@datagrok/sequence-translator 1.9.12 → 1.9.14

package/files/polytool-rules/rules_example.json

@@ -68,6 +68,13 @@
       ],
       "firstLinkingGroup": 3,
       "secondLinkingGroup": 3
+    },
+    {
+      "code": 0,
+      "firstMonomers": [],
+      "secondMonomers": [],
+      "firstLinkingGroup": 1,
+      "secondLinkingGroup": 2
     }
   ],
   "reactionRules": [

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@datagrok/sequence-translator",
   "friendlyName": "Sequence Translator",
-  "version": "1.9.12",
+  "version": "1.9.14",
   "author": {
     "name": "Davit Rizhinashvili",
     "email": "drizhinashvili@datagrok.ai"
@@ -25,7 +25,7 @@
     "@datagrok-libraries/bio": "^5.54.8",
     "@datagrok-libraries/chem-meta": "^1.2.8",
     "@datagrok-libraries/tutorials": "^1.6.1",
-    "@datagrok-libraries/utils": "^4.6.3",
+    "@datagrok-libraries/utils": "^4.6.5",
     "@types/react": "^18.0.15",
     "cash-dom": "^8.1.0",
     "datagrok-api": "^1.25.0",
@@ -54,7 +54,7 @@
     "@typescript-eslint/eslint-plugin": "^7.2.0",
     "@typescript-eslint/parser": "^7.2.0",
     "css-loader": "^6.7.3",
-    "datagrok-tools": "^4.14.48",
+    "datagrok-tools": "^4.14.55",
     "eslint": "^8.57.0",
     "eslint-config-google": "^0.14.0",
     "style-loader": "^3.3.1",

package/src/package.g.ts

@@ -119,8 +119,8 @@ export async function getPolyToolConvertEditor(call: DG.FuncCall) : Promise<any>
 
 //input: dataframe table 
 //input: column seqCol { caption: Sequence }
-//input: bool generateHelm { default: true }
-//input: bool chiralityEngine { default: true }
+//input: bool generateHelm = true 
+//input: bool chiralityEngine = true 
 //input: object rules 
 //output: column result
 //editor: SequenceTranslator:getPolyToolConvertEditor

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

@@ -7,6 +7,7 @@ import {RulesManager} from './rule-manager';
 import {RuleCards} from './pt-rule-cards';
 import {getMonomerLibHelper} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
 import {
+  _package,
   PackageFunctions} from '../../package';
 import {MmcrTemps} from '@datagrok-libraries/bio/src/utils/cell-renderer-consts';
 import {ReactionEditorProps} from './rule-reaction-editor';
@@ -26,6 +27,7 @@ const NAME_FIRST_LINK = 'firstLinkingGroup';
 const NAME_SECOND_LINK = 'secondLinkingGroup';
 
 export class RuleInputs extends ActiveFiles {
+  static ruleDescriptions: Record<string, Promise<HTMLElement>> = {};
   constructor(
     path: string, userStorageName: string, ext: string,
     options?: { onValueChanged: (value: string[]) => void }
@@ -48,8 +50,70 @@ export class RuleInputs extends ActiveFiles {
 
     return res;
   }
+
+  override async getForm(): Promise<HTMLDivElement> {
+    const form = await super.getForm();
+    this.processRulesForm(form);
+    return form;
+  }
+
+  private async processRulesForm(rulesForm: HTMLElement) {
+    const ruleNameLabels = Array.from(rulesForm.getElementsByTagName('label') ?? [])
+      .filter((l) => l.textContent?.endsWith('.json') && l.parentElement != null);
+    for (const label of ruleNameLabels) {
+      const ruleName = label.textContent!.trim();
+      const inputRoot = label.parentElement!.getElementsByTagName('input')[0]!;
+      ui.tooltip.bind(inputRoot, ui.wait(async () => {
+        RuleInputs.ruleDescriptions[ruleName] ??= (async () => {
+          try {
+            const rule = JSON.parse(await grok.dapi.files.readAsText(`${RULES_PATH}/${ruleName}`));
+            const descDiv = ui.divV([ui.h1(ruleName)]);
+            const linkRules: RuleLink[] = rule.linkRules ?? [];
+            // link rules
+            if (linkRules.length > 0) {
+              descDiv.appendChild(ui.h3('Linkage Rules'));
+              const table = ui.table(linkRules, (item) => [
+                item.code?.toString() ?? '',
+                shortenToMaxLen((item.firstMonomers ?? []).join(', ')),
+                shortenToMaxLen((item.secondMonomers ?? []).join(', ')),
+                item.firstLinkingGroup?.toString() ?? '',
+                item.secondLinkingGroup?.toString() ?? ''
+              ], ['Code', 'M1', 'M2', 'L1', 'L2']);
+              descDiv.appendChild(table);
+            }
+            // reaction rules
+            const reactionRules: RuleReaction[] = rule.reactionRules ?? [];
+            if (reactionRules.length > 0) {
+              descDiv.appendChild(ui.h3('Synthesis Rules'));
+              const table = ui.table(reactionRules, (item) => [
+                item.code?.toString() ?? '',
+                shortenToMaxLen((item.firstMonomers ?? []).join(', ')),
+                shortenToMaxLen((item.secondMonomers ?? []).join(', ')),
+                shortenToMaxLen(item.name ?? ''),
+                grok.chem.drawMolecule(item.reaction?.split('>>')[1] ?? '', 70, 70)
+              ], ['Code', 'M1', 'M2', 'Name', 'Product']);
+              descDiv.appendChild(table);
+            }
+            return descDiv;
+          } catch (e: any) {
+            _package.logger.error(`Failed to load rule ${ruleName}: ${e?.toString?.()}`);
+            console.error(e);
+            return ui.divText(`Failed to load rule ${ruleName}`);
+          }
+        })();
+        return await RuleInputs.ruleDescriptions[ruleName];
+      }));
+    }
+  }
 }
 
+
+function shortenToMaxLen(s: string, maxLen: number = 30): string {
+  if (s.length <= maxLen) return s;
+  return `${s.substring(0, maxLen)}...`;
+}
+
+
 export type RuleLink = {
   code: number,
   firstMonomers: string[],

package/src/polytool/pt-convert-editor.ts

@@ -35,7 +35,7 @@ export class PolyToolConvertFuncEditor {
 
   private async initInputs(): Promise<void> {
     const getParam = (pName: string) => this.call.inputParams[pName];
-
+    const rulesForm = await this.ruleInputs.getForm();
     this.inputs = {
       table: (() => {
         const p = getParam(P.table);
@@ -49,7 +49,7 @@ export class PolyToolConvertFuncEditor {
       chiralityEngine: ui.input.forProperty(getParam(P.chiralityEngine).property),
       rules: {
         header: ui.inlineText([PT_UI_RULES_USED]),
-        form: await this.ruleInputs.getForm(),
+        form: rulesForm,
       }
     };
   }