MAAM,EAAE,CAAC;IACvD,eAAe,IAAI,MAAM,EAAE,CAAC;IAC5B,MAAM,CAAC,GAAG,EAAE,WAAW,GAAG,IAAI,CAAC;IAC/B,IAAI,SAAS,IAAI,UAAU,CAAC,GAAG,CAAC,CAAC;CAClC"}
|
|
1
|
+
{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["index.ts"],"names":[],"mappings":"AAIA,OAAO,EAAC,UAAU,EAAC,MAAM,MAAM,CAAC;AAChC,OAAO,EACL,oBAAoB,IAAI,GAAG,EAC3B,kBAAkB,IAAI,GAAG,EAAE,oBAAoB,IAAI,GAAG,EACvD,MAAM,gBAAgB,CAAC;AAExB,KAAK,MAAM,GAAG;IACZ,CAAC,GAAG,CAAC,gBAAgB,CAAC,EAAE,MAAM,CAAC;IAC/B,CAAC,GAAG,CAAC,YAAY,CAAC,EAAE,MAAM,CAAC;IAC3B,CAAC,GAAG,CAAC,cAAc,CAAC,EAAE,MAAM,CAAC;IAC7B,CAAC,GAAG,CAAC,KAAK,CAAC,EAAE,MAAM,CAAC;CACrB,CAAA;AACD,MAAM,MAAM,OAAO,GAAG;IACpB,CAAC,GAAG,CAAC,MAAM,CAAC,EAAE,MAAM,CAAC;IACrB,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE,MAAM,CAAC;IACnB,CAAC,GAAG,CAAC,OAAO,CAAC,EAAE,MAAM,CAAC;IACtB,CAAC,GAAG,CAAC,MAAM,CAAC,EAAE,MAAM,CAAC;IACrB,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,MAAM,CAAC;IACjB,CAAC,GAAG,CAAC,OAAO,CAAC,EAAE,MAAM,EAAE,CAAC;IACxB,CAAC,GAAG,CAAC,MAAM,CAAC,EAAE,MAAM,CAAC;IACrB,CAAC,GAAG,CAAC,YAAY,CAAC,EAAE,MAAM,CAAC;IAC3B,CAAC,GAAG,CAAC,YAAY,CAAC,EAAE,MAAM,CAAC;IAC3B,CAAC,GAAG,CAAC,WAAW,CAAC,EAAE,MAAM,GAAG,IAAI,CAAC;IACjC,CAAC,GAAG,CAAC,cAAc,CAAC,CAAC,EAAE,MAAM,CAAC;IAC9B,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC,EAAE;QAAE,CAAC,QAAQ,EAAE,MAAM,GAAG,GAAG,CAAA;KAAE,CAAA;CACzC,CAAC;AAEF,MAAM,WAAW,WAAW;IAC1B,IAAI,KAAK,IAAI,MAAM,GAAG,SAAS,CAAC;IAChC,UAAU,CAAC,WAAW,EAAE,MAAM,EAAE,aAAa,EAAE,MAAM,GAAG,OAAO,GAAG,IAAI,CAAC;IACvE,2BAA2B,CAAC,WAAW,EAAE,MAAM,GAAG;QAAE,CAAC,aAAa,EAAE,MAAM,GAAG,MAAM,CAAA;KAAE,GAAG,IAAI,CAAC;IAC7F,yBAAyB,CAAC,YAAY,EAAE,MAAM,EAAE,WAAW,EAAE,MAAM,EAAE,OAAO,CAAC,EAAE,MAAM,GAAG,MAAM,EAAE,CAAC;IACjG,uBAAuB,CAAC,WAAW,EAAE,MAAM,GAAG,MAAM,EAAE,CAAC;IACvD,eAAe,IAAI,MAAM,EAAE,CAAC;IAC5B,MAAM,CAAC,GAAG,EAAE,WAAW,GAAG,IAAI,CAAC;IAC/B,IAAI,SAAS,IAAI,UAAU,CAAC,GAAG,CAAC,CAAC;CAClC"}
|
package/src/utils/const.d.ts
CHANGED
|
@@ -48,6 +48,19 @@ export declare const enum HELM_MONOMER_TYPE {
|
|
|
48
48
|
}
|
|
49
49
|
export declare const HELM_CORE_FIELDS: HELM_FIELDS[];
|
|
50
50
|
export declare const SDF_MONOMER_NAME = "MonomerName";
|
|
51
|
+
/** For Enumerator */
|
|
52
|
+
export declare const helmFieldsToEnumeratorInputFields: {
|
|
53
|
+
symbol: string;
|
|
54
|
+
name: string;
|
|
55
|
+
smiles: string;
|
|
56
|
+
};
|
|
57
|
+
/** For Enumerator */
|
|
58
|
+
export declare const rGroupsDummy: {
|
|
59
|
+
capGroupSmiles: string;
|
|
60
|
+
alternateId: string;
|
|
61
|
+
capGroupName: string;
|
|
62
|
+
label: string;
|
|
63
|
+
}[];
|
|
51
64
|
export declare const jsonSdfMonomerLibDict: {
|
|
52
65
|
monomerType: null;
|
|
53
66
|
smiles: null;
|
|
@@ -61,6 +74,19 @@ export declare const jsonSdfMonomerLibDict: {
|
|
|
61
74
|
polymerType: string;
|
|
62
75
|
symbol: string;
|
|
63
76
|
};
|
|
77
|
+
export declare const dummyMonomer: {
|
|
78
|
+
monomerType: string;
|
|
79
|
+
smiles: string;
|
|
80
|
+
name: string;
|
|
81
|
+
author: string;
|
|
82
|
+
molfile: string;
|
|
83
|
+
naturalAnalog: string;
|
|
84
|
+
rgroups: never[];
|
|
85
|
+
createDate: null;
|
|
86
|
+
id: number;
|
|
87
|
+
polymerType: string;
|
|
88
|
+
symbol: string;
|
|
89
|
+
};
|
|
64
90
|
export declare const MONOMER_ENCODE_MIN = 256;
|
|
65
91
|
export declare const MONOMER_ENCODE_MAX = 1034;
|
|
66
92
|
//# sourceMappingURL=const.d.ts.map
|
package/src/utils/const.d.ts.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"const.d.ts","sourceRoot":"","sources":["const.ts"],"names":[],"mappings":"AAIA,eAAO,MAAM,sBAAsB,+BAA+B,CAAC;AAEnE;uFACuF;AACvF,0BAAkB,oBAAoB;IACpC,MAAM,WAAW;IACjB,IAAI,SAAS;IACb,OAAO,YAAY;IACnB,MAAM,WAAW;IACjB,EAAE,OAAO;IACT,OAAO,YAAY;IACnB,MAAM,WAAW;IACjB,YAAY,gBAAgB;IAC5B,YAAY,gBAAgB;IAC5B,WAAW,eAAe;CAC3B;AAED,0BAAkB,oBAAoB;IACpC,cAAc,kBAAkB;IAChC,IAAI,SAAS;CACd;AAED,0BAAkB,WAAW;IAC3B,YAAY,gBAAgB;IAC5B,MAAM,WAAW;IACjB,IAAI,SAAS;IACb,MAAM,WAAW;IACjB,OAAO,YAAY;IACnB,cAAc,kBAAkB;IAChC,OAAO,YAAY;IACnB,WAAW,eAAe;IAC1B,EAAE,OAAO;IACT,YAAY,gBAAgB;IAC5B,MAAM,WAAW;CAClB;AAGD,0BAAkB,kBAAkB;IAClC,gBAAgB,mBAAmB;IACnC,0BAA0B,mBAAmB;IAC7C,YAAY,gBAAgB;IAC5B,cAAc,iBAAiB;IAC/B,KAAK,UAAU;CAChB;AAGD,0BAAkB,iBAAiB;IACjC,OAAO,YAAY;IACnB,GAAG,QAAQ;CACZ;AAED,0BAAkB,iBAAiB;IACjC,QAAQ,aAAa;IACrB,QAAQ,aAAa;IACrB,MAAM,WAAW;CAClB;AAGD,eAAO,MAAM,gBAAgB,eAO5B,CAAC;AAEF,eAAO,MAAM,gBAAgB,gBAAgB,CAAC;
|
|
1
|
+
{"version":3,"file":"const.d.ts","sourceRoot":"","sources":["const.ts"],"names":[],"mappings":"AAIA,eAAO,MAAM,sBAAsB,+BAA+B,CAAC;AAEnE;uFACuF;AACvF,0BAAkB,oBAAoB;IACpC,MAAM,WAAW;IACjB,IAAI,SAAS;IACb,OAAO,YAAY;IACnB,MAAM,WAAW;IACjB,EAAE,OAAO;IACT,OAAO,YAAY;IACnB,MAAM,WAAW;IACjB,YAAY,gBAAgB;IAC5B,YAAY,gBAAgB;IAC5B,WAAW,eAAe;CAC3B;AAED,0BAAkB,oBAAoB;IACpC,cAAc,kBAAkB;IAChC,IAAI,SAAS;CACd;AAED,0BAAkB,WAAW;IAC3B,YAAY,gBAAgB;IAC5B,MAAM,WAAW;IACjB,IAAI,SAAS;IACb,MAAM,WAAW;IACjB,OAAO,YAAY;IACnB,cAAc,kBAAkB;IAChC,OAAO,YAAY;IACnB,WAAW,eAAe;IAC1B,EAAE,OAAO;IACT,YAAY,gBAAgB;IAC5B,MAAM,WAAW;CAClB;AAGD,0BAAkB,kBAAkB;IAClC,gBAAgB,mBAAmB;IACnC,0BAA0B,mBAAmB;IAC7C,YAAY,gBAAgB;IAC5B,cAAc,iBAAiB;IAC/B,KAAK,UAAU;CAChB;AAGD,0BAAkB,iBAAiB;IACjC,OAAO,YAAY;IACnB,GAAG,QAAQ;CACZ;AAED,0BAAkB,iBAAiB;IACjC,QAAQ,aAAa;IACrB,QAAQ,aAAa;IACrB,MAAM,WAAW;CAClB;AAGD,eAAO,MAAM,gBAAgB,eAO5B,CAAC;AAEF,eAAO,MAAM,gBAAgB,gBAAgB,CAAC;AAE9C,sBAAsB;AACtB,eAAO,MAAM,iCAAiC;;;;CAI7C,CAAC;AAEF,sBAAsB;AACtB,eAAO,MAAM,YAAY;;;;;GAaxB,CAAC;AAGF,eAAO,MAAM,qBAAqB;;;;;;;;;;;;CAYjC,CAAC;AAEF,eAAO,MAAM,YAAY;;;;;;;;;;;;CAYxB,CAAC;AAEF,eAAO,MAAM,kBAAkB,MAAQ,CAAC;AACxC,eAAO,MAAM,kBAAkB,OAAQ,CAAC"}
|
package/src/utils/const.js
CHANGED
|
@@ -9,6 +9,27 @@ export const HELM_CORE_FIELDS = [
|
|
|
9
9
|
// supported
|
|
10
10
|
];
|
|
11
11
|
export const SDF_MONOMER_NAME = 'MonomerName';
|
|
12
|
+
/** For Enumerator */
|
|
13
|
+
export const helmFieldsToEnumeratorInputFields = {
|
|
14
|
+
["symbol" /* HELM_REQUIRED_FIELDS.SYMBOL */]: 'Short Name',
|
|
15
|
+
["name" /* HELM_REQUIRED_FIELDS.NAME */]: 'Medium Name',
|
|
16
|
+
["smiles" /* HELM_REQUIRED_FIELDS.SMILES */]: 'SMILES',
|
|
17
|
+
};
|
|
18
|
+
/** For Enumerator */
|
|
19
|
+
export const rGroupsDummy = [
|
|
20
|
+
{
|
|
21
|
+
'capGroupSmiles': '[*:1][H]',
|
|
22
|
+
'alternateId': 'R1-H',
|
|
23
|
+
'capGroupName': 'H',
|
|
24
|
+
'label': 'R1'
|
|
25
|
+
},
|
|
26
|
+
{
|
|
27
|
+
'capGroupSmiles': 'O[*:2]',
|
|
28
|
+
'alternateId': 'R2-OH',
|
|
29
|
+
'capGroupName': 'OH',
|
|
30
|
+
'label': 'R2'
|
|
31
|
+
}
|
|
32
|
+
];
|
|
12
33
|
// todo: ideally, keys should be expressed via constants
|
|
13
34
|
export const jsonSdfMonomerLibDict = {
|
|
14
35
|
'monomerType': null,
|
|
@@ -23,6 +44,19 @@ export const jsonSdfMonomerLibDict = {
|
|
|
23
44
|
'polymerType': 'MonomerType',
|
|
24
45
|
'symbol': 'MonomerCode'
|
|
25
46
|
};
|
|
47
|
+
export const dummyMonomer = {
|
|
48
|
+
'monomerType': 'Backbone',
|
|
49
|
+
'smiles': '',
|
|
50
|
+
'name': '',
|
|
51
|
+
'author': 'Datagrok',
|
|
52
|
+
'molfile': '',
|
|
53
|
+
'naturalAnalog': '',
|
|
54
|
+
'rgroups': [],
|
|
55
|
+
'createDate': null,
|
|
56
|
+
'id': 0,
|
|
57
|
+
'polymerType': 'PEPTIDE',
|
|
58
|
+
'symbol': ''
|
|
59
|
+
};
|
|
26
60
|
// range of hex nubers used in PepSea library to endode monomers
|
|
27
61
|
export const MONOMER_ENCODE_MIN = 0x100;
|
|
28
62
|
export const MONOMER_ENCODE_MAX = 0x40A;
|
package/src/utils/const.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"const.js","sourceRoot":"","sources":["const.ts"],"names":[],"mappings":"AAIA,MAAM,CAAC,MAAM,sBAAsB,GAAG,4BAA4B,CAAC;AAyDnE,oEAAoE;AACpE,MAAM,CAAC,MAAM,gBAAgB,GAAG;;;;;IAK9B,2EAA2E;IAC3E,YAAY;CACb,CAAC;AAEF,MAAM,CAAC,MAAM,gBAAgB,GAAG,aAAa,CAAC;AAE9C,wDAAwD;AACxD,MAAM,CAAC,MAAM,qBAAqB,GAAG;IACnC,aAAa,EAAE,IAAI;IACnB,QAAQ,EAAE,IAAI;IACd,MAAM,EAAE,aAAa;IACrB,QAAQ,EAAE,IAAI;IACd,SAAS,EAAE,UAAU;IACrB,eAAe,EAAE,0BAA0B;IAC3C,SAAS,EAAE,aAAa;IACxB,YAAY,EAAE,IAAI;IAClB,IAAI,EAAE,IAAI;IACV,aAAa,EAAE,aAAa;IAC5B,QAAQ,EAAE,aAAa;CACxB,CAAC;AAEF,gEAAgE;AAChE,MAAM,CAAC,MAAM,kBAAkB,GAAG,KAAK,CAAC;AACxC,MAAM,CAAC,MAAM,kBAAkB,GAAG,KAAK,CAAC"}
|
|
1
|
+
{"version":3,"file":"const.js","sourceRoot":"","sources":["const.ts"],"names":[],"mappings":"AAIA,MAAM,CAAC,MAAM,sBAAsB,GAAG,4BAA4B,CAAC;AAyDnE,oEAAoE;AACpE,MAAM,CAAC,MAAM,gBAAgB,GAAG;;;;;IAK9B,2EAA2E;IAC3E,YAAY;CACb,CAAC;AAEF,MAAM,CAAC,MAAM,gBAAgB,GAAG,aAAa,CAAC;AAE9C,sBAAsB;AACtB,MAAM,CAAC,MAAM,iCAAiC,GAAG;IAC/C,4CAA6B,EAAE,YAAY;IAC3C,wCAA2B,EAAE,aAAa;IAC1C,4CAA6B,EAAE,QAAQ;CACxC,CAAC;AAEF,sBAAsB;AACtB,MAAM,CAAC,MAAM,YAAY,GAAG;IAC1B;QACE,gBAAgB,EAAE,UAAU;QAC5B,aAAa,EAAE,MAAM;QACrB,cAAc,EAAE,GAAG;QACnB,OAAO,EAAE,IAAI;KACd;IACD;QACE,gBAAgB,EAAE,QAAQ;QAC1B,aAAa,EAAE,OAAO;QACtB,cAAc,EAAE,IAAI;QACpB,OAAO,EAAE,IAAI;KACd;CACF,CAAC;AAEF,wDAAwD;AACxD,MAAM,CAAC,MAAM,qBAAqB,GAAG;IACnC,aAAa,EAAE,IAAI;IACnB,QAAQ,EAAE,IAAI;IACd,MAAM,EAAE,aAAa;IACrB,QAAQ,EAAE,IAAI;IACd,SAAS,EAAE,UAAU;IACrB,eAAe,EAAE,0BAA0B;IAC3C,SAAS,EAAE,aAAa;IACxB,YAAY,EAAE,IAAI;IAClB,IAAI,EAAE,IAAI;IACV,aAAa,EAAE,aAAa;IAC5B,QAAQ,EAAE,aAAa;CACxB,CAAC;AAEF,MAAM,CAAC,MAAM,YAAY,GAAG;IAC1B,aAAa,EAAE,UAAU;IACzB,QAAQ,EAAE,EAAE;IACZ,MAAM,EAAE,EAAE;IACV,QAAQ,EAAE,UAAU;IACpB,SAAS,EAAE,EAAE;IACb,eAAe,EAAE,EAAE;IACnB,SAAS,EAAE,EAAE;IACb,YAAY,EAAE,IAAI;IAClB,IAAI,EAAE,CAAC;IACP,aAAa,EAAE,SAAS;IACxB,QAAQ,EAAE,EAAE;CACb,CAAC;AACF,gEAAgE;AAChE,MAAM,CAAC,MAAM,kBAAkB,GAAG,KAAK,CAAC;AACxC,MAAM,CAAC,MAAM,kBAAkB,GAAG,KAAK,CAAC"}
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
{"version":3,"file":"types.d.ts","sourceRoot":"","sources":["types.ts"],"names":[],"mappings":"AAAA,MAAM,MAAM,aAAa,GAAG;IAC1B,YAAY,EAAE,MAAM,CAAC;IACrB,aAAa,EAAE,MAAM,CAAC;IACtB,QAAQ,EAAE,MAAM,CAAC;IACjB,UAAU,EAAE,MAAM,CAAA;CACnB,CAAA"}
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
{"version":3,"file":"types.js","sourceRoot":"","sources":["types.ts"],"names":[],"mappings":""}
|