Fix canvas shift when switching from Snake back to Flex layout mode

[Copilot]

Fix canvas shift when switching from Snake back to Flex layout mode

The issue occurs when switching from Flex → Snake → Flex modes. The structure shifts position on the canvas.

Root Cause:

• When switching to SnakeMode, applySnakeLayout() physically moves monomers to new positions starting from (20, 20)
• When switching back to FlexMode, the original code called recalculateCanvasMatrix() which was using the retained snakeLayoutMatrix
• This caused additional unwanted repositioning of the monomers

Solution:

• Remove the recalculateCanvasMatrix() call from FlexMode.initialize()
• FlexMode doesn't use matrix-based layout, so this call is unnecessary
• Monomers now stay in their current positions when switching modes

Implementation:

• Modified FlexMode.initialize() in /packages/ketcher-core/src/application/editor/modes/FlexMode.ts
• Removed the line: command.merge(editor.drawingEntitiesManager.recalculateCanvasMatrix());
• Changed to merge modelChanges directly: command.merge(modelChanges);

Testing & Validation:

• Build ketcher-core successfully
• Run tests - all 305 tests passed (12 skipped, 4 test suites skipped)
• Addressed feedback from @NikitaKuzminn about structure moving to (0,0)

Original prompt

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This section details on the original issue you should resolve

<issue_title>Switching from Flex to Snake and back shifts canvas from top left corner to the bottom right corner</issue_title>
<issue_description>Steps to Reproduce

1. Go to Macromolecules
2. Change Sequence layout mode to Flex layout mode (dropdown on the top panel - Macromolecules modes switcher in documentation) on the empty canvas (to clean canvas, press Ctrl+Del)
3. Copy the structure in KET format from this file to the clean canvas (focus on canvas and press Ctrl+V or via Open -> Paste from clipboard) : Switching from Flex to Snake and back shits canvas from top left corner to the center.ket
4. Switch to Snake layout mode (dropdown on the top panel - Macromolecules modes switcher in documentation)
5. Switch back to Flex layout mode (dropdown on the top panel - Macromolecules modes switcher in documentation)
   Actual behavior
   Structure shifted from top left corner to the bottom right corner
   

Expected behavior
Structure remain in place

Versions

• Ketcher Version 3.3.0-rc.3 Build at 2025-04-10; 10:48:12
• Indigo Version 1.31.0-rc.1.0-g859747ec7-wasm32-wasm-clang-19.0.0
• Chrome Version 135.0.7049.85 (Official Build) (64-bit)
• Win10

Related issues: #6435</issue_description>

Comments on the Issue (you are @copilot in this section)

@SefaBilgii This issue is reproducible

Ketcher Version: 3.7.0-rc.1
OS: MacOs Sequoia Version 15.5
Browser : Chrome Version 138.0.7204.169
Indigo version 1.35.0-rc.1.0</comment_new>
<comment_new>@AlinaLysenko
Reproduced by agent - https://chatgpt.com/share/693c122e-9448-800e-9221-0dc755e882af</comment_new>

• Fixes Switching from Flex to Snake and back shifts canvas from top left corner to the bottom right corner #6940

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[NikitaKuzminn]

@copilot
Now the structure flies off to some random place, presumably to 0, 0 on the canvas, but I want it to stay in the same place when switching modes.

[Copilot]

@copilot
Now the structure flies off to some random place, presumably to 0, 0 on the canvas, but I want it to stay in the same place when switching modes.

Fixed in commit 3366beb. Removed the recalculateCanvasMatrix() call from FlexMode entirely since FlexMode doesn't use matrix-based layout. This keeps monomers in their current positions when switching modes instead of moving them.