@datagrok/sequence-translator 1.6.0 → 1.6.2

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@datagrok/sequence-translator",
   "friendlyName": "Sequence Translator",
-  "version": "1.6.0",
+  "version": "1.6.2",
   "author": {
     "name": "Leonid Stolbov",
     "email": "lstolbov@datagrok.ai"
@@ -22,7 +22,7 @@
     }
   ],
   "dependencies": {
-    "@datagrok-libraries/bio": "^5.45.6",
+    "@datagrok-libraries/bio": "^5.46.0",
     "@datagrok-libraries/chem-meta": "^1.2.7",
     "@datagrok-libraries/tutorials": "^1.4.3",
     "@datagrok-libraries/utils": "^4.3.7",
@@ -41,7 +41,7 @@
   "devDependencies": {
     "@datagrok-libraries/helm-web-editor": "^1.1.13",
     "@datagrok-libraries/js-draw-lite": "^0.0.10",
-    "@datagrok/bio": "^2.17.0",
+    "@datagrok/bio": "^2.17.2",
     "@datagrok/helm": "^2.5.8",
     "@datagrok/chem": "^1.12.4",
     "@types/jquery": "^3.5.14",

package/src/apps/common/model/oligo-toolkit-package.ts

@@ -1,3 +1,4 @@
+/* eslint-disable max-len */
 import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
@@ -76,7 +77,7 @@ export class OligoToolkitPackage extends DG.Package implements ITranslationHelpe
     if (!this.initLibDataPromise) {
       this.initLibDataPromise = (async () => {
         const packageSettings = await this.getSettings();
-        let monomersPath: string = packageSettings['MonomersPath'];
+        let monomersPath: string = packageSettings instanceof Map ? packageSettings.get('MonomersPath') : packageSettings['MonomersPath'];
         if (!monomersPath || !(await grok.dapi.files.exists(monomersPath))) {
           this.logger.warning(`Monomers path '${monomersPath}' not found. ` +
             `Fallback to monomers sample path '${FALLBACK_LIB_PATH}'.`);

package/src/polytool/conversion/pt-synthetic.ts

@@ -30,6 +30,7 @@ export async function getOverriddenLibrary(rules: Rules): Promise<IMonomerLibBas
       names = [];
       monomers = [];
       console.error(e);
+      grok.shell.warning(e);
     } finally {
       for (let j = 0; j < names.length; j ++)
         argLib[names[j]] = monomers[j];
@@ -52,12 +53,12 @@ export function getNewMonomers(rdkit: RDModule, mLib: IMonomerLib, rule: RuleRea
 
   const monomerNames = new Array<string>(totalLength);
   const resMonomers = new Array<Monomer>(totalLength);
-  const rawMonomers = new Array<string>(totalLength);
+  const monomers = new Array<string>(totalLength);
 
   const mainRxn = getReactionSmirks(rdkit, reacSmarts);
 
-  const reacCutFirst = `${reactants[0]}>>[C:1]`;
-  const reacCutSecond = `${reactants[1]}>>[C:2]`;
+  const reacCutFirst = `${reactants[0]}>>[C:1]C`;
+  const reacCutSecond = `${reactants[1]}>>[C:2]C`;
 
   const rxnCutFirst = getReactionSmirks(rdkit, reacCutFirst);
   const rxnCutSecond = getReactionSmirks(rdkit, reacCutSecond);
@@ -68,7 +69,7 @@ export function getNewMonomers(rdkit: RDModule, mLib: IMonomerLib, rule: RuleRea
     if (!monomer) throw new MonomerNotFoundError('PEPTIDE', rule.firstMonomers[i]);
 
     const sMolBlock = cutReactant(rdkit, monomer.molfile, rxnCutFirst, monomer.name);
-    rawMonomers[counter] = sMolBlock;
+    monomers[counter] = sMolBlock;
     monomerNames[counter] = `${monomer.symbol}_${monomerName}`;
     counter++;
   }
@@ -77,7 +78,7 @@ export function getNewMonomers(rdkit: RDModule, mLib: IMonomerLib, rule: RuleRea
     if (!monomer) throw new MonomerNotFoundError('PEPTIDE', rule.secondMonomers[i]);
 
     const sMolBlock = cutReactant(rdkit, monomer.molfile, rxnCutSecond, monomer.name);
-    rawMonomers[counter] = sMolBlock;
+    monomers[counter] = sMolBlock;
     monomerNames[counter] = `${monomer.symbol}_${monomerName}`;
     counter++;
   }
@@ -97,20 +98,22 @@ export function getNewMonomers(rdkit: RDModule, mLib: IMonomerLib, rule: RuleRea
     mol?.delete();
   }
   //pMolblock = reactionMembers[1]//cutProduct(rdkit, monomer1?.molfile, monomer2?.molfile, mainRxn, monomerName);
-  rawMonomers[counter] = pMolblock;
+  monomers[counter] = pMolblock;
   monomerNames[counter] = monomerName;
 
-  //after RDKit works
-  for (let i = 0; i < totalLength - 1; i ++)
-    rawMonomers[i] = rawMonomers[i].replace('0.0000 C   ', '0.0000 R#  ').replace('M  RGP  2', 'M  RGP  3   1   3');
-  rawMonomers[totalLength - 1] = modProduct(rawMonomers[totalLength - 1]);
+  //after RDKit works - [X:N] is first atom which is exploited
+  for (let i = 0; i < totalLength - 1; i ++) {
+    monomers[i] = monomers[i].replace('    0.0000    0.0000    0.0000 C   ', '    0.0000    0.0000    0.0000 R#  ')
+      .replace('M  RGP  2', 'M  RGP  3   2   3');
+  }
+  monomers[totalLength - 1] = modProduct(monomers[totalLength - 1]);
 
   for (let i = 0; i < totalLength; i ++) {
     const isProduct = i == totalLength - 1 ? true : false;
     const resMonomer: Monomer = {
       [REQ.SYMBOL]: monomerNames[i],
       [REQ.NAME]: monomerNames[i],
-      [REQ.MOLFILE]: rawMonomers[i],
+      [REQ.MOLFILE]: monomers[i],
       [REQ.AUTHOR]: '',
       [REQ.ID]: 0,
       [REQ.RGROUPS]: getNewGroups(isProduct),

package/src/polytool/conversion/rule-manager.ts

@@ -87,16 +87,33 @@ export class RulesManager {
       reactionRules: this.rules.reactionRules,
     };
 
-    const rrrr = JSON.stringify(saveable, undefined, 2);
-    _package.files.writeAsText(`polytool-rules/${this.fileName}`, rrrr);
+    const json = JSON.stringify(saveable, undefined, 2);
+    _package.files.writeAsText(`polytool-rules/${this.fileName}`, json);
     grok.shell.info(`Polytool rules at ${this.fileName} was updated`);
   }
 
-  private createGridDiv(name: string, grid: DG.Grid) {
+  private createGridDiv(name: string, grid: DG.Grid, buttons: HTMLButtonElement[] = []) {
     const header = ui.h1(name, 'polytool-grid-header');
-    grid.root.prepend(header);
+    header.style.marginTop = '10px';
+    header.style.marginRight = '10px';
     grid.root.style.height = '100%';
-    return grid.root;
+
+    buttons.forEach((b) => {
+      b.style.marginLeft = '5px';
+      b.style.marginRight = '10px';
+    });
+
+    const gridDiv = ui.splitV([
+      ui.box(
+        ui.divH([header, ...buttons]),
+        {style: {maxHeight: '60px'}},
+      ),
+      grid.root,
+    ]);
+
+    gridDiv.style.height = '100%';
+
+    return gridDiv;
   };
 
   async getLinkExamplesGrid() {
@@ -160,69 +177,48 @@ export class RulesManager {
   async getForm() {
     inputsTabControl: DG.TabControl;
 
+    const saveLinksButton = ui.bigButton('Save', () => { this.save(); });
+    const addLinkButton = ui.button('Add rule', () => { this.linkRuleDataFrame.rows.addNew(); });
+    const linksGridDiv = this.createGridDiv('Rules',
+      this.linkRuleDataFrame.plot.grid({showAddNewRowIcon: true}), [saveLinksButton, addLinkButton]);
+    const linkExamples = this.createGridDiv('Examples', await this.getLinkExamplesGrid());
+    linksGridDiv.style.width = '50%';
+    linkExamples.style.width = '50%';
+    const links = ui.divH([linksGridDiv, linkExamples]);
+
+    const saveReactionsButton = ui.bigButton('Save', () => { this.save(); });
+    const addReactionButton = ui.button('Add rule', () => { this.synthRuleDataFrame.rows.addNew(); });
+    const reactionsGridDiv = this.createGridDiv('Rules',
+      this.synthRuleDataFrame.plot.grid({showAddNewRowIcon: true}), [saveReactionsButton, addReactionButton]);
+    const reactionExamples = this.createGridDiv('Examples', await this.getReactionExamplesGrid());
+    reactionsGridDiv.style.width = '50%';
+    reactionExamples.style.width = '50%';
+    const reactions = ui.divH([reactionsGridDiv, reactionExamples]);
+
     const dimerInputsDiv = ui.divV([
       this.homoDimerInput,
       this.heteroDimerInput,
     ]);
 
-    const linkExamples = await this.getLinkExamplesGrid();
-    const reactionExamples = await this.getReactionExamplesGrid();
-
     const inputsTabControl = ui.tabControl({
-      'Links': linkExamples,
-      'Reactions': reactionExamples,
+      'Links': links,
+      'Reactions': reactions,
       'Dimers': dimerInputsDiv,
     }, false);
 
-    inputsTabControl.root.style.height = '90%';
+    inputsTabControl.root.style.height = '100%';
     inputsTabControl.root.style.width = '100%';
     inputsTabControl.root.classList.add('rules-manager-form-tab-control');
     inputsTabControl.header.style.marginBottom = '10px';
 
-    const linksGridDiv = this.createGridDiv('Link rules', this.linkRuleDataFrame.plot.grid({showAddNewRowIcon: true}));
-    const reactionsGridDiv =
-      this.createGridDiv('Reaction rules', this.synthRuleDataFrame.plot.grid({showAddNewRowIcon: true}));
-
-    linksGridDiv.style.width = '100%';
-    reactionsGridDiv.style.width = '100%';
-
-    const divs = [linksGridDiv, reactionsGridDiv, ui.div()];
-    divs[0].style.removeProperty('display');
-    divs[1].style.display = 'none';
-    divs[2].style.display = 'none';
-
-    inputsTabControl.onTabChanged.subscribe(() => {
-      this.currentTab = inputsTabControl.currentPane.name;
-
-      const idx = inputsTabControl.panes.findIndex((p) => p.name == this.currentTab);
-
-      for (let i = 0; i < divs.length; i++) {
-        if (i == idx)
-          divs[i].style.removeProperty('display');
-        else
-          divs[i].style.display = 'none';
-      }
-    });
-
-    const saveButton = ui.bigButton('Save changes', () => {
-      this.save();
-    });
-
-
     const panel = ui.divV([
       inputsTabControl.root,
-      saveButton
     ]);
 
     panel.style.height = '100%';
     panel.style.alignItems = 'center';
 
-    const form = ui.splitH([
-      panel,
-      ui.divV(divs, {style: {width: '100%'}})
-    ], {style: {width: '100%'}}, true);
-    form.style.height = '100%';
-    return form;
+    return inputsTabControl.root;
   }
 }
 

package/src/polytool/pt-dialog.ts

@@ -99,8 +99,8 @@ export async function getPolyToolConvertDialog(srcCol?: DG.Column): Promise<DG.D
     const generateHelmInput = ui.input.bool(PT_UI_GET_HELM, {value: true});
     ui.tooltip.bind(generateHelmInput.root, PT_UI_ADD_HELM);
 
-    const chiralityEngineInput = ui.input.bool(PT_UI_USE_CHIRALITY, {value: false});
-    const highlightMonomersInput = ui.input.bool(PT_UI_HIGHLIGHT_MONOMERS, {value: false});
+    const chiralityEngineInput = ui.input.bool(PT_UI_USE_CHIRALITY, {value: true});
+    const highlightMonomersInput = ui.input.bool(PT_UI_HIGHLIGHT_MONOMERS, {value: true});
     let ruleFileList: string[];
     const ruleInputs = new RuleInputs(RULES_PATH, RULES_STORAGE_NAME, '.json', {
       onValueChanged: (value: string[]) => { ruleFileList = value; }

package/src/tests/toAtomicLevel-tests.ts

@@ -85,8 +85,8 @@ category('toAtomicLevel', () => {
     try {
       const molInchi = mol.get_inchi();
       const molInchiKey = rdKitModule.get_inchikey_for_inchi(molInchi);
-      expect(mol.get_num_bonds(), 6);
-      expect(mol.get_num_atoms(), 7);
+      expect(mol.get_num_bonds(), 7);
+      expect(mol.get_num_atoms(), 8);
       // TODO: Check inchi key for the new monomer molfile
       // expect(molInchiKey, 'V2H10N2O3S-UHFFFAOYSA-N');
     } finally {

package/src/utils/cell-renderer-cyclized.ts

@@ -5,20 +5,20 @@ import * as DG from 'datagrok-api/dg';
 import {MonomerPlacer} from '@datagrok-libraries/bio/src/utils/cell-renderer-monomer-placer';
 import {monomerToShort} from '@datagrok-libraries/bio/src/utils/macromolecule';
 import {ISeqHelper} from '@datagrok-libraries/bio/src/utils/seq-helper';
-
 import {_package} from '../package';
 
 export class CyclizedCellRendererBack extends MonomerPlacer {
-
   constructor(
     gridCol: DG.GridColumn | null, tableCol: DG.Column,
     maxLengthOfMonomer: number, seqHelper: ISeqHelper
   ) {
     super(gridCol, tableCol, _package.logger, maxLengthOfMonomer, () => {
       const sh = seqHelper.getSeqHandler(tableCol);
+      const {font, fontWidth} = MonomerPlacer.getFontSettings(tableCol);
       return {
         seqHandler: sh,
-        monomerCharWidth: 7,
+        font: font,
+        fontCharWidth: fontWidth,
         separatorWidth: 11,
         monomerToShort: monomerToShort,
       };
@@ -26,12 +26,12 @@ export class CyclizedCellRendererBack extends MonomerPlacer {
   }
 
   override onMouseMove(gridCell: DG.GridCell, e: MouseEvent) {
-    const gridCellBounds: DG.Rect = gridCell.bounds;
-    const argsX = e.offsetX - gridCell.gridColumn.left + (gridCell.gridColumn.left - gridCellBounds.x);
-    const left: number | null = this.getPosition(gridCell.tableRowIndex!, argsX, gridCellBounds.width);
-    if(left != null) {
+    // const gridCellBounds: DG.Rect = gridCell.bounds;
+    // const argsX = e.offsetX - gridCell.gridColumn.left + (gridCell.gridColumn.left - gridCellBounds.x);
+    // const left: number | null = this.getPosition(gridCell.tableRowIndex!, argsX, gridCellBounds.width);
+    // if(left != null) {
 
-    }
+    // }
     super.onMouseMove(gridCell, e);
   }
 }