@datagrok-libraries/bio 5.42.7 → 5.42.9

package/CHANGELOG.md

@@ -1,5 +1,17 @@
 # bio changelog
 
+## 5.42.9
+
+### Features
+
+* HWE option for continuous monomer numbering
+* Add HelmInput mouse events redraw, showTooltip
+* Bump HWE dependencies versions
+
+## 5.42.8 (2024-08-14)
+
+Fix monomer substitution matrix calculation
+
 ## 5.42.7 (2024-08-12)
 
 ### Features

package/package.json

@@ -8,7 +8,7 @@
     "access": "public"
   },
   "friendlyName": "Datagrok bio library",
-  "version": "5.42.7",
+  "version": "5.42.9",
   "description": "Bio utilities, types supporting Macromolecule, Molecule3D data",
   "dependencies": {
     "@datagrok-libraries/gridext": "^1.3.71",
@@ -26,8 +26,8 @@
     "wu": "latest"
   },
   "devDependencies": {
-    "@datagrok-libraries/helm-web-editor": "^1.1.7",
-    "@datagrok-libraries/js-draw-lite": "^0.0.5",
+    "@datagrok-libraries/helm-web-editor": "^1.1.8",
+    "@datagrok-libraries/js-draw-lite": "^0.0.6",
     "@types/signals": "1.0.1",
     "@types/three": "^0.159.0",
     "@types/uuid": "^9.0.1",
@@ -46,7 +46,7 @@
     "link-utils": "npm link @datagrok-libraries/utils",
     "link-all": "npm link datagrok-api @datagrok-libraries/gridext @datagrok-libraries/utils @datagrok-libraries/ml",
     "build-bio": "git clean -f -X -d ./src && tsc",
-    "build": "git clean -f -X -d ./src && tsc",
+    "build": "tsc",
     "build-all": "npm --prefix ./../../js-api run build && npm --prefix ./../../libraries/gridext run build && npm --prefix ./../../libraries/utils run build && npm --prefix ./../../libraries/ml run build && npm run build",
     "lint": "eslint \"./src/**/*.ts\"",
     "lint-fix": "eslint \"./src/**/*.ts\" --fix"

package/src/helm/consts.d.ts

@@ -1,3 +1,4 @@
 import { HelmTypes, MonomerTypes, PolymerTypes } from '@datagrok-libraries/js-draw-lite/src/types/org';
-export { HelmTypes, MonomerTypes, PolymerTypes };
+import { MonomerNumberingTypes } from '@datagrok-libraries/helm-web-editor/src/types/org-helm';
+export { HelmTypes, MonomerTypes, PolymerTypes, MonomerNumberingTypes };
 //# sourceMappingURL=consts.d.ts.map

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

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package/src/helm/consts.js.map

@@ -1 +1 @@
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package/src/helm/helm-helper.d.ts

@@ -1,21 +1,29 @@
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 import type { App } from '@datagrok-libraries/helm-web-editor/helm/App';
-import { MonomersFuncs, HelmMol, HelmString, IHelmWebEditor } from './types';
+import { MonomersFuncs, HelmMol, HelmString, IHelmWebEditor, HelmAtom, IHelmDrawOptions } from './types';
 import { IMonomerLib } from '../types/index';
-export type IHelmInputInitOptions = ui.input.IInputInitOptions<HelmString | HelmMol>;
+import { Observable } from 'rxjs';
+export type IHelmInputInitOptions = ui.input.IInputInitOptions<HelmString | HelmMol> & {
+    editable: boolean;
+};
 export declare abstract class HelmInputBase extends DG.JsInputBase<HelmString> {
     abstract get molValue(): HelmMol;
     abstract set molValue(value: HelmMol);
+    abstract get onMouseMove(): Observable<MouseEvent>;
+    abstract get onClick(): Observable<MouseEvent>;
+    abstract redraw(): void;
+    abstract showTooltip(content: HTMLElement | string, a: HelmAtom): void;
 }
 export interface IHelmHelper {
     createHelmInput(name: string, options?: IHelmInputInitOptions): HelmInputBase;
-    createHelmWebEditor(host?: HTMLElement): IHelmWebEditor;
+    createHelmWebEditor(host?: HTMLElement, drawOptions?: Partial<IHelmDrawOptions>): IHelmWebEditor;
     createWebEditorApp(host: HTMLDivElement, helm?: string): App;
     get originalMonomersFuncs(): MonomersFuncs | null;
     buildMonomersFuncsFromLib(monomerLib: IMonomerLib): MonomersFuncs;
     overrideMonomersFuncs(monomersFuncs: MonomersFuncs): MonomersFuncs;
     revertOriginalMonomersFuncs(): MonomersFuncs;
+    getHoveredAtom(x: number, y: number, mol: HelmMol, height: number): HelmAtom | null;
 }
 export declare function getHelmHelper(): Promise<IHelmHelper>;
 declare module 'datagrok-api/ui' {

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

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

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

@@ -4,7 +4,7 @@ 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 { HelmAtom, HelmBond, HelmMol, HelmString, IOrgHelmWebEditor, IOrgHelmMonomers, GetMonomerFunc, GetMonomerResType, MonomersFuncs } from '@datagrok-libraries/helm-web-editor/src/types/org-helm';
+import type { HelmAtom, HelmBond, HelmMol, HelmEditor, HelmString, IOrgHelmWebEditor, IOrgHelmMonomers, GetMonomerFunc, GetMonomerResType, MonomersFuncs, IHelmDrawOptions } from '@datagrok-libraries/helm-web-editor/src/types/org-helm';
 import type { HweWindow } from '@datagrok-libraries/helm-web-editor/src/types';
 import type { MonomerExplorer } from '@datagrok-libraries/helm-web-editor/helm/MonomerExplorer';
 import type { App } from '@datagrok-libraries/helm-web-editor/helm/App';
@@ -15,8 +15,8 @@ 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, MonomerExplorer };
-export { HelmAtom, HelmBond, HelmMol, HelmString };
-export { IWebEditorMonomer, IMonomerColors, IOrgHelmWebEditor, IOrgHelmMonomers, App, Monomers, GetMonomerFunc, GetMonomerResType };
+export { HelmAtom, HelmBond, HelmMol, HelmEditor, HelmString };
+export { IWebEditorMonomer, IMonomerColors, IOrgHelmWebEditor, IOrgHelmMonomers, IHelmDrawOptions, App, Monomers, GetMonomerFunc, GetMonomerResType };
 export { DojoType, DojoxType };
 export { HweWindow, ScilModuleType, JSDraw2ModuleType, OrgType };
 export interface ISeqMonomer {
@@ -24,7 +24,7 @@ export interface ISeqMonomer {
     symbol: string;
 }
 export interface IHelmWebEditor {
-    get editor(): Editor<HelmType>;
+    get editor(): HelmEditor;
     get host(): HTMLDivElement;
     resizeEditor(width: number, height: number): void;
 }

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

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

@@ -211,7 +211,8 @@ export async function getMonomerSubstitutionMatrix(monomerSet, fingerprintType =
     const monomerLib = libHelper.getMonomerLib();
     const scoringMatrix = new Array(monomerSet.length).fill(0).map(() => new Array(monomerSet.length).fill(0));
     const alphabetIndexes = {};
-    const monomerMolecules = monomerSet.map((monomer) => monomerLib.getMonomer('PEPTIDE', monomer)?.smiles ?? '');
+    // note, below specifically boolean OR is used to get either molfile or smiles, because we want to skip '' molfiles
+    const monomerMolecules = monomerSet.map((monomer) => monomerLib.getMonomer('PEPTIDE', monomer)?.molfile || monomerLib.getMonomer('PEPTIDE', monomer)?.smiles || '');
     const fingerprintsFunc = DG.Func.find({ package: 'Chem', name: 'getFingerprints' })[0];
     if (!fingerprintsFunc) {
         console.warn('Function "Chem:getFingerprints" is not found in chem package. falling back to Morgan fingerprints');

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

@@ -1 +1 @@
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