@datagrok-libraries/bio 5.41.11 → 5.42.0

package/.eslintrc.json

@@ -17,6 +17,7 @@
   "rules": {
     "indent": ["error", 2, {"SwitchCase": 0}],
     "max-len": ["error", 120],
+    "no-throw-literal": "error",
     "no-unused-vars": "off",
     "@typescript-eslint/no-unused-vars": [
       "warn", {"varsIgnorePattern": "^(_|ui$|grok$|DG$)", "argsIgnorePattern": "^_"}

package/CHANGELOG.md

@@ -1,5 +1,16 @@
 # bio changelog
 
+## 5.42.0 (2024-06-21)
+
+Use types of forked JSDraw.Lite and HELMWebEditor
+
+## 5.41.12 (2024-06-12)
+
+### Bug fixes
+
+* Fix .pdbqt to .pdb sorting atoms, add tests
+* Fix cell renderer async base to reset errorCount
+
 ## 5.41.11 (2024-06-11)
 
 ### Bug fixes

package/package.json

@@ -8,12 +8,12 @@
     "access": "public"
   },
   "friendlyName": "Datagrok bio library",
-  "version": "5.41.11",
+  "version": "5.42.0",
   "description": "Bio utilities, types supporting Macromolecule, Molecule3D data",
   "dependencies": {
     "@datagrok-libraries/gridext": "^1.3.71",
-    "@datagrok-libraries/utils": "^4.2.2",
-    "@datagrok-libraries/ml": "^6.6.5",
+    "@datagrok-libraries/ml": "^6.6.11",
+    "@datagrok-libraries/utils": "^4.2.11",
     "@deck.gl/core": "8.8.12",
     "cash-dom": "latest",
     "datagrok-api": "^1.18.6",
@@ -26,12 +26,15 @@
     "wu": "latest"
   },
   "devDependencies": {
-    "@types/three": "^0.159.0",
+    "@datagrok-libraries/helm-web-editor": "^1.1.4",
+    "@datagrok-libraries/js-draw-lite": "^0.0.2",
     "@types/signals": "1.0.1",
+    "@types/three": "^0.159.0",
     "@types/uuid": "^9.0.1",
     "@types/wu": "latest",
     "@typescript-eslint/eslint-plugin": "latest",
     "@typescript-eslint/parser": "latest",
+    "datagrok-tools": "latest",
     "eslint": "latest",
     "eslint-config-google": "latest",
     "ts-loader": "^9.2.6",

package/src/helm/consts.d.ts

@@ -0,0 +1,3 @@
+import { HelmTypes, MonomerTypes, PolymerTypes } from '@datagrok-libraries/js-draw-lite/src/types/org';
+export { HelmTypes, MonomerTypes, PolymerTypes };
+//# sourceMappingURL=consts.d.ts.map

package/src/helm/consts.d.ts.map

@@ -0,0 +1 @@
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package/src/helm/consts.js

@@ -0,0 +1,2 @@
+export {};
+//# sourceMappingURL=consts.js.map

package/src/helm/consts.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"consts.js","sourceRoot":"","sources":["consts.ts"],"names":[],"mappings":""}

package/src/helm/helm-helper.d.ts

@@ -1,9 +1,15 @@
-import '../types/helm';
-import * as org from 'org';
-import { IHelmWebEditor } from './types';
+import type { App } from '@datagrok-libraries/helm-web-editor/helm/App';
+import { Atom, HelmType, IHelmWebEditor, IWebEditorMonomer } from './types';
+import { IMonomerLib } from '../types/index';
+export type GetMonomerResType = IWebEditorMonomer | null;
+export type GetMonomerFunc = (a: Atom<HelmType> | HelmType, name?: string) => GetMonomerResType;
 export interface IHelmHelper {
     createHelmWebEditor(): IHelmWebEditor;
-    createWebEditorApp(host: HTMLDivElement, helm?: string): org.helm.IWebEditorApp;
+    createWebEditorApp(host: HTMLDivElement, helm?: string): App;
+    get originalGetMonomer(): GetMonomerFunc | null;
+    buildGetMonomerFromLib(monomerLib: IMonomerLib): GetMonomerFunc;
+    overrideGetMonomer(getMonomerFunc: GetMonomerFunc): GetMonomerFunc;
+    revertOriginalGetMonomer(): GetMonomerFunc;
 }
 export declare function getHelmHelper(): Promise<IHelmHelper>;
 //# sourceMappingURL=helm-helper.d.ts.map

package/src/helm/helm-helper.d.ts.map

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package/src/helm/helm-helper.js

@@ -1,5 +1,4 @@
 import * as DG from 'datagrok-api/dg';
-import '../types/helm';
 export async function getHelmHelper() {
     const packageName = 'Helm';
     const funcList = DG.Func.find({ package: packageName, name: `getHelmHelper` });

package/src/helm/helm-helper.js.map

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package/src/helm/types.d.ts

@@ -1,7 +1,23 @@
-import '../types/jsdraw2';
-import * as JSDraw2 from 'JSDraw2';
+import type { HelmType, PolymerType, MonomerType, IWebEditorMonomer, WebEditorRGroups } from '@datagrok-libraries/js-draw-lite/src/types/org';
+import type { Atom } from '@datagrok-libraries/js-draw-lite/src/Atom';
+import type { IJsAtom } from '@datagrok-libraries/js-draw-lite/src/types/jsdraw2';
+import type { Bond } from '@datagrok-libraries/js-draw-lite/src/Bond';
+import type { Mol } from '@datagrok-libraries/js-draw-lite/src/Mol';
+import type { Editor } from '@datagrok-libraries/js-draw-lite/src/JSDraw.Editor';
+import type { App } from '@datagrok-libraries/helm-web-editor/helm/App';
+import type { IOrgHelmWebEditor, IOrgHelmMonomers } from '@datagrok-libraries/helm-web-editor/src/types/org-helm';
+import type { HweWindow } from '@datagrok-libraries/helm-web-editor/src/types';
+import type { JSDraw2ModuleType, ScilModuleType } from '@datagrok-libraries/js-draw-lite/src/types';
+import type { OrgType } from '@datagrok-libraries/helm-web-editor/src/types/org-helm';
+import type { Monomers } from '@datagrok-libraries/helm-web-editor/helm/Monomers';
+import type { DojoType, DojoxType } from '@datagrok-libraries/js-draw-lite/src/types/dojo';
+export { HelmType, PolymerType, MonomerType, WebEditorRGroups };
+export { Atom, IJsAtom, Bond, Mol, Editor };
+export { IWebEditorMonomer, IOrgHelmWebEditor, IOrgHelmMonomers, App, Monomers };
+export { DojoType, DojoxType };
+export { HweWindow, ScilModuleType, JSDraw2ModuleType, OrgType };
 export interface IHelmWebEditor {
-    get editor(): JSDraw2.Editor;
+    get editor(): Editor<HelmType>;
     get host(): HTMLDivElement;
     resizeEditor(width: number, height: number): void;
 }

package/src/helm/types.d.ts.map

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package/src/helm/types.js

@@ -1,2 +1,2 @@
-import '../types/jsdraw2';
+export {};
 //# sourceMappingURL=types.js.map

package/src/helm/types.js.map

@@ -1 +1 @@
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+{"version":3,"file":"types.js","sourceRoot":"","sources":["types.ts"],"names":[],"mappings":""}

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package/src/monomer-works/monomer-utils.js

@@ -230,6 +230,7 @@ export async function getMonomerSubstitutionMatrix(monomerSet, fingerprintType =
         for (let j = i + 1; j < fingerPrints.length; ++j) {
             if (!fingerPrints[j])
                 continue;
+            // @ts-ignore
             scoringMatrix[i][j] = scoringMatrix[j][i] = tanimotoSimilarity(fingerPrints[i], fingerPrints[j]);
         }
     }

package/src/monomer-works/monomer-utils.js.map

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package/src/monomer-works/monomer-works.d.ts

@@ -1,4 +1,5 @@
-import { IMonomerLib, HelmType, PolymerType } from '../types';
+import { IMonomerLib } from '../types';
+import { HelmType, PolymerType } from '../helm/types';
 /** Hypothetical interface to convert mol block notation.
  * It should be placed in the chem-meta package, and have an implementation in the Chem package.
  * So dependency of MonomerWorks on molfile conversion operation becomes explicit.

package/src/monomer-works/monomer-works.d.ts.map

@@ -1 +1 @@
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package/src/monomer-works/monomer-works.js.map

@@ -1 +1 @@
-{"version":3,"file":"monomer-works.js","sourceRoot":"","sources":["monomer-works.ts"],"names":[],"mappings":"AAiBA,MAAM,OAAO,YAAY;IAGvB,8CAA8C;IAE9C,YAAY,UAAuB,CAAA,yCAAyC;QAC1E,IAAI,CAAC,UAAU,GAAG,UAAU,CAAC;QAC7B,2CAA2C;IAC7C,CAAC;IAED,qCAAqC;IAC9B,uBAAuB,CAAC,WAAwB,EAAE,WAAmB;QAC1E,sCAAsC;QACtC,MAAM,OAAO,GAAG,IAAI,CAAC,UAAU,CAAC,UAAU,CAAC,WAAW,EAAE,WAAW,CAAC,CAAC;QACrE,IAAI,OAAO;YACT,OAAO,OAAO,CAAC,OAAO,CAAC,CAAC,UAAU;QAEpC,OAAO,IAAI,CAAC;IACd,CAAC;CACF;AAED,MAAM,UAAU,qBAAqB,CAAC,QAAkB;IACtD,IAAI,WAAW,GAA4B,SAAS,CAAC;IACrD,QAAQ,QAAQ,EAAE;QAClB,sCAAoB;QACpB,wCAAqB,CAAC,8BAA8B;QACpD,0CAAsB,CAAC,gBAAgB;QACvC,iDAA0B;QACxB,aAAa;QACf,KAAK,YAAY;YACf,WAAW,+BAAmB,CAAC;YAC/B,MAAM;QACR;YACE,WAAW,uCAAuB,CAAC;YACnC,MAAM;QACR;YACE,WAAW,iCAAoB,CAAC;YAChC,MAAM;QACR;YACE,WAAW,iCAAoB,CAAC;YAChC,MAAM;QACR;YACE,WAAW,uCAAuB,CAAC;YACnC,OAAO,CAAC,IAAI,CAAC,wBAAwB,QAAQ,GAAG,CAAC,CAAC;KACnD;IACD,OAAO,WAAW,CAAC;AACrB,CAAC"}
+{"version":3,"file":"monomer-works.js","sourceRoot":"","sources":["monomer-works.ts"],"names":[],"mappings":"AAkBA,MAAM,OAAO,YAAY;IAGvB,8CAA8C;IAE9C,YAAY,UAAuB,CAAA,yCAAyC;QAC1E,IAAI,CAAC,UAAU,GAAG,UAAU,CAAC;QAC7B,2CAA2C;IAC7C,CAAC;IAED,qCAAqC;IAC9B,uBAAuB,CAAC,WAAwB,EAAE,WAAmB;QAC1E,sCAAsC;QACtC,MAAM,OAAO,GAAG,IAAI,CAAC,UAAU,CAAC,UAAU,CAAC,WAAW,EAAE,WAAW,CAAC,CAAC;QACrE,IAAI,OAAO;YACT,OAAO,OAAO,CAAC,OAAO,CAAC,CAAC,UAAU;QAEpC,OAAO,IAAI,CAAC;IACd,CAAC;CACF;AAED,MAAM,UAAU,qBAAqB,CAAC,QAAkB;IACtD,IAAI,WAAW,GAA4B,SAAS,CAAC;IACrD,QAAQ,QAAQ,EAAE;QAClB,sCAAoB;QACpB,wCAAqB,CAAC,8BAA8B;QACpD,0CAAsB,CAAC,gBAAgB;QACvC,iDAA0B;QACxB,aAAa;QACf,KAAK,YAAY;YACf,WAAW,+BAAmB,CAAC;YAC/B,MAAM;QACR;YACE,WAAW,uCAAuB,CAAC;YACnC,MAAM;QACR;YACE,WAAW,iCAAoB,CAAC;YAChC,MAAM;QACR;YACE,WAAW,iCAAoB,CAAC;YAChC,MAAM;QACR;YACE,WAAW,uCAAuB,CAAC;YACnC,OAAO,CAAC,IAAI,CAAC,wBAAwB,QAAQ,GAAG,CAAC,CAAC;KACnD;IACD,OAAO,WAAW,CAAC;AACrB,CAAC"}

package/src/pdb/format/types-base.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"types-base.d.ts","sourceRoot":"","sources":["types-base.ts"],"names":[],"mappings":"AAIA,OAAO,EAAC,SAAS,EAAE,WAAW,EAAE,QAAQ,EAAC,MAAM,SAAS,CAAC;AAEzD,qBAAa,QAAQ;aAED,SAAS,EAAE,MAAM;gBAAjB,SAAS,EAAE,MAAM;IAGnC,MAAM,CAAC,OAAO,CAAC,IAAI,EAAE,MAAM,GAAG,QAAQ;IAMtC,KAAK,IAAI,MAAM;CAQhB;AAQD,WAAW;AACX,qBAAa,QAAS,SAAQ,QAAS,YAAW,SAAS;aAYvC,MAAM,EAAE,MAAM;aACA,WAAW,EAAE,MAAM;aACK,QAAQ,EAAE,MAAM;aACtD,MAAM,EAAE,MAAM;aACY,OAAO,EAAE,MAAM;aACzC,KAAK,EAAE,MAAM;aACb,SAAS,EAAE,MAAM;aACjB,OAAO,EAAE,MAAM;IAlBjC;;;;;;;;OAQG;gBAED,CAAC,EAAE,QAAQ,EACK,MAAM,EAAE,MAAM,EACA,WAAW,EAAE,MAAM,EACK,QAAQ,EAAE,MAAM,EACtD,MAAM,EAAE,MAAM,EACY,OAAO,EAAE,MAAM,EACzC,KAAK,EAAE,MAAM,EACb,SAAS,EAAE,MAAM,EACjB,OAAO,EAAE,MAAM;IAKjC,MAAM,CAAC,OAAO,CAAC,IAAI,EAAE,MAAM,GAAG,QAAQ;IAetC,OAAO,CAAC,CAAC,EAAE,QAAQ,GAAG,MAAM;IAmC5B,KAAK,IAAI,MAAM;CAgBhB;AAED,WAAW;AACX,qBAAa,cAAe,SAAQ,QAAS,YAAW,WAAW;aAY/C,CAAC,EAAE,MAAM;aACT,CAAC,EAAE,MAAM;aACT,CAAC,EAAE,MAAM;aACT,SAAS,EAAE,MAAM;aACjB,OAAO,EAAE,MAAM;IAfjC;;;;;;;;OAQG;gBAED,CAAC,EAAE,QAAQ,EACK,CAAC,EAAE,MAAM,EACT,CAAC,EAAE,MAAM,EACT,CAAC,EAAE,MAAM,EACT,SAAS,EAAE,MAAM,EACjB,OAAO,EAAE,MAAM;IAKjC,MAAM,CAAC,OAAO,CAAC,IAAI,EAAE,MAAM,GAAG,cAAc;IAa5C,OAAO,IAAI,OAAO;IAgBlB,KAAK,IAAI,MAAM;CAahB;AAED,qBAAa,WAAY,SAAQ,QAAS,YAAW,QAAQ;CAAG"}
+{"version":3,"file":"types-base.d.ts","sourceRoot":"","sources":["types-base.ts"],"names":[],"mappings":"AAIA,OAAO,EAAC,SAAS,EAAE,WAAW,EAAE,QAAQ,EAAC,MAAM,SAAS,CAAC;AAEzD,qBAAa,QAAQ;aAED,SAAS,EAAE,MAAM;gBAAjB,SAAS,EAAE,MAAM;IAGnC,MAAM,CAAC,OAAO,CAAC,IAAI,EAAE,MAAM,GAAG,QAAQ;IAMtC,KAAK,IAAI,MAAM;CAQhB;AASD,WAAW;AACX,qBAAa,QAAS,SAAQ,QAAS,YAAW,SAAS;aAYvC,MAAM,EAAE,MAAM;aACA,WAAW,EAAE,MAAM;aACK,QAAQ,EAAE,MAAM;aACtD,MAAM,EAAE,MAAM;aACY,OAAO,EAAE,MAAM;aACzC,KAAK,EAAE,MAAM;aACb,SAAS,EAAE,MAAM;aACjB,OAAO,EAAE,MAAM;IAlBjC;;;;;;;;OAQG;gBAED,CAAC,EAAE,QAAQ,EACK,MAAM,EAAE,MAAM,EACA,WAAW,EAAE,MAAM,EACK,QAAQ,EAAE,MAAM,EACtD,MAAM,EAAE,MAAM,EACY,OAAO,EAAE,MAAM,EACzC,KAAK,EAAE,MAAM,EACb,SAAS,EAAE,MAAM,EACjB,OAAO,EAAE,MAAM;IAKjC,MAAM,CAAC,OAAO,CAAC,IAAI,EAAE,MAAM,GAAG,QAAQ;IAetC,OAAO,CAAC,CAAC,EAAE,QAAQ,GAAG,MAAM;IAyD5B,KAAK,IAAI,MAAM;CAgBhB;AAED,WAAW;AACX,qBAAa,cAAe,SAAQ,QAAS,YAAW,WAAW;aAY/C,CAAC,EAAE,MAAM;aACT,CAAC,EAAE,MAAM;aACT,CAAC,EAAE,MAAM;aACT,SAAS,EAAE,MAAM;aACjB,OAAO,EAAE,MAAM;IAfjC;;;;;;;;OAQG;gBAED,CAAC,EAAE,QAAQ,EACK,CAAC,EAAE,MAAM,EACT,CAAC,EAAE,MAAM,EACT,CAAC,EAAE,MAAM,EACT,SAAS,EAAE,MAAM,EACjB,OAAO,EAAE,MAAM;IAKjC,MAAM,CAAC,OAAO,CAAC,IAAI,EAAE,MAAM,GAAG,cAAc;IAa5C,OAAO,IAAI,OAAO;IAgBlB,KAAK,IAAI,MAAM;CAahB;AAED,qBAAa,WAAY,SAAQ,QAAS,YAAW,QAAQ;CAAG"}

package/src/pdb/format/types-base.js

@@ -16,7 +16,8 @@ export class LineBase {
 }
 const backboneRanks = { 'N': 1, 'CA': 2, 'C': 3, 'O': 4 };
 const atomNameRanks = {
-    '': 0, 'A': 1, 'B': 2, 'G': 3, 'D': 4, 'E': 5, 'Z': 6, 'H': 7,
+    /* backbone */ '': 0, /**/ 'N': 0,
+    'A': 1, 'B': 2, 'G': 3, 'D': 4, 'E': 5, 'Z': 6, 'H': 7,
     /* terminal */ 'X': 1000
 };
 /** 1-27 */
@@ -51,6 +52,7 @@ export class AtomBase extends LineBase {
         /* resNumber */ parseInt(line.slice(23 - 1, 26)), `${line.slice(27 - 1, 27).trim()}`);
     }
     compare(b) {
+        // https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/pdbintro.html
         const a = this;
         if (a.chain != b.chain)
             return a.chain.localeCompare(b.chain);
@@ -68,18 +70,40 @@ export class AtomBase extends LineBase {
             else if (bBackboneRank !== -1)
                 return +1;
             else {
-                const aAtomNameRank = atomNameRanks[a.atomName.replaceAll(/\d+/g, '').slice(0, 1)];
-                const bAtomNameRank = atomNameRanks[b.atomName.replaceAll(/\d+/g, '').slice(0, 1)];
-                if (aAtomNameRank === undefined)
-                    throw new Error(`Unexpected atom element ${a.atomElement} name ${a.atomName}`);
-                if (bAtomNameRank === undefined)
-                    throw new Error(`Unexpected atom element ${b.atomElement} name ${b.atomName}`);
-                if (aAtomNameRank !== bAtomNameRank)
-                    return aAtomNameRank - bAtomNameRank;
+                const aElement = a.atomElement.replaceAll(/\d+/g, '');
+                const bElement = b.atomElement.replaceAll(/\d+/g, '');
+                const aRemoteness = a.atomName.replaceAll(/\d+/g, '').slice(0, 1);
+                const bRemoteness = b.atomName.replaceAll(/\d+/g, '').slice(0, 1);
+                const aAtomNameRank = atomNameRanks[aRemoteness];
+                const bAtomNameRank = atomNameRanks[bRemoteness];
+                if (aAtomNameRank === undefined || bAtomNameRank === undefined) {
+                    return a.atomName.localeCompare(b.atomName);
+                }
+                if (aElement !== 'H' && bElement !== 'H') {
+                    // Both atoms are not hydrogen
+                    if (aAtomNameRank !== bAtomNameRank)
+                        return aAtomNameRank - bAtomNameRank;
+                    else {
+                        const aAtomNameNum = parseInt(a.atomName.slice(1));
+                        const bAtomNameNum = parseInt(b.atomName.slice(1));
+                        if (aAtomNameNum !== bAtomNameNum)
+                            return aAtomNameNum - bAtomNameNum;
+                        return a.atomName.localeCompare(b.atomName);
+                    }
+                }
+                else if (a.atomElement !== 'H' && b.atomElement === 'H')
+                    return -1;
+                else if (a.atomElement === 'H' && b.atomElement !== 'H')
+                    return +1;
                 else {
-                    const aAtomNameNum = parseInt(a.atomName.slice(1));
-                    const bAtomNameNum = parseInt(b.atomName.slice(1));
-                    return aAtomNameNum - bAtomNameNum;
+                    // Both atoms are hydrogen
+                    if (aAtomNameRank !== bAtomNameRank)
+                        return aAtomNameRank - bAtomNameRank;
+                    else {
+                        const aAtomNameNum = parseInt(a.atomName.slice(1));
+                        const bAtomNameNum = parseInt(b.atomName.slice(1));
+                        return aAtomNameNum - bAtomNameNum;
+                    }
                 }
             }
         }

package/src/pdb/format/types-base.js.map

@@ -1 +1 @@
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package/src/types/index.d.ts

@@ -1,12 +1,6 @@
 import * as DG from 'datagrok-api/dg';
-import './helm';
-import * as org from 'org';
-import PolymerType = org.helm.PolymerType;
-import HelmType = org.helm.HelmType;
-import MonomerType = org.helm.MonomerType;
-import WebEditorMonomer = org.helm.WebEditorMonomer;
-export { WebEditorMonomer, PolymerType, HelmType, MonomerType };
 import { Observable } from 'rxjs';
+import { IWebEditorMonomer, MonomerType, PolymerType } from '../helm/types';
 import { HELM_REQUIRED_FIELD as REQ, HELM_RGROUP_FIELDS as RGP, HELM_OPTIONAL_FIELDS as OPT, HELM_POLYMER_TYPE } from '../utils/const';
 export type RGroup = {
     [RGP.CAP_GROUP_SMILES]: string;
@@ -31,7 +25,7 @@ export type Monomer = {
         [property: string]: any;
     };
     lib?: IMonomerLib;
-    wem?: WebEditorMonomer;
+    wem?: IWebEditorMonomer;
 };
 export type MonomerLibSummaryType = {
     [polymerType: string]: number;
@@ -39,7 +33,7 @@ export type MonomerLibSummaryType = {
 export interface IMonomerLib {
     get source(): string | undefined;
     get error(): string | undefined;
-    getMonomer(polymerType: PolymerType, monomerSymbol: string): Monomer | null;
+    getMonomer(polymerType: PolymerType | null, monomerSymbol: string): Monomer | null;
     addMissingMonomer(polymerType: PolymerType, monomerSymbol: string): Monomer;
     getMonomerMolsByPolymerType(polymerType: PolymerType): {
         [monomerSymbol: string]: string;

package/src/types/index.d.ts.map

@@ -1 +1 @@
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package/src/types/index.js

@@ -1,4 +1,3 @@
-import './helm';
 import { ALPHABET } from '../utils/macromolecule';
 export const alphabetPolymerTypes = {
     [ALPHABET.DNA]: "RNA" /* HELM_POLYMER_TYPE.RNA */,

package/src/types/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["index.ts"],"names":[],"mappings":"AAWA,OAAO,EAAC,QAAQ,EAAC,MAAM,wBAAwB,CAAC;AAyDhD,MAAM,CAAC,MAAM,oBAAoB,GAAG;IAClC,CAAC,QAAQ,CAAC,GAAG,CAAC,mCAAuB;IACrC,CAAC,QAAQ,CAAC,GAAG,CAAC,mCAAuB;IACrC,CAAC,QAAQ,CAAC,EAAE,CAAC,2CAA2B;IACxC,CAAC,QAAQ,CAAC,EAAE,CAAC,2CAA2B;CACzC,CAAC"}

package/src/utils/cell-renderer-async-base.d.ts

@@ -42,7 +42,7 @@ export declare abstract class RenderServiceBase<TProps extends PropsBase, TAux>
     protected toLog(): string;
     get errorCount(): number;
     /** Disposes MolstarViewer to free WebGL context */
-    abstract reset(): Promise<void>;
+    reset(): Promise<void>;
     /** Queues render tasks
      * @param consumerId   Identifier of the consumer of this render service
      * @param task         Task to render

package/src/utils/cell-renderer-async-base.d.ts.map

@@ -1 +1 @@
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package/src/utils/cell-renderer-async-base.js

@@ -37,6 +37,10 @@ export class RenderServiceBase {
         return `${this.constructor.name}<${this.viewerId}>`;
     }
     get errorCount() { return this._errorCount; }
+    /** Disposes MolstarViewer to free WebGL context */
+    async reset() {
+        this._errorCount = 0;
+    }
     /** Queues render tasks
      * @param consumerId   Identifier of the consumer of this render service
      * @param task         Task to render

package/src/utils/cell-renderer-async-base.js.map

@@ -1 +1 @@
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package/src/utils/const.d.ts

@@ -1,11 +1,6 @@
-import '../types/helm';
-import * as org from 'org';
-import PolymerTypes = org.helm.PolymerTypes;
-import HelmTypes = org.helm.HelmTypes;
-import MonomerTypes = org.helm.MonomerTypes;
-export { PolymerTypes, HelmTypes, MonomerTypes };
-import HELM_POLYMER_TYPE = org.helm.PolymerTypes;
-import HELM_MONOMER_TYPE = org.helm.MonomerTypes;
+import { MonomerTypes, PolymerTypes } from '../helm/consts';
+import HELM_POLYMER_TYPE = PolymerTypes;
+import HELM_MONOMER_TYPE = MonomerTypes;
 import { RGroup } from '../types';
 export { HELM_POLYMER_TYPE, HELM_MONOMER_TYPE };
 /** Required HELM library monomer fields:
@@ -62,7 +57,7 @@ export declare const jsonSdfMonomerLibDict: {
     symbol: string;
 };
 export declare const DUMMY_MONOMER: {
-    monomerType: "Backbone" | "Branch" | "Terminal";
+    monomerType: "Backbone" | "Branch" | "Terminal" | "Undefined";
     smiles: string;
     name: string;
     author: string;
@@ -71,7 +66,7 @@ export declare const DUMMY_MONOMER: {
     rgroups: RGroup[];
     createDate: null;
     id: number;
-    polymerType: "G" | "RNA" | "PEPTIDE" | "CHEM" | "BLOB";
+    polymerType: "G" | "PEPTIDE" | "RNA" | "CHEM" | "BLOB";
     symbol: string;
 };
 export declare const MONOMER_ENCODE_MIN = 256;

package/src/utils/const.d.ts.map

@@ -1 +1 @@
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package/src/utils/const.js

@@ -1,4 +1,3 @@
-import '../types/helm';
 // core fields of HELM library object used in toAtomicLevel function
 export const HELM_CORE_FIELDS = [
     "symbol" /* HELM_FIELDS.SYMBOL */,

package/src/utils/const.js.map

@@ -1 +1 @@
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package/src/utils/generator.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"generator.d.ts","sourceRoot":"","sources":["generator.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAItC,OAAO,EAAC,QAAQ,EAAe,QAAQ,EAAO,MAAM,iBAAiB,CAAC;AAGtE,OAAO,EAAC,WAAW,EAAC,MAAM,gBAAgB,CAAC;AAG3C,wBAAgB,qBAAqB,IAAI,EAAE,CAAC,MAAM,EAAE,CAQnD;AAED,sGAAsG;AACtG,wBAAgB,oBAAoB,CAAC,MAAM,GAAE,MAAgB,GAAG,EAAE,CAAC,MAAM,EAAE,CAc1E;AAED,wBAAgB,qBAAqB,CACnC,QAAQ,GAAE,QAA6B,EAAE,QAAQ,GAAE,QAAsB,EACzE,SAAS,GAAE,MAAM,GAAG,SAA+D,EACnF,UAAU,GAAE,WAAW,GAAG,SAAqB,EAC/C,OAAO,GAAE,MAAc,EAAE,QAAQ,GAAE,MAAY,EAAE,SAAS,GAAE,MAAgB,GAC3E,EAAE,CAAC,MAAM,CAqBX"}

package/src/utils/generator.js

@@ -1,6 +1,6 @@
 import * as DG from 'datagrok-api/dg';
-import { ALPHABET, getAlphabet, NOTATION, TAGS } from './macromolecule';
 import wu from 'wu';
+import { ALPHABET, getAlphabet, NOTATION, TAGS } from './macromolecule';
 import { GapOriginals, SeqHandler } from './seq-handler';
 import { StringListSeqSplitted } from './macromolecule/utils';
 export function generateManySequences() {

package/src/utils/generator.js.map

@@ -1 +1 @@
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+{"version":3,"file":"generator.js","sourceRoot":"","sources":["generator.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAEtC,OAAO,EAAE,MAAM,IAAI,CAAC;AAEpB,OAAO,EAAC,QAAQ,EAAE,WAAW,EAAE,QAAQ,EAAE,IAAI,EAAC,MAAM,iBAAiB,CAAC;AACtE,OAAO,EAAC,YAAY,EAAE,UAAU,EAAC,MAAM,eAAe,CAAC;AACvD,OAAO,EAAC,qBAAqB,EAAC,MAAM,uBAAuB,CAAC;AAI5D,MAAM,UAAU,qBAAqB;IACnC,MAAM,OAAO,GAAgB,EAAE,CAAC;IAChC,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,MAAM,CAAC,QAAQ,CAAC,QAAQ,EAAE,KAAK,EAC7C,IAAI,KAAK,CAAC,EAAE,IAAI,CAAC,CAAC,CAAC,IAAI,CACrB,0FAA0F,CAAC,CAAC,CAC/F,CAAC;IACF,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,MAAM,CAAC,QAAQ,CAAC,EAAE,CAAC,WAAW,CAAC,KAAK,EAAE,UAAU,EAAE,IAAI,KAAK,CAAC,EAAE,IAAI,CAAC,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC;IACrG,OAAO,OAAO,CAAC;AACjB,CAAC;AAED,sGAAsG;AACtG,MAAM,UAAU,oBAAoB,CAAC,SAAiB,EAAE,IAAI,CAAC;IAC3D,MAAM,YAAY,GAChB,4DAA4D,CAAC,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,MAAM,GAAG,EAAE,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC;IAC3G,MAAM,MAAM,GAAG,EAAE,CAAC,MAAM,CAAC,QAAQ,CAAC,EAAE,CAAC,WAAW,CAAC,MAAM,EAAE,KAAK,EAAE,IAAI,KAAK,CAAC,EAAE,IAAI,CAAC,CAAC,CAAC,IAAI,CAAC,YAAY,CAAC,CAAC,CAAC;IACvG,MAAM,CAAC,OAAO,GAAG,EAAE,CAAC,OAAO,CAAC,aAAa,CAAC;IAC1C,MAAM,CAAC,MAAM,CAAC,EAAE,CAAC,IAAI,CAAC,KAAK,EAAE,QAAQ,CAAC,SAAS,CAAC,CAAC;IACjD,MAAM,CAAC,MAAM,CAAC,IAAI,CAAC,SAAS,EAAE,GAAG,CAAC,CAAC;IACnC,MAAM,CAAC,MAAM,CAAC,IAAI,CAAC,QAAQ,EAAE,QAAQ,CAAC,EAAE,CAAC,CAAC;IAC1C,MAAM,CAAC,MAAM,CAAC,IAAI,CAAC,mBAAmB,EAAE,MAAM,CAAC,CAAC;IAEhD,MAAM,OAAO,GAAgB,EAAE,CAAC;IAChC,OAAO,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC;IACrB,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,MAAM,CAAC,QAAQ,CAAC,EAAE,CAAC,WAAW,CAAC,KAAK,EAAE,UAAU,EAAE,IAAI,KAAK,CAAC,EAAE,IAAI,CAAC,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC;IACrG,OAAO,OAAO,CAAC;AACjB,CAAC;AAED,MAAM,UAAU,qBAAqB,CACnC,WAAqB,QAAQ,CAAC,SAAS,EAAE,WAAqB,QAAQ,CAAC,EAAE,EACzE,YAAgC,CAAC,QAAQ,KAAK,QAAQ,CAAC,SAAS,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,SAAS,CAAC,EACnF,aAAsC,SAAS,EAC/C,UAAkB,KAAK,EAAE,WAAmB,GAAG,EAAE,YAAoB,EAAE,IAAI,CAAC;IAE5E,MAAM,WAAW,GAAa,QAAQ,KAAK,QAAQ,CAAC,EAAE,CAAC,CAAC;QACtD,UAAU,EAAE,uBAAuB,sCAAsB,IAAI,EAAE,CAAC,CAAC,CAAC,KAAK,CAAC,IAAI,CAAC,WAAW,CAAC,QAAQ,CAAC,CAAC,CAAC;IACtG,MAAM,YAAY,GAAG,WAAW,CAAC,MAAM,CAAC;IAExC,MAAM,GAAG,GAAG,EAAE,CAAC,MAAM,CAAC,QAAQ,CAAC,EAAE,CAAC,WAAW,CAAC,MAAM,EAAE,OAAO,EAAE,QAAQ,CAAC,CAAC;IACzE,GAAG,CAAC,OAAO,GAAG,EAAE,CAAC,OAAO,CAAC,aAAa,CAAC;IACvC,GAAG,CAAC,MAAM,CAAC,EAAE,CAAC,IAAI,CAAC,KAAK,EAAE,QAAQ,CAAC,CAAC;IACpC,GAAG,CAAC,MAAM,CAAC,IAAI,CAAC,QAAQ,EAAE,QAAQ,CAAC,CAAC;IACpC,IAAI,QAAQ,IAAI,QAAQ,CAAC,SAAS;QAAE,GAAG,CAAC,MAAM,CAAC,IAAI,CAAC,SAAS,EAAE,SAAU,CAAC,CAAC;IAE3E,MAAM,EAAE,GAAG,UAAU,CAAC,SAAS,CAAC,GAAG,CAAC,CAAC;IACrC,KAAK,IAAI,IAAI,GAAG,CAAC,EAAE,IAAI,GAAG,QAAQ,EAAE,IAAI,EAAE,EAAE;QAC1C,MAAM,QAAQ,GAAa,EAAE,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,SAAS,CAAC;aACnD,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,GAAG,OAAO,WAAW,CAAC,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,MAAM,EAAE,GAAG,YAAY,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;aAC7E,OAAO,EAAE,CAAC;QACb,MAAM,GAAG,GAAG,EAAE,CAAC,MAAM,CAAC,IAAI,qBAAqB,CAAC,QAAQ,EAAE,YAAY,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC;QACnF,GAAG,CAAC,GAAG,CAAC,IAAI,EAAE,GAAG,CAAC,CAAC;KACpB;IAED,OAAO,GAAG,CAAC;AACb,CAAC"}

package/src/viewers/helm-service.d.ts

@@ -1,13 +1,12 @@
 import * as DG from 'datagrok-api/dg';
-import '../types/jsdraw2';
-import * as JSDraw2 from 'JSDraw2';
+import { HelmType, Mol } from '../helm/types';
 import { PropsBase, RenderServiceBase } from '../utils/cell-renderer-async-base';
 export declare class HelmProps extends PropsBase {
     readonly helm: string;
     constructor(helm: string, backColor: number, width: number, height: number);
 }
 export type HelmAux = {
-    /** The molecule made of atoms (monomers) and bonds */ mol: JSDraw2.IEditorMol;
+    /** The molecule made of atoms (monomers) and bonds */ mol: Mol<HelmType>;
     /** SVG bounding box */ bBox: DG.Rect;
     /** Cell box {0, 0, w, h} */ cBox: DG.Rect;
 };

package/src/viewers/helm-service.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"helm-service.d.ts","sourceRoot":"","sources":["helm-service.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAEtC,OAAO,kBAAkB,CAAC;AAC1B,OAAO,KAAK,OAAO,MAAM,SAAS,CAAC;AAEnC,OAAO,EAAC,SAAS,EAAE,iBAAiB,EAAC,MAAM,mCAAmC,CAAC;AAE/E,qBAAa,SAAU,SAAQ,SAAS;aAEpB,IAAI,EAAE,MAAM;gBAAZ,IAAI,EAAE,MAAM,EAC5B,SAAS,EAAE,MAAM,EAAE,KAAK,EAAE,MAAM,EAAE,MAAM,EAAE,MAAM;CAInD;AAED,MAAM,MAAM,OAAO,GAAG;IACpB,sDAAsD,CAAC,GAAG,EAAE,OAAO,CAAC,UAAU,CAAC;IAC/E,uBAAuB,CAAC,IAAI,EAAE,EAAE,CAAC,IAAI,CAAC;IACtC,4BAA4B,CAAC,IAAI,EAAE,EAAE,CAAC,IAAI,CAAC;CAC5C,CAAA;AAED,8BAAsB,eAAgB,SAAQ,iBAAiB,CAAC,SAAS,EAAE,OAAO,CAAC;CAAG;AAEtF,wBAAsB,cAAc,IAAI,OAAO,CAAC,eAAe,CAAC,CAO/D"}
+{"version":3,"file":"helm-service.d.ts","sourceRoot":"","sources":["helm-service.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAGtC,OAAO,EAAC,QAAQ,EAAE,GAAG,EAAC,MAAM,eAAe,CAAC;AAC5C,OAAO,EAAC,SAAS,EAAE,iBAAiB,EAAC,MAAM,mCAAmC,CAAC;AAE/E,qBAAa,SAAU,SAAQ,SAAS;aAEpB,IAAI,EAAE,MAAM;gBAAZ,IAAI,EAAE,MAAM,EAC5B,SAAS,EAAE,MAAM,EAAE,KAAK,EAAE,MAAM,EAAE,MAAM,EAAE,MAAM;CAInD;AAED,MAAM,MAAM,OAAO,GAAG;IACpB,sDAAsD,CAAC,GAAG,EAAE,GAAG,CAAC,QAAQ,CAAC,CAAC;IAC1E,uBAAuB,CAAC,IAAI,EAAE,EAAE,CAAC,IAAI,CAAC;IACtC,4BAA4B,CAAC,IAAI,EAAE,EAAE,CAAC,IAAI,CAAC;CAC5C,CAAA;AAED,8BAAsB,eAAgB,SAAQ,iBAAiB,CAAC,SAAS,EAAE,OAAO,CAAC;CAAG;AAEtF,wBAAsB,cAAc,IAAI,OAAO,CAAC,eAAe,CAAC,CAO/D"}

package/src/viewers/helm-service.js

@@ -1,5 +1,4 @@
 import * as DG from 'datagrok-api/dg';
-import '../types/jsdraw2';
 import { PropsBase, RenderServiceBase } from '../utils/cell-renderer-async-base';
 export class HelmProps extends PropsBase {
     constructor(helm, backColor, width, height) {

package/src/viewers/helm-service.js.map

@@ -1 +1 @@
-{"version":3,"file":"helm-service.js","sourceRoot":"","sources":["helm-service.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAEtC,OAAO,kBAAkB,CAAC;AAG1B,OAAO,EAAC,SAAS,EAAE,iBAAiB,EAAC,MAAM,mCAAmC,CAAC;AAE/E,MAAM,OAAO,SAAU,SAAQ,SAAS;IACtC,YACkB,IAAY,EAC5B,SAAiB,EAAE,KAAa,EAAE,MAAc;QAEhD,KAAK,CAAC,SAAS,EAAE,KAAK,EAAE,MAAM,CAAC,CAAC;QAHhB,SAAI,GAAJ,IAAI,CAAQ;IAI9B,CAAC;CACF;AAQD,MAAM,OAAgB,eAAgB,SAAQ,iBAAqC;CAAG;AAEtF,MAAM,CAAC,KAAK,UAAU,cAAc;IAClC,MAAM,QAAQ,GAAG,EAAE,CAAC,IAAI,CAAC,IAAI,CAAC,EAAC,OAAO,EAAE,MAAM,EAAE,IAAI,EAAE,gBAAgB,EAAC,CAAC,CAAC;IACzE,IAAI,QAAQ,CAAC,MAAM,KAAK,CAAC;QACvB,MAAM,IAAI,KAAK,CAAC,qDAAqD,CAAC,CAAC;IAEzE,MAAM,GAAG,GAAoB,CAAC,MAAM,QAAQ,CAAC,CAAC,CAAC,CAAC,OAAO,EAAE,CAAC,IAAI,EAAE,CAAC,CAAC,mBAAmB,EAAqB,CAAC;IAC3G,OAAO,GAAG,CAAC;AACb,CAAC"}
+{"version":3,"file":"helm-service.js","sourceRoot":"","sources":["helm-service.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAItC,OAAO,EAAC,SAAS,EAAE,iBAAiB,EAAC,MAAM,mCAAmC,CAAC;AAE/E,MAAM,OAAO,SAAU,SAAQ,SAAS;IACtC,YACkB,IAAY,EAC5B,SAAiB,EAAE,KAAa,EAAE,MAAc;QAEhD,KAAK,CAAC,SAAS,EAAE,KAAK,EAAE,MAAM,CAAC,CAAC;QAHhB,SAAI,GAAJ,IAAI,CAAQ;IAI9B,CAAC;CACF;AAQD,MAAM,OAAgB,eAAgB,SAAQ,iBAAqC;CAAG;AAEtF,MAAM,CAAC,KAAK,UAAU,cAAc;IAClC,MAAM,QAAQ,GAAG,EAAE,CAAC,IAAI,CAAC,IAAI,CAAC,EAAC,OAAO,EAAE,MAAM,EAAE,IAAI,EAAE,gBAAgB,EAAC,CAAC,CAAC;IACzE,IAAI,QAAQ,CAAC,MAAM,KAAK,CAAC;QACvB,MAAM,IAAI,KAAK,CAAC,qDAAqD,CAAC,CAAC;IAEzE,MAAM,GAAG,GAAoB,CAAC,MAAM,QAAQ,CAAC,CAAC,CAAC,CAAC,OAAO,EAAE,CAAC,IAAI,EAAE,CAAC,CAAC,mBAAmB,EAAqB,CAAC;IAC3G,OAAO,GAAG,CAAC;AACb,CAAC"}

package/src/types/helm-web-editor.d.ts

@@ -1,26 +0,0 @@
-export interface IEditorOptions {
-    width: number;
-    height: number;
-}
-export interface IEditor {
-    get options(): IEditorOptions;
-    get div(): HTMLDivElement;
-    get m(): IEditorMol;
-    resize(width: number, height: number): void;
-    /** Clear all contents */ clear(redraw: boolean, fireevents: boolean): void;
-    /** Resets and clears undo and redo buffers */ reset(): void;
-    setData(data: string, format: string): void;
-}
-export interface IEditorMol {
-    get atoms(): IEditorMolAtom[];
-    clone(selectedOnly: boolean): IEditorMol;
-}
-export interface IEditorMolAtom {
-    get p(): IEditorPoint;
-    get elem(): string;
-}
-export interface IEditorPoint {
-    get x(): number;
-    get y(): number;
-}
-//# sourceMappingURL=helm-web-editor.d.ts.map

package/src/types/helm-web-editor.d.ts.map

@@ -1 +0,0 @@
-{"version":3,"file":"helm-web-editor.d.ts","sourceRoot":"","sources":["helm-web-editor.ts"],"names":[],"mappings":"AAIA,MAAM,WAAW,cAAc;IAC7B,KAAK,EAAE,MAAM,CAAC;IACd,MAAM,EAAE,MAAM,CAAC;CAChB;AAED,MAAM,WAAW,OAAO;IACtB,IAAI,OAAO,IAAI,cAAc,CAAC;IAE9B,IAAI,GAAG,IAAI,cAAc,CAAC;IAC1B,IAAI,CAAC,IAAI,UAAU,CAAC;IAEpB,MAAM,CAAC,KAAK,EAAE,MAAM,EAAE,MAAM,EAAE,MAAM,GAAG,IAAI,CAAC;IAC5C,yBAAyB,CAAC,KAAK,CAAC,MAAM,EAAE,OAAO,EAAE,UAAU,EAAE,OAAO,GAAG,IAAI,CAAC;IAC5E,8CAA8C,CAAC,KAAK,IAAI,IAAI,CAAC;IAC7D,OAAO,CAAC,IAAI,EAAE,MAAM,EAAE,MAAM,EAAE,MAAM,GAAG,IAAI,CAAC;CAC7C;AAED,MAAM,WAAW,UAAU;IACzB,IAAI,KAAK,IAAI,cAAc,EAAE,CAAC;IAE9B,KAAK,CAAC,YAAY,EAAE,OAAO,GAAG,UAAU,CAAC;CAC1C;AAED,MAAM,WAAW,cAAc;IAC7B,IAAI,CAAC,IAAI,YAAY,CAAC;IAEtB,IAAI,IAAI,IAAI,MAAM,CAAC;CACpB;AAED,MAAM,WAAW,YAAY;IAC3B,IAAI,CAAC,IAAI,MAAM,CAAC;IAEhB,IAAI,CAAC,IAAI,MAAM,CAAC;CACjB"}

package/src/types/helm-web-editor.js

@@ -1,2 +0,0 @@
-export {};
-//# sourceMappingURL=helm-web-editor.js.map

package/src/types/helm-web-editor.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"helm-web-editor.js","sourceRoot":"","sources":["helm-web-editor.ts"],"names":[],"mappings":""}

package/src/types/helm.d.ts

@@ -1,122 +0,0 @@
-declare module 'scil' {
-    function apply<T>(dest: T, atts: Partial<T>, defaults?: Partial<T>): void;
-    interface IUtils {
-        alert: (s: string) => void;
-        isNullOrEmpty(s: string): boolean;
-        endswith(s: string, token: string, casesensitive?: boolean): boolean;
-    }
-    const Utils: IUtils;
-}
-declare module 'org' {
-    import * as JSDraw2 from 'JSDraw2';
-    namespace helm {
-        type WebEditorRGroups = {
-            [group: string]: string;
-        };
-        type WebEditorMonomer = {
-            /** symbol */ id: string;
-            /** name */ n?: string;
-            /** natural analog */ na?: string;
-            /** polymer type */ type?: PolymerType;
-            /** monomer type */ mt?: MonomerType;
-            /** molfile */ m?: string;
-            /** substituents */ at: WebEditorRGroups;
-            /** number of substituents */ get rs(): number;
-        };
-        interface IPistoiaBase {
-            get T(): string;
-        }
-        interface IMonomer {
-        }
-        interface IAppOptions {
-            showabout: boolean;
-            mexfontsize: string;
-            mexrnapinontab: boolean;
-            topmargin: number;
-            mexmonomerstab: boolean;
-            sequenceviewonly: boolean;
-            mexfavoritefirst: boolean;
-            mexfilter: boolean;
-        }
-        interface IWebEditorHelm {
-            setSequence(seq: string, format: string, sugar?: string, linker?: string, append?: boolean, separator?: string): boolean;
-        }
-        interface IWebEditorCanvas {
-            get helm(): IWebEditorHelm;
-            getHelm(ret: boolean): string;
-            resize(width: number, height: number): void;
-        }
-        interface IWebEditorSizes {
-            get rightwidth(): number;
-            get topheight(): number;
-            get bottomheight(): number;
-        }
-        interface IWebEditorAppProperties {
-            parent: HTMLElement;
-        }
-        interface IWebEditorApp {
-            notation: HTMLElement;
-            sequence: HTMLElement;
-            properties: IWebEditorAppProperties;
-            get toolbarheight(): number;
-            get canvas(): IWebEditorCanvas;
-            get structureview(): any;
-            get mex(): any;
-            calculateSizes(): IWebEditorSizes;
-        }
-        interface IApp {
-            new (host: HTMLDivElement, options: IAppOptions): IWebEditorApp;
-        }
-        interface IMolViewer {
-            molscale: number;
-        }
-        interface IMonomers {
-            addOneMonomer(monomer: IMonomer): void;
-            getMonomer(a: JSDraw2.Atom<HelmType> | HelmType, elem: string | undefined): WebEditorMonomer | null;
-            getMonomerSet(biotype: string): any;
-            clear(): void;
-        }
-        interface IWebEditorIO {
-            trimBracket(s: string): string;
-        }
-        const enum MonomerTypes {
-            BACKBONE = "Backbone",
-            BRANCH = "Branch",
-            TERMINAL = "Terminal"
-        }
-        /** 'Backbone' | 'Branch' | 'Terminal' */
-        type MonomerType = `${MonomerTypes}`;
-        const enum PolymerTypes {
-            RNA = "RNA",
-            PEPTIDE = "PEPTIDE",
-            CHEM = "CHEM",
-            BLOB = "BLOB",
-            G = "G"
-        }
-        /** 'RNA' | 'PEPTIDE' | 'CHEM' | 'BLOB' | 'G' */
-        type PolymerType = `${PolymerTypes}`;
-        const enum HelmTypes {
-            BASE = "HELM_BASE",
-            SUGAR = "HELM_SUGAR",
-            LINKER = "HELM_LINKER",
-            AA = "HELM_AA",
-            CHEM = "HELM_CHEM",
-            BLOB = "HELM_BLOB",
-            NUCLEOTIDE = "HELM_NUCLETIDE"
-        }
-        /** 'HELM_BASE' | 'HELM_SUGAR' | 'HELM_LINKER' | 'HELM_AA' | 'HELM_CHEM' | 'HELM_BLOB' | 'HELM_NUCLETIDE' */
-        type HelmType = `${HelmTypes}`;
-        type IHelmTypes = Record<HelmTypes, HelmType>;
-        interface IOrgHelmWebEditor {
-            readonly App: IApp;
-            readonly Monomers: IMonomers;
-            readonly MolViewer: IMolViewer;
-            readonly IO: IWebEditorIO;
-            kCaseSensitive: boolean;
-            readonly HELM: IHelmTypes;
-            monomerTypeList(): string[];
-        }
-        const webeditor: IOrgHelmWebEditor;
-    }
-}
-//# sourceMappingURL=helm.d.ts.map

package/src/types/helm.d.ts.map

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package/src/types/helm.js

@@ -1,2 +0,0 @@
-"use strict";
-//# sourceMappingURL=helm.js.map

package/src/types/helm.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"helm.js","sourceRoot":"","sources":["helm.ts"],"names":[],"mappings":""}

package/src/types/jsdraw2.d.ts

@@ -1,80 +0,0 @@
-declare module 'JSDraw2' {
-    interface IEditorOptions {
-        width: number;
-        height: number;
-        skin: string;
-        viewonly: boolean;
-    }
-    interface IEditorPoint {
-        get x(): number;
-        get y(): number;
-    }
-    interface IAtomBio {
-        type: 'HELM_BASE' | 'HELM_SUGAR' | 'HELM_LINKER' | 'HELM_AA' | 'HELM_CHEM' | 'HELM_BLOB' | 'HELM_NUCLETIDE';
-    }
-    interface IEditorMolAtom {
-        get p(): IEditorPoint;
-        get elem(): string;
-        get bio(): IAtomBio;
-    }
-    interface IEditorMolBond {
-        get a1(): IEditorMolAtom;
-        get a2(): IEditorMolAtom;
-        get type(): number;
-    }
-    interface IEditorMol {
-        get atoms(): IEditorMolAtom[];
-        get bonds(): IEditorMolBond[];
-        clone(selectedOnly: boolean): IEditorMol;
-    }
-    class Editor {
-        get options(): IEditorOptions;
-        get div(): HTMLDivElement;
-        get m(): IEditorMol;
-        resize(width: number, height: number): void;
-        /** Clear all contents */ clear(redraw: boolean, fireevents: boolean): void;
-        /** Resets and clears undo and redo buffers */ reset(): void;
-        setData(data: string, format: string): void;
-        setHelm(helm: string): void;
-        setSize(w: number, h: number): void;
-        getMolfile(): string;
-        constructor(host: HTMLElement, options?: Partial<IEditorOptions>);
-    }
-    interface IPistoiaBase {
-        get T(): string;
-    }
-    const enum BioTypes {
-        AA = "AA",
-        ANTIBODY = "ANTIBODY",
-        PROTEIN = "PROTEIN",
-        GENE = "GENE",
-        DNA = "DNA",
-        RNA = "RNA",
-        BASE_DNA = "BASEDNA",
-        BASE_RNA = "BASERNA"
-    }
-    type BioType = `${BioTypes}`;
-    interface IBio<TBio> {
-        id?: number | null;
-        type: TBio;
-        ambiguity?: string | null;
-        annotation?: string | null;
-        annotationshowright?: string | null;
-    }
-    abstract class JsAtom<TBio> implements IPistoiaBase {
-        get T(): 'ATOM';
-        get p(): Point;
-        get elem(): string;
-        get bio(): IBio<TBio>;
-    }
-    class Atom<TBio> extends JsAtom<TBio> {
-        biotype(): TBio;
-        constructor(p: Point, elem: string, bio: IBio<TBio>);
-    }
-    class Point {
-        x: number;
-        y: number;
-        constructor(x: number, y: number);
-    }
-}
-//# sourceMappingURL=jsdraw2.d.ts.map

package/src/types/jsdraw2.d.ts.map

@@ -1 +0,0 @@
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package/src/types/jsdraw2.js

@@ -1,2 +0,0 @@
-"use strict";
-//# sourceMappingURL=jsdraw2.js.map

package/src/types/jsdraw2.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"jsdraw2.js","sourceRoot":"","sources":["jsdraw2.ts"],"names":[],"mappings":""}