Squashed commit of the following:

commit 42a2a6c Author: Roman Rodionov <[email protected]> Date: Thu Dec 12 11:29:11 2024 +0100 #6109 - Antisense of layout doesn't work on flex mode after load (#6114) (#6138) * #6109 - Antisense of layout doesn't work on flex mode after load - applied snake layout in flex mode if open/paste file with antisense chain - fixed open file implementation * #6083 - Creation of antisense chain causes monomer re-arrangement on the flex canvas - applied zoom to left top corner of the structures after antisense chains creation - updated ketcher version to 2.28.0-rc.2 commit 6c4a38b Author: Roman Rodionov <[email protected]> Date: Thu Dec 12 11:28:28 2024 +0100 #6107 - Create Antisense Strand doesn't work in some cases (#6116) (#6120) - changed implementation of searching first monomers in selection (in this case monomer can be in the middle of the chain and does not have free r1 attachment point) - changed antisense base for Adenine commit c7d3f22 Author: Roman Rodionov <[email protected]> Date: Thu Dec 12 11:27:46 2024 +0100 #5032 - Selection of monomers should disappear when the user moves the cursor (#6136) commit 8862787 Author: Roman Rodionov <[email protected]> Date: Wed Dec 11 23:06:58 2024 +0100 Backmerge: #5949 - Delete of micromolecules bonds works wrong (or doesn't work) (#6124) * #5949 - Delete of micromolecules bonds works wrong (or doesn't work) - added invertAfterAllOperations method to atom and bonds operations to allow renderers rely on final state of model before rendering - added deleting of atoms and bonds from molecules struct to synchronize molecules and macromolecules modes - reworked bonds/atoms deletion logic - moved post execution logic from renderer to command commit dc4cfdc Author: Igor Kostrubin <[email protected]> Date: Wed Dec 11 20:54:17 2024 +0100 #5796 - Indigo functions doesn't work if monomer on micro canvas - system throws an error: Error: Cannot deserialize input JSON. (#6130) commit 014472b Author: Roman Rodionov <[email protected]> Date: Wed Dec 11 17:50:13 2024 +0100 #5317 - Some side chain bonds are not shown in Sequence mode for bases, CHEMs, phosphates and sugars (#6054) commit b236964 Author: Maksim Labovich <[email protected]> Date: Wed Dec 11 18:55:54 2024 +0300 #5476 - Copy/Cut and Paste using Ctrl+C/X and Ctrl+V doesn't work for static elements in Mozilla Firefox (#6121) * #5476 - save to text/plain in KET format instead of RXN - Firefox doesn't support MIME types other than text/plain in ClipboardItem, and RXN format saved by default to text/plain supports only chemical elements * #5476 - added comment, added stringify for data object to avoid [object Object] in console commit fa13b99 Author: Roman Rodionov <[email protected]> Date: Wed Dec 11 15:48:24 2024 +0100 #6086 - Unable to create antisense chains for ambiguous monomers from the library (#6113) (#6118) - added antisense creation for chains with ambiguous bases commit 668758d Author: Roman Rodionov <[email protected]> Date: Wed Dec 11 15:34:37 2024 +0100 #6096 - Antisense creation works wrong in case of partial selection (#6122) (#6123) - fixed creation of antisense for partial selection by several pieces in one chain commit 89f5ce6 Author: Ruslan <[email protected]> Date: Wed Dec 11 13:14:21 2024 +0500 #6127 - Hover mouse over ambiguous monomer on Micromolecules canvas causes app crash (#6128) commit cca5f90 Author: Anrei Menshikov <[email protected]> Date: Wed Dec 11 12:05:35 2024 +0400 #5978-entire-element-bounding-box-should-be-clickable-not-only-black-dots (#6059) * 5978-entire-element-bounding-box-should-be-clickable-not-only-black-dots * Refactoring * fix test * add new metod bondHoverablePath after review * createBondHoverablePath new logic * add type,const and refctoring createBondHoverablePath * commit TODO for mouseEvents * add ?? operand --------- Co-authored-by: Andrey Menshikov <[email protected]> commit 932ed0f Author: Roman Rodionov <[email protected]> Date: Tue Dec 10 12:49:17 2024 +0100 Backmerge: #6068 - Same chain configuration imported by different HELM layouted differently (anyway - both are wrong) (#6111) * #6068 - Same chain configuration imported by different HELM layouted differently (anyway - both are wrong) (#6099) #6074 - System doesn't flip chain if connected to monomer but not to base (2) #6068 - Same chain configuration imported by different HELM layouted differently (anyway - both are wrong) #6074 - System doesn't flip chain if connected to monomer but not to base (2) #6080 - System doesn't flip chain if connected to monomer but not to base (3) #6081 - Smaller chain should be at the bottom #6087 - Antisense layout is wrong for any ambiguouse base from the library #6077 - H-bond is not alligned to Snake mode view in some cases #6076 - Two-to-one base H-bond connection layouted wrong #6075 - In case of multipal H-bonds system should arrange antisence chain to first base of bottom chain #6070 - System doesn't flip chain if connected to monomer but not to base #6067 - Two chains connected by H-bond arranged wrong if third bond present on the canvas #6061 - RNA chain remain flipped after hydrogen bond removal - reworked antisense chains calculation * - fixed flacky test
epam · Dec 12, 2024 · 7590a7f · 7590a7f
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diff --git a/packages/ketcher-core/package.json b/packages/ketcher-core/package.json
@@ -1,6 +1,6 @@
 {
   "name": "ketcher-core",
-  "version": "2.28.0-rc.1",
+  "version": "2.28.0-rc.2",
   "description": "Web-based molecule sketcher",
   "license": "Apache-2.0",
   "homepage": "http://lifescience.opensource.epam.com/ketcher",

diff --git a/packages/ketcher-core/src/application/editor/Editor.ts b/packages/ketcher-core/src/application/editor/Editor.ts
@@ -41,7 +41,12 @@ import assert from 'assert';
 import { SequenceType, Struct, Vec2 } from 'domain/entities';
 import { BaseMonomer } from 'domain/entities/BaseMonomer';
 import { Command } from 'domain/entities/Command';
-import { DrawingEntitiesManager } from 'domain/entities/DrawingEntitiesManager';
+import {
+  DrawingEntitiesManager,
+  MONOMER_START_X_POSITION,
+  MONOMER_START_Y_POSITION,
+  SNAKE_LAYOUT_CELL_WIDTH,
+} from 'domain/entities/DrawingEntitiesManager';
 import { PolymerBond } from 'domain/entities/PolymerBond';
 import { AttachmentPointName, MonomerItemType } from 'domain/types';
 import { DOMSubscription } from 'subscription';
@@ -416,6 +421,7 @@ export class CoreEditor {
 
     this.renderersContainer.update(modelChanges);
     history.update(modelChanges);
+    this.scrollToTopLeftCorner();
   }
 
   private onSelectMonomer(monomer: MonomerItemType) {
@@ -786,4 +792,17 @@ export class CoreEditor {
 
     ZoomTool.instance.zoomStructureToFitHalfOfCanvas(structureBbox);
   }
+
+  public scrollToTopLeftCorner() {
+    const drawnEntitiesBoundingBox =
+      RenderersManager.getRenderedStructuresBbox();
+
+    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,
+      false,
+    );
+  }
 }
diff --git a/packages/ketcher-core/src/application/editor/modes/FlexMode.ts b/packages/ketcher-core/src/application/editor/modes/FlexMode.ts
@@ -30,7 +30,25 @@ export class FlexMode extends BaseMode {
   }
 
   applyAdditionalPasteOperations() {
-    return new Command();
+    const command = new Command();
+    const editor = CoreEditor.provideEditorInstance();
+
+    editor.drawingEntitiesManager.recalculateAntisenseChains();
+
+    if (!editor.drawingEntitiesManager.hasAntisenseChains) {
+      return command;
+    }
+
+    command.merge(
+      editor.drawingEntitiesManager.applySnakeLayout(
+        editor.canvas.width.baseVal.value,
+        true,
+        true,
+        true,
+      ),
+    );
+
+    return command;
   }
 
   isPasteAllowedByMode(): boolean {

diff --git a/packages/ketcher-core/src/application/editor/modes/SequenceMode.ts b/packages/ketcher-core/src/application/editor/modes/SequenceMode.ts
@@ -804,12 +804,14 @@ export class SequenceMode extends BaseMode {
         shortcut: ['ArrowUp'],
         handler: () => {
           SequenceRenderer.moveCaretUp();
+          this.unselectAllEntities();
         },
       },
       'move-caret-down': {
         shortcut: ['ArrowDown'],
         handler: () => {
           SequenceRenderer.moveCaretDown();
+          this.unselectAllEntities();
         },
       },
       'move-caret-forward': {
@@ -818,8 +820,10 @@ export class SequenceMode extends BaseMode {
           if (!this.isEditMode) {
             return;
           }
+
           SequenceRenderer.moveCaretForward();
           SequenceRenderer.resetLastUserDefinedCaretPosition();
+          this.unselectAllEntities();
         },
       },
       'move-caret-back': {
@@ -828,8 +832,11 @@ export class SequenceMode extends BaseMode {
           if (!this.isEditMode) {
             return;
           }
+
           SequenceRenderer.moveCaretBack();
           SequenceRenderer.resetLastUserDefinedCaretPosition();
+
+          this.unselectAllEntities();
         },
       },
       'add-sequence-item': {

diff --git a/packages/ketcher-core/src/application/editor/modes/SnakeMode.ts b/packages/ketcher-core/src/application/editor/modes/SnakeMode.ts
@@ -7,11 +7,6 @@ import { Command } from 'domain/entities/Command';
 import { ReinitializeModeOperation } from 'application/editor/operations/modes';
 import { Vec2 } from 'domain/entities';
 import { RenderersManager } from 'application/render/renderers/RenderersManager';
-import {
-  MONOMER_START_X_POSITION,
-  MONOMER_START_Y_POSITION,
-  SNAKE_LAYOUT_CELL_WIDTH,
-} from 'domain/entities/DrawingEntitiesManager';
 
 export class SnakeMode extends BaseMode {
   constructor(previousMode?: LayoutMode) {
@@ -33,22 +28,10 @@ export class SnakeMode extends BaseMode {
         );
 
     editor.drawingEntitiesManager.applyFlexLayoutMode();
-
     command.merge(modelChanges);
     editor.renderersContainer.update(modelChanges);
     command.setUndoOperationReverse();
-
-    const drawnEntitiesBoundingBox =
-      RenderersManager.getRenderedStructuresBbox();
-    const zoom = ZoomTool.instance;
-
-    zoom.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,
-      false,
-    );
+    editor.scrollToTopLeftCorner();
 
     return command;
   }

diff --git a/packages/ketcher-core/src/domain/entities/DrawingEntitiesManager.ts b/packages/ketcher-core/src/domain/entities/DrawingEntitiesManager.ts
@@ -2647,7 +2647,7 @@ export class DrawingEntitiesManager {
 
   private get antisenseChainBasesMap() {
     return {
-      [RnaDnaNaturalAnaloguesEnum.ADENINE]: RnaDnaNaturalAnaloguesEnum.THYMINE,
+      [RnaDnaNaturalAnaloguesEnum.ADENINE]: RnaDnaNaturalAnaloguesEnum.URACIL,
       [RnaDnaNaturalAnaloguesEnum.CYTOSINE]: RnaDnaNaturalAnaloguesEnum.GUANINE,
       [RnaDnaNaturalAnaloguesEnum.GUANINE]: RnaDnaNaturalAnaloguesEnum.CYTOSINE,
       [RnaDnaNaturalAnaloguesEnum.THYMINE]: RnaDnaNaturalAnaloguesEnum.ADENINE,
@@ -2824,6 +2824,12 @@ export class DrawingEntitiesManager {
     return command;
   }
 
+  public get hasAntisenseChains() {
+    return [...this.monomers.values()].some(
+      (monomer) => monomer.monomerItem.isAntisense,
+    );
+  }
+
   private getAntisenseBaseLabel(rnaBase: RNABase | AmbiguousMonomer) {
     return this.antisenseChainBasesMap[
       rnaBase instanceof AmbiguousMonomer

diff --git a/packages/ketcher-core/src/domain/entities/monomer-chains/ChainsCollection.ts b/packages/ketcher-core/src/domain/entities/monomer-chains/ChainsCollection.ts
@@ -14,6 +14,7 @@ import {
 } from 'domain/entities';
 import {
   getNextMonomerInChain,
+  getPreviousMonomerInChain,
   getRnaBaseFromSugar,
   isMonomerConnectedToR2RnaBase,
   isRnaBaseOrAmbiguousRnaBase,
@@ -128,15 +129,15 @@ export class ChainsCollection {
       chainsCollection.add(new Chain(monomer, !!IsChainCycled.CYCLED));
     });
 
-    if (
-      firstMonomersInRegularChains.length === 0 &&
-      firstMonomersInCycledChains.length === 0
-    ) {
-      const topLeftMonomer = this.getMonomerWithLowerCoordsFromMonomerList(
-        filteredMonomers.filter((monomer) => !(monomer instanceof RNABase)),
-      );
+    const firstMonomersInMiddleOfChains =
+      this.getFirstMonomersInMiddleOfChains(filteredMonomers);
 
-      chainsCollection.add(new Chain(topLeftMonomer));
+    if (firstMonomersInMiddleOfChains.length) {
+      firstMonomersInMiddleOfChains.forEach(
+        (firstMonomerInMiddleOfChain: BaseMonomer) => {
+          chainsCollection.add(new Chain(firstMonomerInMiddleOfChain));
+        },
+      );
     }
 
     return chainsCollection;
@@ -184,6 +185,42 @@ export class ChainsCollection {
     return firstMonomersInChains;
   }
 
+  private static getFirstMonomersInMiddleOfChains(monomers: BaseMonomer[]) {
+    const initialMonomersSet = new Set(monomers);
+    const handledMonomers = new Set<BaseMonomer>();
+    const firstMonomersInMiddleOfChains: BaseMonomer[] = [];
+
+    monomers.forEach((monomer) => {
+      if (handledMonomers.has(monomer)) {
+        return;
+      }
+
+      handledMonomers.add(monomer);
+
+      let previousMonomerInChain = getPreviousMonomerInChain(monomer);
+
+      while (
+        previousMonomerInChain &&
+        !handledMonomers.has(previousMonomerInChain) &&
+        !initialMonomersSet.has(previousMonomerInChain)
+      ) {
+        const previousMonomer = getPreviousMonomerInChain(
+          previousMonomerInChain,
+        );
+
+        handledMonomers.add(previousMonomerInChain);
+
+        if (!previousMonomer) {
+          firstMonomersInMiddleOfChains.push(previousMonomerInChain);
+        } else {
+          previousMonomerInChain = previousMonomer;
+        }
+      }
+    });
+
+    return firstMonomersInMiddleOfChains;
+  }
+
   public get firstNode() {
     return this.chains[0]?.subChains[0]?.nodes[0];
   }

diff --git a/packages/ketcher-core/src/domain/helpers/monomers.ts b/packages/ketcher-core/src/domain/helpers/monomers.ts
@@ -73,6 +73,24 @@ export function isMonomerConnectedToR2RnaBase(monomer?: BaseMonomer) {
   );
 }
 
+export function getPreviousMonomerInChain(monomer: BaseMonomer) {
+  const r1PolymerBond = monomer.attachmentPointsToBonds.R1;
+  const previousMonomer =
+    r1PolymerBond instanceof PolymerBond
+      ? r1PolymerBond?.getAnotherMonomer(monomer)
+      : undefined;
+
+  if (!previousMonomer || !(r1PolymerBond instanceof PolymerBond)) {
+    return undefined;
+  }
+
+  return previousMonomer &&
+    previousMonomer.getAttachmentPointByBond(r1PolymerBond) ===
+      AttachmentPointName.R2
+    ? previousMonomer
+    : undefined;
+}
+
 export function getNextMonomerInChain(
   monomer?: BaseMonomer,
   firstMonomer?: BaseMonomer | null,

diff --git a/packages/ketcher-macromolecules/package.json b/packages/ketcher-macromolecules/package.json
@@ -1,6 +1,6 @@
 {
   "name": "ketcher-macromolecules",
-  "version": "2.28.0-rc.1",
+  "version": "2.28.0-rc.2",
   "description": "Web-based molecule sketcher",
   "license": "Apache-2.0",
   "homepage": "http://lifescience.opensource.epam.com/ketcher",

diff --git a/packages/ketcher-macromolecules/src/components/modal/Open/Open.tsx b/packages/ketcher-macromolecules/src/components/modal/Open/Open.tsx
@@ -29,6 +29,7 @@ import {
   macromoleculesFilesInputFormats,
   ModeTypes,
   SnakeMode,
+  FlexMode,
 } from 'ketcher-core';
 import { IndigoProvider } from 'ketcher-react';
 import { RequiredModalProps } from '../modalContainer';
@@ -175,6 +176,22 @@ const addToCanvas = ({
   const editorHistory = new EditorHistory(editor);
   const isSequenceMode = editor.mode instanceof SequenceMode;
   const isSnakeMode = editor.mode instanceof SnakeMode;
+  const isFlexMode = editor.mode instanceof FlexMode;
+
+  if (isFlexMode) {
+    editor.drawingEntitiesManager.recalculateAntisenseChains();
+
+    if (editor.drawingEntitiesManager.hasAntisenseChains) {
+      modelChanges.merge(
+        editor.drawingEntitiesManager.applySnakeLayout(
+          editor.canvas.width.baseVal.value,
+          true,
+          true,
+          true,
+        ),
+      );
+    }
+  }
 
   editor.renderersContainer.update(modelChanges);
   editorHistory.update(modelChanges);

diff --git a/packages/ketcher-react/package.json b/packages/ketcher-react/package.json
@@ -1,6 +1,6 @@
 {
   "name": "ketcher-react",
-  "version": "2.28.0-rc.1",
+  "version": "2.28.0-rc.2",
   "description": "Web-based molecule sketcher",
   "license": "Apache-2.0",
   "homepage": "http://lifescience.opensource.epam.com/ketcher",

diff --git a/packages/ketcher-standalone/package.json b/packages/ketcher-standalone/package.json
@@ -1,6 +1,6 @@
 {
   "name": "ketcher-standalone",
-  "version": "2.28.0-rc.1",
+  "version": "2.28.0-rc.2",
   "description": "Web-based molecule sketcher",
   "license": "Apache-2.0",
   "homepage": "http://lifescience.opensource.epam.com/ketcher",