Indigo functions doesn't work prorerly: Aromatize, Dearomatize, Layout, Clean Up, Hydrogens, Auto-Mapping Tool

[ivanmaslow]

Steps to Reproduce

1. Add a reaction with Benzene Rings and Multi-Tailed Arrow:
2. Corrupt one Benzene Ring:
   
3. Click on Indigo actions: Aromatize, Dearomatize, Layout, Clean Up, Hydrogens, Auto-Mapping Tool:
   
   

Actual behavior

• When clicking on Aromatize/Dearomatize - nothing happens
• When clicking on Layout - reaction is moved to the center, arrows are changed sizes, but benzene ring is still corrupted:
  
• When clicking on Clean Up - nothing happens, benzene ring is still corrupted
• When clicking on Add/Remove Explicit Hydrogens - nothing happens
• When clicking on Reaction Auto-Mapping Tool - error message "array: invalid index 1 (size=0)" is displayed:
  

Expected behavior

• When clicking on Aromatize/Dearomatize - benzene rings are aromatized/dearomatized for separate benzene ring

• When clicking on Layout - benzene ring is fixed, arrows sized are changed, reaction is moved to the center

• When clicking on Clean up - benzene ring is fixed, all elements are on the same positions

• When clicking on Add/Remove Explicit Hydrogens - hydrogens are added/removed as it works for separate benzene ring

• When clicking on Reaction Auto-Mapping Tool - it should work as for usual reaction with benzene rings

• aromatize/dearomatize/cip/calculate props - no changes to layout

• For layout for each molecule call layout separately. Tree (margin components, arrow size, etc) is recalculated

• For clean-up for each molecule call clean-up separately. Tree is not recalculated

Environment details

• Tested on CI-CD 2237-detect-pathway SA environment
• Ketcher [Version 2.25.0-rc.2] Build at 2024-09-24; 02:30:35
• Indigo Version 1.25.0-dev.1.58-ga966745f-wasm32-wasm-clang-12.0.0
• Windows 11 Enterprise
• Chrome Version 129.0.6668.59 (Official Build) (64-bit)

Notes

• Issue is detected during exploratory testing of Import/Export of Multi-Tailed Arrow in cascade reactions - Import/export multi-tails in KET #2236

[ivanmaslow]

Exploratory testing is completed on Remote env:

• Ketcher [Version 2.26.0-rc.3] Build at 2024-10-16; 14:42:10
• Indigo Version 1.25.0-rc.2.0-g867ae250b-x86_64-linux-gnu-11.2.1
• Desktop, Windows 11 Enterprise
• Chrome Version 130.0.6723.59 (Official Build) (64-bit)

Tests below are completed and updated in xls:

• Aromatize /Dearomatize actions for Benzene Rings when Cascade Reaction with Multi-Tailed arrow on Canvas:
  
  
• Layout actions for different combinations of single/cascade reaction with different positioning of reactants and products:
  
  
  • Issues:
    • User can't correctly save (or make a layout) to RDF/RXN reaction several products or with separate positioned molecules #2412
    • Reaction with the single arrow is changed to reaction with Multi-Tailed Arrow after layout action #2451
    • Reactions change the ordering on canvas after layout or save/load to/from RDF actions #2452
    • Layout and Save to RXN/RDF works not correctly when Multi-Tailed Arrow is on canvas without elements near tails or head, If no elements are near multi-tailed arrow, layout action should consider it as empty elements #2424
    • Intermediate reaction products can't be recognized on Save to RDF/Layout if there are more than one product #2416
    • Several cascade reactions are not aligned after layout or save/load to/from RDF actions #2498
• Clean up action for corrupted elements of cascade reaction with Multi-Tailed Arrow - elements are fixed and positioning isn't changed;
• Calculate CIP action works correctly for cascade reaction with Multi-Tailed Arrow:
  
  
• Check Structure and Calculate Values actions work correctly for cascade reactions with Multi-Tailed Arrow and it doesn't affect the reaction on Canvas
• Explicit Hydrogens can be added/removed to Cascade Reaction with Multi-Tailed Arrow -
  
• 3D view doesn't work correctly for cascade reaction because of existing issue - Static objects (shapes, images, arrows, plus, text) and elements are lost after 3D-mode applying on Canvas with chemical elements and static objects ketcher#5388
• Reaction Auto-Mapping Tool doesn't work correctly, defect is reported - Reaction Auto-Mapping Tool doesn't work for single and cascade reactions with Multi-Tailed Arrow #2556

All detected defects should be automated after fixing

[ivanmaslow]

New issues related to layout are detected:

• The ordering of several separate reactions is changed after layout and save/load to/from RDF actions #2584
• The ordering of reactions is changed after Undo/Redo of adding from file and Layout or Save/Load actions to/from RDF #2585