@datagrok-libraries/bio 3.3.1 → 4.0.0

package/README.md

@@ -1,3 +1,3 @@
 # bio
 
-bio is a [package](https://datagrok.ai/help/develop/develop#packages) for the [Datagrok](https://datagrok.ai) platform.
+bio is a [library](https://datagrok.ai/help/develop/develop#libraries) for the [Datagrok](https://datagrok.ai) platform.

package/package.json

@@ -5,11 +5,10 @@
   },
   "beta": true,
   "friendlyName": "Datagrok bio library",
-  "version": "3.3.1",
+  "version": "4.0.0",
   "description": "",
   "dependencies": {
     "@datagrok-libraries/utils": "^1.6.2",
-    "@types/wu": "latest",
     "cash-dom": "latest",
     "datagrok-api": "^1.6.0",
     "dayjs": "latest",
@@ -17,6 +16,7 @@
     "wu": "latest"
   },
   "devDependencies": {
+    "@types/wu": "latest",
     "@typescript-eslint/eslint-plugin": "latest",
     "@typescript-eslint/parser": "latest",
     "eslint": "latest",
@@ -29,14 +29,8 @@
     "link-api": "npm link datagrok-api",
     "link-utils": "npm link @datagrok-libraries/utils",
     "link-all": "npm link datagrok-api @datagrok-libraries/utils",
-    "debug-bio": "grok publish",
-    "release-bio": "grok publish --release",
     "build-bio": "tsc",
     "build": "tsc",
-    "debug-bio-public": "grok publish public",
-    "release-bio-public": "grok publish public --release",
-    "debug-bio-local": "grok publish local",
-    "release-bio-local": "grok publish local --release",
     "lint": "eslint \"./src/**/*.ts\"",
     "lint-fix": "eslint \"./src/**/*.ts\" --fix"
   }

package/src/rdkit-api.d.ts

@@ -1,63 +0,0 @@
-export interface RDModule {
-    get_mol(molString: string, options?: string): RDMol;
-    get_qmol(smarts: string): RDMol;
-    get_inchikey_for_inchi(input: string): string;
-    version(): string;
-    prefer_coordgen(prefer: boolean): void;
-}
-export interface RDMol {
-    d_defaultWidth: number;
-    d_default_Height: number;
-    get_smiles(): string;
-    get_cxsmiles(): string;
-    get_smarts(): string;
-    get_cxsmarts(): string;
-    get_molblock(): string;
-    get_v3Kmolblock(): string;
-    get_inchi(): string;
-    get_json(): string;
-    get_svg(width?: number, height?: number): string;
-    get_svg_with_highlightes(details: string): string;
-    get_substruct_match(qmol: RDMol): string;
-    get_substruct_matches(qmol: RDMol): string;
-    get_descriptors(): string;
-    get_morgan_fp(radius?: number, len?: number): string;
-    get_morgan_fp_as_uint8array(radius?: number, len?: number): Uint8Array;
-    get_pattern_fp(len?: number): string;
-    get_pattern_fp_as_uint8array(len?: number): Uint8Array;
-    condense_abbreviations(maxCoverage?: number, useLinkers?: boolean): string;
-    condense_abbreviations_from_defs(definitions: string, maxCoverage: number, areLinkers: boolean): string;
-    generate_aligned_coords(template: RDMol, useCoordGen?: boolean, allowOptionalAttachments?: boolean, acceptFailure?: boolean): string;
-    draw_to_canvas_with_offset(canvas: HTMLCanvasElement, offsetX: number, offsetY: number, width: number, height: number): string;
-    draw_to_canvas(canvas: HTMLCanvasElement, width: number, height: number): string;
-    draw_to_canvas_with_highlights(canvas: HTMLCanvasElement, details: string): string;
-    get_morgan_fp_as_uint8array(radius: number, fplen: number): Uint8Array;
-    is_valid(): boolean;
-    has_coords(): boolean;
-    get_stereo_tags(): string;
-    get_aromatic_form(): string;
-    get_kekule_from(): string;
-    get_new_coords(useCoordGen?: boolean): string;
-    set_new_coords(useCoordGen?: boolean): boolean;
-    remove_hs(): string;
-    add_hs(): string;
-    normalize_depiction(): void;
-    straighten_depiction(): void;
-    compute_hash(): string;
-    /** Reclaims the memory used for that molecule. */
-    delete(): void;
-}
-export interface SubstructLibrary {
-    d_num_bits: number;
-    d_defaultNumBits: number;
-    d_defaultUseChirality: boolean;
-    d_defaultNumThreads: number;
-    d_defaultMaxResults: number;
-    add_mol(mol: RDMol): number;
-    add_smiles(smiles: string): number;
-    add_trusted_smiles(smiles: string): number;
-    get_mol(i: number): RDMol;
-    get_matches(qmol: RDMol, useChirality?: boolean, numThreads?: number, maxResults?: number): string;
-    count_matches(qmol: RDMol, useChirality?: boolean, numThreads?: number): number;
-}
-//# sourceMappingURL=rdkit-api.d.ts.map

package/src/rdkit-api.d.ts.map

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package/src/rdkit-api.js

@@ -1,2 +0,0 @@
-export {};
-//# sourceMappingURL=data:application/json;base64,eyJ2ZXJzaW9uIjozLCJmaWxlIjoicmRraXQtYXBpLmpzIiwic291cmNlUm9vdCI6IiIsInNvdXJjZXMiOlsicmRraXQtYXBpLnRzIl0sIm5hbWVzIjpbXSwibWFwcGluZ3MiOiIiLCJzb3VyY2VzQ29udGVudCI6WyJleHBvcnQgaW50ZXJmYWNlIFJETW9kdWxlIHtcbiAgZ2V0X21vbChtb2xTdHJpbmc6IHN0cmluZywgb3B0aW9ucz86IHN0cmluZyk6IFJETW9sO1xuICBnZXRfcW1vbChzbWFydHM6IHN0cmluZyk6IFJETW9sO1xuICBnZXRfaW5jaGlrZXlfZm9yX2luY2hpKGlucHV0OiBzdHJpbmcpOiBzdHJpbmc7XG4gIHZlcnNpb24oKTogc3RyaW5nO1xuICBwcmVmZXJfY29vcmRnZW4ocHJlZmVyOiBib29sZWFuKTogdm9pZDtcbn1cblxuZXhwb3J0IGludGVyZmFjZSBSRE1vbCB7XG4gIGRfZGVmYXVsdFdpZHRoOiBudW1iZXI7XG4gIGRfZGVmYXVsdF9IZWlnaHQ6IG51bWJlcjtcblxuICBnZXRfc21pbGVzKCk6IHN0cmluZztcbiAgZ2V0X2N4c21pbGVzKCk6IHN0cmluZztcbiAgZ2V0X3NtYXJ0cygpOiBzdHJpbmc7XG4gIGdldF9jeHNtYXJ0cygpOiBzdHJpbmc7XG4gIGdldF9tb2xibG9jaygpOiBzdHJpbmc7XG4gIGdldF92M0ttb2xibG9jaygpOiBzdHJpbmc7XG4gIGdldF9pbmNoaSgpOiBzdHJpbmc7XG4gIGdldF9qc29uKCk6IHN0cmluZztcbiAgZ2V0X3N2Zyh3aWR0aD86IG51bWJlciwgaGVpZ2h0PzogbnVtYmVyKTogc3RyaW5nO1xuICBnZXRfc3ZnX3dpdGhfaGlnaGxpZ2h0ZXMoZGV0YWlsczogc3RyaW5nKTogc3RyaW5nO1xuICBnZXRfc3Vic3RydWN0X21hdGNoKHFtb2w6IFJETW9sKSA6IHN0cmluZztcbiAgZ2V0X3N1YnN0cnVjdF9tYXRjaGVzKHFtb2w6IFJETW9sKTogc3RyaW5nO1xuICBnZXRfZGVzY3JpcHRvcnMoKTogc3RyaW5nO1xuXG4gIGdldF9tb3JnYW5fZnAocmFkaXVzPzogbnVtYmVyLCBsZW4/OiBudW1iZXIpOiBzdHJpbmc7XG4gIGdldF9tb3JnYW5fZnBfYXNfdWludDhhcnJheShyYWRpdXM/OiBudW1iZXIsIGxlbj86IG51bWJlcik6IFVpbnQ4QXJyYXk7XG4gIGdldF9wYXR0ZXJuX2ZwKGxlbj86IG51bWJlcik6IHN0cmluZztcbiAgZ2V0X3BhdHRlcm5fZnBfYXNfdWludDhhcnJheShsZW4/OiBudW1iZXIpOiBVaW50OEFycmF5O1xuXG4gIGNvbmRlbnNlX2FiYnJldmlhdGlvbnMobWF4Q292ZXJhZ2U/OiBudW1iZXIsIHVzZUxpbmtlcnM/OiBib29sZWFuKTogc3RyaW5nO1xuICBjb25kZW5zZV9hYmJyZXZpYXRpb25zX2Zyb21fZGVmcyhkZWZpbml0aW9uczogc3RyaW5nLCBtYXhDb3ZlcmFnZTogbnVtYmVyLCBhcmVMaW5rZXJzOiBib29sZWFuKTogc3RyaW5nO1xuICBnZW5lcmF0ZV9hbGlnbmVkX2Nvb3JkcyhcbiAgICAgIHRlbXBsYXRlOiBSRE1vbCwgdXNlQ29vcmRHZW4/OiBib29sZWFuLCBhbGxvd09wdGlvbmFsQXR0YWNobWVudHM/OiBib29sZWFuLCBhY2NlcHRGYWlsdXJlPzogYm9vbGVhbik6IHN0cmluZztcblxuICBkcmF3X3RvX2NhbnZhc193aXRoX29mZnNldChcbiAgICAgIGNhbnZhczogSFRNTENhbnZhc0VsZW1lbnQsIG9mZnNldFg6IG51bWJlciwgb2Zmc2V0WTogbnVtYmVyLCB3aWR0aDogbnVtYmVyLCBoZWlnaHQ6IG51bWJlcik6IHN0cmluZztcbiAgZHJhd190b19jYW52YXMoY2FudmFzOiBIVE1MQ2FudmFzRWxlbWVudCwgd2lkdGg6IG51bWJlciwgaGVpZ2h0OiBudW1iZXIpOiBzdHJpbmc7XG4gIGRyYXdfdG9fY2FudmFzX3dpdGhfaGlnaGxpZ2h0cyhjYW52YXM6IEhUTUxDYW52YXNFbGVtZW50LCBkZXRhaWxzOiBzdHJpbmcpOiBzdHJpbmc7XG4gIGdldF9tb3JnYW5fZnBfYXNfdWludDhhcnJheShyYWRpdXM6IG51bWJlciwgZnBsZW46IG51bWJlcik6IFVpbnQ4QXJyYXk7XG5cbiAgaXNfdmFsaWQoKTogYm9vbGVhbjtcbiAgaGFzX2Nvb3JkcygpOiBib29sZWFuO1xuXG4gIGdldF9zdGVyZW9fdGFncygpOiBzdHJpbmc7XG4gIGdldF9hcm9tYXRpY19mb3JtKCk6IHN0cmluZztcbiAgZ2V0X2tla3VsZV9mcm9tKCk6IHN0cmluZztcbiAgZ2V0X25ld19jb29yZHModXNlQ29vcmRHZW4/OiBib29sZWFuKTogc3RyaW5nO1xuICBzZXRfbmV3X2Nvb3Jkcyh1c2VDb29yZEdlbj86IGJvb2xlYW4pOiBib29sZWFuO1xuICByZW1vdmVfaHMoKTogc3RyaW5nO1xuICBhZGRfaHMoKTogc3RyaW5nO1xuXG4gIG5vcm1hbGl6ZV9kZXBpY3Rpb24oKTogdm9pZDtcbiAgc3RyYWlnaHRlbl9kZXBpY3Rpb24oKTogdm9pZDtcbiAgY29tcHV0ZV9oYXNoKCk6IHN0cmluZztcblxuICAvKiogUmVjbGFpbXMgdGhlIG1lbW9yeSB1c2VkIGZvciB0aGF0IG1vbGVjdWxlLiAqL1xuICBkZWxldGUoKTogdm9pZDtcbn1cblxuZXhwb3J0IGludGVyZmFjZSBTdWJzdHJ1Y3RMaWJyYXJ5IHtcbiAgZF9udW1fYml0czogbnVtYmVyO1xuICBkX2RlZmF1bHROdW1CaXRzOiBudW1iZXI7XG4gIGRfZGVmYXVsdFVzZUNoaXJhbGl0eTogYm9vbGVhbjtcbiAgZF9kZWZhdWx0TnVtVGhyZWFkczogbnVtYmVyO1xuICBkX2RlZmF1bHRNYXhSZXN1bHRzOiBudW1iZXI7XG5cbiAgYWRkX21vbChtb2w6IFJETW9sKTogbnVtYmVyO1xuICBhZGRfc21pbGVzKHNtaWxlczogc3RyaW5nKTogbnVtYmVyO1xuICBhZGRfdHJ1c3RlZF9zbWlsZXMoc21pbGVzOiBzdHJpbmcpOiBudW1iZXI7XG4gIGdldF9tb2woaTogbnVtYmVyKTogUkRNb2w7XG4gIGdldF9tYXRjaGVzKHFtb2w6IFJETW9sLCB1c2VDaGlyYWxpdHk/OiBib29sZWFuLCBudW1UaHJlYWRzPzogbnVtYmVyLCBtYXhSZXN1bHRzPzogbnVtYmVyKTogc3RyaW5nO1xuICBjb3VudF9tYXRjaGVzKHFtb2w6IFJETW9sLCB1c2VDaGlyYWxpdHk/OiBib29sZWFuLCBudW1UaHJlYWRzPzogbnVtYmVyKTogbnVtYmVyO1xufVxuXG4iXX0=