#6026 - Bond length is different for monomers loaded from HELM and from the library

packages/ketcher-core/src/application/editor/Editor.ts

@@ -45,7 +45,7 @@ import {
   DrawingEntitiesManager,
   MONOMER_START_X_POSITION,
   MONOMER_START_Y_POSITION,
-  SNAKE_LAYOUT_CELL_WIDTH,
+  CELL_WIDTH,
 } from 'domain/entities/DrawingEntitiesManager';
 import { PolymerBond } from 'domain/entities/PolymerBond';
 import { AttachmentPointName, MonomerItemType } from 'domain/types';
@@ -800,8 +800,8 @@ export class CoreEditor {
     ZoomTool.instance.scrollTo(
       new Vec2(drawnEntitiesBoundingBox.left, drawnEntitiesBoundingBox.top),
       false,
-      MONOMER_START_X_POSITION - SNAKE_LAYOUT_CELL_WIDTH / 4,
-      MONOMER_START_Y_POSITION - SNAKE_LAYOUT_CELL_WIDTH / 4,
+      MONOMER_START_X_POSITION - CELL_WIDTH / 4,
+      MONOMER_START_Y_POSITION - CELL_WIDTH / 4,
       false,
     );
   }

packages/ketcher-core/src/application/editor/tools/RnaPreset.ts

@@ -24,8 +24,8 @@ import { monomerFactory } from '../operations/monomer/monomerFactory';
 import { RNABase } from 'domain/entities/RNABase';
 import { Phosphate } from 'domain/entities/Phosphate';
 import { Coordinates } from '../shared/coordinates';
+import { CELL_WIDTH } from 'domain/entities/DrawingEntitiesManager';
 
-export const RNA_MONOMER_DISTANCE = 22.5;
 class RnaPresetTool implements Tool {
   rnaBase: MonomerItemType | undefined;
   sugar: MonomerItemType | undefined;
@@ -78,9 +78,7 @@ class RnaPresetTool implements Tool {
         phosphatePosition: this.phosphatePreviewRenderer
           ? Coordinates.canvasToModel(
               new Vec2(
-                this.editor.lastCursorPositionOfCanvas.x +
-                  this.sugarPreviewRenderer?.width +
-                  RNA_MONOMER_DISTANCE,
+                this.editor.lastCursorPositionOfCanvas.x + CELL_WIDTH,
                 this.editor.lastCursorPositionOfCanvas.y,
               ),
             )
@@ -90,9 +88,7 @@ class RnaPresetTool implements Tool {
           ? Coordinates.canvasToModel(
               new Vec2(
                 this.editor.lastCursorPositionOfCanvas.x,
-                this.editor.lastCursorPositionOfCanvas.y +
-                  this.sugarPreviewRenderer.height +
-                  RNA_MONOMER_DISTANCE,
+                this.editor.lastCursorPositionOfCanvas.y + CELL_WIDTH,
               ),
             )
           : undefined,

packages/ketcher-core/src/application/render/renderers/PolymerBondRenderer/SnakeModePolymerBondRenderer.ts

@@ -14,7 +14,7 @@ import {
   ConnectionDirectionInDegrees,
   ConnectionDirectionOfLastCell,
 } from 'domain/entities/canvas-matrix/Connection';
-import { SNAKE_LAYOUT_CELL_WIDTH } from 'domain/entities/DrawingEntitiesManager';
+import { CELL_WIDTH } from 'domain/entities/DrawingEntitiesManager';
 import { DrawingEntity } from 'domain/entities/DrawingEntity';
 import { PolymerBond } from 'domain/entities/PolymerBond';
 import { getSugarFromRnaBase } from 'domain/helpers/monomers';
@@ -171,7 +171,7 @@ export class SnakeModePolymerBondRenderer extends BaseRenderer {
   ): string {
     const sin = Math.sin((direction * Math.PI) / 180);
     const cos = Math.cos((direction * Math.PI) / 180);
-    const xOffset = (SNAKE_LAYOUT_CELL_WIDTH / 2) * cos;
+    const xOffset = (CELL_WIDTH / 2) * cos;
     const yOffset = (CELL_HEIGHT / 2) * sin;
     const maxXOffset = cell.connections.reduce(
       (max: number, connection: Connection): number => {

packages/ketcher-core/src/domain/entities/DrawingEntitiesManager.ts

@@ -98,11 +98,10 @@ import { Chain } from 'domain/entities/monomer-chains/Chain';
 const VERTICAL_DISTANCE_FROM_ROW_WITHOUT_RNA = 30;
 const VERTICAL_OFFSET_FROM_ROW_WITH_RNA = 142;
 const DISTANCE_FROM_RIGHT = 55;
-export const SNAKE_LAYOUT_CELL_WIDTH = 60;
-export const SNAKE_LAYOUT_Y_OFFSET_BETWEEN_CHAINS =
-  SNAKE_LAYOUT_CELL_WIDTH * 2 + 30;
-export const MONOMER_START_X_POSITION = 20 + SNAKE_LAYOUT_CELL_WIDTH / 2;
-export const MONOMER_START_Y_POSITION = 20 + SNAKE_LAYOUT_CELL_WIDTH / 2;
+export const CELL_WIDTH = 60;
+export const SNAKE_LAYOUT_Y_OFFSET_BETWEEN_CHAINS = CELL_WIDTH * 2 + 30;
+export const MONOMER_START_X_POSITION = 20 + CELL_WIDTH / 2;
+export const MONOMER_START_Y_POSITION = 20 + CELL_WIDTH / 2;
 
 type RnaPresetAdditionParams = {
   sugar: MonomerItemType;
@@ -1246,7 +1245,7 @@ export class DrawingEntitiesManager {
   ) {
     const command = new Command();
     const heightMonomerWithBond =
-      SNAKE_LAYOUT_CELL_WIDTH / 2 + VERTICAL_DISTANCE_FROM_ROW_WITHOUT_RNA;
+      CELL_WIDTH / 2 + VERTICAL_DISTANCE_FROM_ROW_WITHOUT_RNA;
     const isNewRow = lastPosition.x === MONOMER_START_X_POSITION;
 
     maxVerticalDistance =
@@ -1314,7 +1313,7 @@ export class DrawingEntitiesManager {
     const oldSugarPosition = nucleotideOrNucleoside.sugar.position;
     const rnaBasePosition = new Vec2(
       lastPosition.x,
-      lastPosition.y + (isAntisense ? -1 : 1) * SNAKE_LAYOUT_CELL_WIDTH,
+      lastPosition.y + (isAntisense ? -1 : 1) * CELL_WIDTH,
     );
 
     if (needRepositionMonomers) {
@@ -1338,7 +1337,7 @@ export class DrawingEntitiesManager {
     if (nucleotideOrNucleoside instanceof Nucleotide) {
       nucleotideOrNucleoside.phosphate.isMonomerInRnaChainRow = true;
       const phosphatePosition = new Vec2(
-        lastPosition.x + SNAKE_LAYOUT_CELL_WIDTH,
+        lastPosition.x + CELL_WIDTH,
         lastPosition.y,
       );
 
@@ -1363,8 +1362,8 @@ export class DrawingEntitiesManager {
         maxVerticalDistance,
         restOfRowsWithAntisense,
         nucleotideOrNucleoside instanceof Nucleotide
-          ? SNAKE_LAYOUT_CELL_WIDTH * 2
-          : SNAKE_LAYOUT_CELL_WIDTH,
+          ? CELL_WIDTH * 2
+          : CELL_WIDTH,
       );
 
     const nextMonomer = getNextMonomerInChain(
@@ -1497,9 +1496,7 @@ export class DrawingEntitiesManager {
     needRepositionMonomers = true,
   ) {
     const command = new Command();
-    let lastPosition = startPosition.add(
-      new Vec2(0, SNAKE_LAYOUT_CELL_WIDTH * 3),
-    );
+    let lastPosition = startPosition.add(new Vec2(0, CELL_WIDTH * 3));
     let rowsUsedByAntisense = 1;
 
     antisenseChain.forEachNode(({ node }) => {
@@ -1856,15 +1853,12 @@ export class DrawingEntitiesManager {
     lastPosition: Vec2,
     height: number,
     canvasWidth: number,
-    width = SNAKE_LAYOUT_CELL_WIDTH,
+    width = CELL_WIDTH,
     restOfRowsWithAntisense: number,
   ) {
-    const isMonomerFitCanvas =
-      lastPosition.x +
-        width +
-        DISTANCE_FROM_RIGHT +
-        SNAKE_LAYOUT_CELL_WIDTH / 2 <
-      canvasWidth;
+    const monomerOccupiedWidth =
+      lastPosition.x + width + DISTANCE_FROM_RIGHT + CELL_WIDTH / 2;
+    const isMonomerFitCanvas = monomerOccupiedWidth < canvasWidth;
 
     if (!isMonomerFitCanvas) {
       return {

packages/ketcher-core/src/domain/entities/Nucleoside.ts

@@ -15,9 +15,9 @@ import { Command } from 'domain/entities/Command';
 import { getRnaPartLibraryItem } from 'domain/helpers/rna';
 import { BaseMonomer } from 'domain/entities/BaseMonomer';
 import { AmbiguousMonomer } from 'domain/entities/AmbiguousMonomer';
-import { RNA_MONOMER_DISTANCE } from 'application/editor/tools/RnaPreset';
 import { SugarRenderer } from 'application/render';
 import { RNA_DNA_NON_MODIFIED_PART } from 'domain/constants/monomers';
+import { CELL_WIDTH } from './DrawingEntitiesManager';
 import { KetMonomerClass } from 'application/formatters';
 
 export class Nucleoside {
@@ -64,7 +64,7 @@ export class Nucleoside {
     const topLeftItemPosition = position;
     const bottomItemPosition = position.add(
       Coordinates.canvasToModel(
-        new Vec2(0, RNA_MONOMER_DISTANCE + SugarRenderer.monomerSize.height),
+        new Vec2(0, CELL_WIDTH + SugarRenderer.monomerSize.height),
       ),
     );
     const modelChanges = new Command();

packages/ketcher-core/src/domain/entities/Nucleotide.ts

@@ -15,9 +15,8 @@ import { getRnaPartLibraryItem } from 'domain/helpers/rna';
 import { RNA_DNA_NON_MODIFIED_PART } from 'domain/constants/monomers';
 import { BaseMonomer } from 'domain/entities/BaseMonomer';
 import { AmbiguousMonomer } from 'domain/entities/AmbiguousMonomer';
-import { RNA_MONOMER_DISTANCE } from 'application/editor/tools/RnaPreset';
 import { SugarRenderer } from 'application/render';
-import { SNAKE_LAYOUT_CELL_WIDTH } from 'domain/entities/DrawingEntitiesManager';
+import { CELL_WIDTH } from 'domain/entities/DrawingEntitiesManager';
 import { KetMonomerClass } from 'application/formatters';
 
 export class Nucleotide {
@@ -76,7 +75,7 @@ export class Nucleotide {
     const topLeftItemPosition = position;
     const bottomItemPosition = position.add(
       Coordinates.canvasToModel(
-        new Vec2(0, RNA_MONOMER_DISTANCE + SugarRenderer.monomerSize.height),
+        new Vec2(0, CELL_WIDTH + SugarRenderer.monomerSize.height),
       ),
     );
 
@@ -88,7 +87,7 @@ export class Nucleotide {
         rnaBasePosition: bottomItemPosition,
         phosphate: phosphateLibraryItem,
         phosphatePosition: topLeftItemPosition.add(
-          Coordinates.canvasToModel(new Vec2(SNAKE_LAYOUT_CELL_WIDTH, 0)),
+          Coordinates.canvasToModel(new Vec2(CELL_WIDTH, 0)),
         ),
       });