@datagrok/helm 2.13.1 → 2.13.3

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@datagrok/helm",
   "friendlyName": "Helm",
-  "version": "2.13.1",
+  "version": "2.13.3",
   "author": {
     "name": "Maria Dolotova",
     "email": "mdolotova@datagrok.ai"
@@ -16,27 +16,28 @@
     "css/helm.css"
   ],
   "dependencies": {
-    "@datagrok-libraries/bio": "^5.61.1",
+    "@datagrok-libraries/bio": "^5.63.5",
     "@datagrok-libraries/chem-meta": "^1.2.9",
     "@datagrok-libraries/helm-web-editor": "^1.1.16",
     "@datagrok-libraries/utils": "^4.6.9",
     "cash-dom": "^8.1.1",
-    "datagrok-api": "^1.25.0",
+    "datagrok-api": "^1.26.0",
     "dayjs": "^1.10.6",
     "lru-cache": "^10.4.3",
     "rxjs": "^6.5.5",
-    "wu": "^2.1.0"
+    "wu": "^2.1.0",
+    "@datagrok-libraries/test": "^1.1.0"
   },
   "devDependencies": {
     "@datagrok-libraries/js-draw-lite": "^0.0.10",
     "@datagrok/bio": "^2.25.1",
-    "@datagrok/chem": "^1.13.0",
+    "@datagrok/chem": "^1.17.0",
     "@types/node": "17.0.45",
     "@types/webpack-env": "^1.18.5",
     "@types/wu": "^2.1.44",
     "@typescript-eslint/eslint-plugin": "^7.16.0",
     "@typescript-eslint/parser": "^7.16.0",
-    "datagrok-tools": "^4.14.65",
+    "datagrok-tools": "^5.0.0",
     "eslint": "^8.57.1",
     "eslint-config-google": "^0.14.0",
     "eslint-plugin-deprecation": "^3.0.0",
@@ -79,5 +80,8 @@
     "url": "https://github.com/datagrok-ai/public.git",
     "directory": "packages/Helm"
   },
-  "category": "Bioinformatics"
+  "category": "Bioinformatics",
+  "overrides": {
+    "datagrok-api": "$datagrok-api"
+  }
 }

package/src/helm-helper.ts

@@ -387,46 +387,87 @@ export class HelmHelper implements IHelmHelper {
     for (let aI: number = mol.atoms.length - 1; aI >= 0; --aI) {
       const a = mol.atoms[aI];
       if (a.elem === HELM_GAP_SYMBOL /* '*' - original */) {
-        const leftBondList: { aI: number, bI: number }[] = [];
-        const rightBondList: { aI: number, bI: number }[] = [];
+        // Collect all bonds connected to this gap atom, tracking which side the gap is on
+        const connectedBonds: { bI: number, gapSide: 1 | 2 }[] = [];
         for (let bI: number = mol.bonds.length - 1; bI >= 0; --bI) {
           const b = mol.bonds[bI];
-          if (b.a1 !== a && b.a2 === a) leftBondList.push({aI, bI});
-          if (b.a1 === a && b.a2 !== a) rightBondList.push({aI, bI});
+          if (b.a1 === a) connectedBonds.push({bI, gapSide: 1}); // gap is a1
+          else if (b.a2 === a) connectedBonds.push({bI, gapSide: 2}); // gap is a2
         }
-        if (leftBondList.length > 1 || rightBondList.length > 1)
-          throw new HelmNotSupportedError(`Removing a gap monomer #${aI} with more than two bonds is unsupported.`);
-
-        const lb = leftBondList[0];
-        const rb = rightBondList[0];
-        if (lb && !rb) {
-          mol.bonds.splice(lb.bI, 1);
-          mol.atoms.splice(lb.aI, 1);
-        } else if (!lb && rb) {
-          const rb = rightBondList[0];
-          mol.bonds.splice(rb.bI, 1);
-          mol.atoms.splice(rb.aI, 1);
-        } else {
-          if (lb.aI !== rb.aI)
-            throw new Error('Something is really wrong here.');
-
-          // is not enough, breaks the simple polymer
-          //mol.delAtom(a, true);
-
-          const leftBond = mol.bonds[lb.bI];
-          const rightBond = mol.bonds[rb.bI];
-          const a2 = leftBond.a2 = rightBond.a2; // right atom
-          leftBond.r2 = rightBond.r2;
-          leftBond.apo2 = rightBond.apo2;
-
-          if (a2.bonds)
-            throw new Error('Bond list of the atom is not corrected.');
-          // a2.bonds!.splice(a2.bonds!.indexOf(rightBond), 1); // remove the right bond from links of the right atom
-          // a2.bonds!.push(leftBond); // put the left bond to links of the right atom
-
-          mol.bonds.splice(rb.bI, 1); // remove right bond
-          mol.atoms.splice(lb.aI, 1);
+
+        if (connectedBonds.length > 2) {
+          throw new HelmNotSupportedError(
+            `Removing gap monomer #${aI} with ${connectedBonds.length} bonds is unsupported (max 2).`);
+        }
+
+        // Separate into backbone bonds (R1/R2) and other bonds (R3+ cross-polymer)
+        // A backbone bond connects to the gap's R1 or R2 attachment point
+        let backboneR1Bond: { bI: number, gapSide: 1 | 2 } | null = null; // bond using gap's R1
+        let backboneR2Bond: { bI: number, gapSide: 1 | 2 } | null = null; // bond using gap's R2
+        const otherBonds: number[] = []; // bond indices to just remove
+
+        for (const cb of connectedBonds) {
+          const bond = mol.bonds[cb.bI];
+          // The R-group on the gap's side tells us which attachment point is used
+          const gapR = cb.gapSide === 1 ? bond.r1 : bond.r2;
+          const gapRNum = typeof gapR === 'string' ? parseInt(gapR.replace(/\D/g, '')) : gapR;
+          if (gapRNum === 1)
+            backboneR1Bond = cb;
+          else if (gapRNum === 2)
+            backboneR2Bond = cb;
+          else
+            otherBonds.push(cb.bI);
         }
+
+        // Remove other (non-backbone) bonds first (iterate in reverse to keep indices valid)
+        otherBonds.sort((a, b) => b - a);
+        for (const bI of otherBonds)
+          mol.bonds.splice(bI, 1);
+
+        // Recalculate bond indices after splice (otherBonds were removed)
+        // We need to adjust backboneR1Bond/R2Bond indices
+        const adjustIdx = (origBi: number): number => {
+          let adj = origBi;
+          for (const removedBi of otherBonds)
+            if (removedBi < origBi) adj--;
+          return adj;
+        };
+
+        const r1 = backboneR1Bond ? {...backboneR1Bond, bI: adjustIdx(backboneR1Bond.bI)} : null;
+        const r2 = backboneR2Bond ? {...backboneR2Bond, bI: adjustIdx(backboneR2Bond.bI)} : null;
+
+        if (r1 && r2) {
+          // Re-link: the neighbor on the R1 side connects directly to the neighbor on the R2 side
+          const r1Bond = mol.bonds[r1.bI];
+          const r2Bond = mol.bonds[r2.bI];
+          // The "other" atom (not the gap) on each bond
+          const r1Neighbor = r1.gapSide === 1 ? r1Bond.a2 : r1Bond.a1;
+          const r2Neighbor = r2.gapSide === 1 ? r2Bond.a2 : r2Bond.a1;
+          const r1NeighborR = r1.gapSide === 1 ? r1Bond.r2 : r1Bond.r1;
+          const r1NeighborApo = r1.gapSide === 1 ? r1Bond.apo2 : r1Bond.apo1;
+          const r2NeighborR = r2.gapSide === 1 ? r2Bond.r2 : r2Bond.r1;
+          const r2NeighborApo = r2.gapSide === 1 ? r2Bond.apo2 : r2Bond.apo1;
+
+          // Rewrite the R1 bond to connect r1Neighbor ↔ r2Neighbor directly
+          r1Bond.a1 = r1Neighbor;
+          r1Bond.r1 = r1NeighborR;
+          r1Bond.apo1 = r1NeighborApo;
+          r1Bond.a2 = r2Neighbor;
+          r1Bond.r2 = r2NeighborR;
+          r1Bond.apo2 = r2NeighborApo;
+
+          // Remove the R2 bond (no longer needed)
+          mol.bonds.splice(r2.bI, 1);
+        } else if (r1 && !r2) {
+          // Gap at the end (only R1 bond) — just remove
+          mol.bonds.splice(r1.bI, 1);
+        } else if (!r1 && r2) {
+          // Gap at the start (only R2 bond) — just remove
+          mol.bonds.splice(r2.bI, 1);
+        }
+        // else: isolated gap, no backbone bonds — just remove atom
+
+        mol.atoms.splice(aI, 1);
       }
     }
 

package/src/package-test.ts

@@ -5,7 +5,7 @@ import * as grok from 'datagrok-api/grok';
 // import {JSDraw2ModuleType} from '@datagrok/js-draw-lite/src/types/jsdraw2';
 // import {HelmType, OrgHelmModuleType} from '@datagrok/helm-web-editor/src/types/org-helm';
 
-import {runTests, tests, TestContext, initAutoTests as initTests} from '@datagrok-libraries/utils/src/test';
+import {runTests, tests, TestContext, initAutoTests as initTests} from '@datagrok-libraries/test/src/test';
 
 import './tests/_first-tests';
 import './tests/helm-tests';

package/src/package-utils.ts

@@ -5,7 +5,8 @@ import * as DG from 'datagrok-api/dg';
 
 import {Unsubscribable} from 'rxjs';
 
-import {delay, timeout} from '@datagrok-libraries/utils/src/test';
+import {timeout} from '@datagrok-libraries/utils/src/test';
+
 import {errorToConsole} from '@datagrok-libraries/utils/src/to-console';
 import {errInfo} from '@datagrok-libraries/bio/src/utils/err-info';
 import {
@@ -152,7 +153,7 @@ export async function initHelmLoadAndPatchDojo(): Promise<void> {
             `Loading Helm Web Editor ${dojoProgress}/${dojoTargetList.length}`);
           _package.logger.debug(`${logPrefix}, dojo loading ... ` +
             `${dojoNotReadyList.map((m) => `'${m}'`).join(',')} ...`);
-          await delay(100);
+          await DG.delay(100);
         }
         _package.logger.debug(`${logPrefix}, dojo ready all modules`);
       }, 60000, 'timeout dojox.gfx.svg');

package/src/package.g.ts

@@ -1,7 +1,7 @@
 import {PackageFunctions} from './package';
 import * as DG from 'datagrok-api/dg';
 
-//tags: init
+//meta.role: init
 export async function initHelm() : Promise<void> {
   await PackageFunctions.initHelm();
 }
@@ -12,18 +12,18 @@ export async function getHelmService() : Promise<any> {
   return await PackageFunctions.getHelmService();
 }
 
-//tags: cellRenderer
 //output: grid_cell_renderer result
 //meta.columnTags: quality=Macromolecule, units=helm
 //meta.cellType: helm
+//meta.role: cellRenderer
 export function helmCellRenderer() : any {
   return PackageFunctions.helmCellRenderer();
 }
 
 //description: Macromolecule
-//tags: cellEditor
 //input: grid_cell cell 
 //meta.columnTags: quality=Macromolecule, units=helm
+//meta.role: cellEditor
 export function editMoleculeCell(cell: any) : void {
   PackageFunctions.editMoleculeCell(cell);
 }
@@ -37,9 +37,10 @@ export function openEditor(mol: DG.SemanticValue) : void {
 }
 
 //name: Properties
-//tags: panel, bio, helm, widgets
 //input: semantic_value sequence { semType: Macromolecule }
 //output: widget result
+//meta.role: widgets,panel
+//meta.domain: bio
 export function propertiesWidget(sequence: DG.SemanticValue) : any {
   return PackageFunctions.propertiesWidget(sequence);
 }
@@ -50,12 +51,12 @@ export function getMolfiles(col: DG.Column<any>) : any {
   return PackageFunctions.getMolfiles(col);
 }
 
-//tags: valueEditor
 //input: string name { optional: true }
 //input: object options { optional: true }
 //output: object result
 //meta.propertyType: string
 //meta.semType: Macromolecule
+//meta.role: valueEditor
 export function helmInput(name: string, options: any) : any {
   return PackageFunctions.helmInput(name, options);
 }

package/src/package.ts

@@ -142,10 +142,10 @@ export class PackageFunctions {
   }
 
   @grok.decorators.func({
-    'tags': ['cellRenderer'],
     'meta': {
       'columnTags': 'quality=Macromolecule, units=helm',
-      'cellType': 'helm'
+      'cellType': 'helm',
+      'role': 'cellRenderer'
     },
     'outputs': [{name: 'result', type: 'grid_cell_renderer'}]
   })
@@ -158,8 +158,10 @@ export class PackageFunctions {
 
 
   @grok.decorators.func({
-    'meta': {'columnTags': 'quality=Macromolecule, units=helm'},
-    'tags': ['cellEditor'],
+    'meta': {
+      'columnTags': 'quality=Macromolecule, units=helm',
+      'role': 'cellEditor'
+    },
     'description': 'Macromolecule'
   })
   static editMoleculeCell(
@@ -193,12 +195,8 @@ export class PackageFunctions {
 
 
   @grok.decorators.panel({
-    'tags': [
-      'bio',
-      'helm',
-      'widgets'
-    ],
-    'name': 'Properties'
+    'name': 'Properties',
+    'meta': {role: 'widgets', domain: 'bio'},
   })
   static propertiesWidget(
     @grok.decorators.param({'options': {'semType': 'Macromolecule'}}) sequence: DG.SemanticValue): DG.Widget {
@@ -218,9 +216,9 @@ export class PackageFunctions {
   @grok.decorators.func({
     'meta': {
       'propertyType': 'string',
-      'semType': 'Macromolecule'
+      'semType': 'Macromolecule',
+      'role': 'valueEditor'
     },
-    'tags': ['valueEditor'],
     'outputs': [{'type': 'object', 'name': 'result'}]
   })
   static helmInput(

package/src/tests/_first-tests.ts

@@ -2,7 +2,7 @@ import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
-import {category, test} from '@datagrok-libraries/utils/src/test';
+import {category, test} from '@datagrok-libraries/test/src/test';
 
 category('_first', () => {
   /** The first test of the package to evaluate problems with imports. */

package/src/tests/findMonomers-tests.ts

@@ -2,7 +2,7 @@ import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
-import {after, before, category, delay, expect, expectObject, test} from '@datagrok-libraries/utils/src/test';
+import {after, before, category, delay, expect, expectObject, test} from '@datagrok-libraries/test/src/test';
 import {UserLibSettings} from '@datagrok-libraries/bio/src/monomer-works/types';
 import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/types/monomer-library';
 import {

package/src/tests/get-molfiles-tests.ts

@@ -2,7 +2,7 @@ import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
-import {after, before, category, delay, expect, test, expectArray, testEvent} from '@datagrok-libraries/utils/src/test';
+import {after, before, category, delay, expect, test, expectArray, testEvent} from '@datagrok-libraries/test/src/test';
 import {getHelmHelper} from '@datagrok-libraries/bio/src/helm/helm-helper';
 import {
   getUserLibSettings, setUserLibSettings,

package/src/tests/get-monomer-tests.ts

@@ -6,7 +6,7 @@ import wu from 'wu';
 
 import {
   after, before, category, delay, expect, test, expectArray, testEvent, expectFloat, timeout
-} from '@datagrok-libraries/utils/src/test';
+} from '@datagrok-libraries/test/src/test';
 import {getHelmHelper, getMonomerHandleArgs} from '@datagrok-libraries/bio/src/helm/helm-helper';
 import {errInfo} from '@datagrok-libraries/bio/src/utils/err-info';
 import {Atom, HelmType, IJsAtom, GetMonomerFunc, HelmAtom} from '@datagrok-libraries/bio/src/helm/types';

package/src/tests/helm-activity-cliffs.ts

@@ -1,7 +1,7 @@
 import * as grok from 'datagrok-api/grok';
 import * as DG from 'datagrok-api/dg';
 
-import {after, awaitCheck, before, category, test} from '@datagrok-libraries/utils/src/test';
+import {after, awaitCheck, before, category, test} from '@datagrok-libraries/test/src/test';
 
 import {BitArrayMetricsNames} from '@datagrok-libraries/ml/src/typed-metrics';
 import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/types/monomer-library';
@@ -11,7 +11,7 @@ import {
 import {UserLibSettings} from '@datagrok-libraries/bio/src/monomer-works/types';
 import {DimReductionMethods} from '@datagrok-libraries/ml/src/multi-column-dimensionality-reduction/types';
 import {getHelmHelper, IHelmHelper} from '@datagrok-libraries/bio/src/helm/helm-helper';
-import {expect} from '@datagrok-libraries/utils/src/test';
+import {expect} from '@datagrok-libraries/test/src/test';
 import {MmDistanceFunctionsNames} from '@datagrok-libraries/ml/src/macromolecule-distance-functions';
 import {BitArrayMetrics} from '@datagrok-libraries/ml/src/typed-metrics';
 import {BYPASS_LARGE_DATA_WARNING} from '@datagrok-libraries/ml/src/functionEditors/consts';

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

@@ -3,7 +3,7 @@ import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
 /* eslint-disable max-len */
-import {after, before, category, delay, expect, expectArray, test, testEvent} from '@datagrok-libraries/utils/src/test';
+import {after, before, category, delay, expect, expectArray, test, testEvent} from '@datagrok-libraries/test/src/test';
 import {HelmNotSupportedError, HelmNotSupportedErrorType, IHelmHelper} from '@datagrok-libraries/bio/src/helm/helm-helper';
 import {getHelmHelper} from '@datagrok-libraries/bio/src/helm/helm-helper';
 import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/types/monomer-library';

package/src/tests/helm-input-tests.ts

@@ -4,7 +4,7 @@ import * as DG from 'datagrok-api/dg';
 
 import $ from 'cash-dom';
 
-import {after, before, category, delay, expect, test, testEvent} from '@datagrok-libraries/utils/src/test';
+import {after, before, category, delay, expect, test, testEvent} from '@datagrok-libraries/test/src/test';
 import {IHelmHelper, getHelmHelper} from '@datagrok-libraries/bio/src/helm/helm-helper';
 import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/types/monomer-library';
 import {

package/src/tests/helm-service-tests.ts

@@ -6,7 +6,7 @@ import {Subject} from 'rxjs';
 
 import {
   category, expect, test, awaitCheck, delay, testEvent, before, after
-} from '@datagrok-libraries/utils/src/test';
+} from '@datagrok-libraries/test/src/test';
 import {getHelmHelper} from '@datagrok-libraries/bio/src/helm/helm-helper';
 import {
   getHelmService, HelmServiceBase, HelmAux, HelmProps

package/src/tests/helm-substructure-filter.ts

@@ -4,7 +4,7 @@ import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
-import {after, before, category, test, expect, delay, testEvent} from '@datagrok-libraries/utils/src/test';
+import {after, before, category, test, expect, delay, testEvent} from '@datagrok-libraries/test/src/test';
 import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/types/monomer-library';
 import {
   getUserLibSettings, setUserLibSettings

package/src/tests/helm-tests.ts

@@ -2,7 +2,7 @@ import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
-import {after, before, category, delay, expect, test, expectArray} from '@datagrok-libraries/utils/src/test';
+import {after, before, category, delay, expect, test, expectArray} from '@datagrok-libraries/test/src/test';
 
 import {parseHelm} from '../utils';
 import {initHelmMainPackage} from './utils';

package/src/tests/helm-web-editor-tests.ts

@@ -2,7 +2,7 @@ import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
-import {after, before, category, delay, expect, test, expectArray} from '@datagrok-libraries/utils/src/test';
+import {after, before, category, delay, expect, test, expectArray} from '@datagrok-libraries/test/src/test';
 import {IHelmHelper, getHelmHelper} from '@datagrok-libraries/bio/src/helm/helm-helper';
 import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/types/monomer-library';
 import {UserLibSettings} from '@datagrok-libraries/bio/src/monomer-works/types';

package/src/tests/parse-helm-tests.ts

@@ -3,7 +3,7 @@ import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
 
-import {after, before, category, delay, expect, test, expectArray, timeout} from '@datagrok-libraries/utils/src/test';
+import {after, before, category, delay, expect, test, expectArray, timeout} from '@datagrok-libraries/test/src/test';
 import {HelmMol, HelmType, IHelmBio, IHelmEditorOptions, Mol, OrgType} from '@datagrok-libraries/bio/src/helm/types';
 import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/types/monomer-library';
 import {UserLibSettings} from '@datagrok-libraries/bio/src/monomer-works/types';

package/src/tests/properties-widget-tests.ts

@@ -2,7 +2,7 @@ import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 import * as grok from 'datagrok-api/grok';
 
-import {after, before, category, expect, expectObject, test, timeout} from '@datagrok-libraries/utils/src/test';
+import {after, before, category, expect, expectObject, test, timeout} from '@datagrok-libraries/test/src/test';
 import {ALPHABET, NOTATION, TAGS as bioTAGS} from '@datagrok-libraries/bio/src/utils/macromolecule';
 import {
   getUserLibSettings, setUserLibSettings

package/src/tests/renderers-tests.ts

@@ -7,7 +7,7 @@ import {fromEvent} from 'rxjs';
 
 import {
   after, before, category, test, expect, awaitCheck, delay, testEvent
-} from '@datagrok-libraries/utils/src/test';
+} from '@datagrok-libraries/test/src/test';
 import {NOTATION} from '@datagrok-libraries/bio/src/utils/macromolecule';
 import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/types/monomer-library';
 import {UserLibSettings} from '@datagrok-libraries/bio/src/monomer-works/types';

package/src/tests/to-atomic-level-ui-non-linear.ts

@@ -1,7 +1,7 @@
 import * as DG from 'datagrok-api/dg';
 import * as grok from 'datagrok-api/grok';
 
-import {after, before, category, expect, test} from '@datagrok-libraries/utils/src/test';
+import {after, before, category, expect, test} from '@datagrok-libraries/test/src/test';
 import {IMonomerLib} from '@datagrok-libraries/bio/src/types/monomer-library';
 import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/types/monomer-library';
 import {getUserLibSettings, setUserLibSettings} from '@datagrok-libraries/bio/src/monomer-works/lib-settings';

package/src/tests/utils.ts

@@ -2,7 +2,7 @@ import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
-import {delay, testEvent} from '@datagrok-libraries/utils/src/test';
+import {delay, testEvent} from '@datagrok-libraries/test/src/test';
 import {getHelmHelper} from '@datagrok-libraries/bio/src/helm/helm-helper';
 import {_package} from '../package-test';