The ordering of branches of cascade reactions and reactions themselves should be the same on Load/Save from/to RDF

[ivanmaslow]

Expected pathway reaction ordering
Idea is to follow reactant’s order: first reactant in a reaction must be "at the top" position of a multi-tailed arrow, as upper molecule in a reaction (reactant near multi-tailed arrow) must be the first reactant in RXN format.

Steps to Reproduce 1

1. Load from RDF file with the single cascade reaction with several branches:
   !Synthia_path_5_tails.zip

Actual Result

• The first branch of cascade reactions in RDF file is the second on Canvas:
  

Expected Result

• The first branch of cascade reactions in the RDF file is the first on Canvas

2. Save to RDF and Load again

Actual Result

• Positioning of elements is changed after Save/Load, but it should like after the first load:
  

Expected Result

• Positioning of elements isn't changed after Save/Load, it's displayed like after the first load

Steps to Reproduce 2

1. Load from RDF file with several single reactions:
   rdf-rxn-v2000-reactions-1x1-2x2-3x3.zip

Actual Result

• The first reaction in RDF file is the third on Canvas, the third reaction in RDF is the first on Canvas:
  

Expected Result

• Reactions should be displayed on Canvas as in RDF file 1:1, 2:2, 3:3

2. Save to RDF

Actual Result

• It can't be saved as separate reactions:
  

Expected Result

• It can be saved as separate reactions 1:1, 2:2, 3:3
• It will be fixed in scope of User can't correctly save (or make a layout) to RDF/RXN reaction several products or with separate positioned molecules #2412

Steps to Reproduce 3 - Ordering of elements

1. Load from KET reaction:ket-cascade-reaction-3-1-2-1-1.zip
   
2. Click on Layout or make Save/Load to/from RDF:

Actual result:

• Arrow is changed according to indigo default sizes, elements are aligned, cyclopropane changes the position:
  

Expected result:

• Arrow is changed according to indigo default sizes, elements are aligned, cyclopropane doesn't change the position:
  

Environment details:

• Tested on CI CD master SA environment
• Ketcher [Version 2.25.0-rc.1] Build at 2024-09-18; 05:59:24
• Indigo Version 1.25.0-dev.1.38-gdbf49deb-wasm32-wasm-clang-12.0.0
• Windows 11 Enterprise
• Chrome Version 128.0.6613.138 (Official Build) (64-bit)

Notes

• Tests are added to xls and have to be automated after fixing
• Also, position of branches shouldn't be changed on Layout action
• Issue is detected during exploratory testing of Save RDF feature for cascade reactions - Save multi reactions (pathway, single, edge cases) to RDF #2237

[ivanmaslow]

Tested on CI CD env with 2309-update-layout:

• Ketcher [Version 2.25.0-rc.2] Build at 2024-09-30; 06:32:00
• Version 1.25.0-dev.2.6-g0e1cfa10-wasm32-wasm-clang-12.0.0
• Desktop, Windows 11 Enterprise
• Chrome Version 129.0.6668.71 (Official Build) (64-bit)

The second part of the defect isn't fixed:
Reactions are still not in order as in RDF, also the displaying for reactions with several products is broken:

[yauhen-karmyzau]

Cases are not fixed.

[ivanmaslow]

Pre-tested on aws_ci environment with Ketcher master and Indigo 2407-branch-ordering branches:

• Ketcher [Version 2.26.0-rc.1] Build at 2024-10-24; 12:25:38;
• Indigo Version 1.25.0-rc.3.18-gcdee98d4-wasm32-wasm-clang-12.0.0
• Desktop, Windows 11 Enterprise
• Chrome Version 130.0.6723.70 (Official Build) (64-bit)

In the first case, the ordering of branches isn't changed after layout actions on save/load to/from RDF:

But still the first branch in the file not the first branch on Canvas, you can see below screenshot how RXN reactions are positioned in RDF file:

The second case is fixed partially, so it can be loaded with correct ordering for this specific case:

But it still can be reproduced for other cases - mentioned in #2452 - ordering is changed after layout or save/load to/from RDF actions:


ketcher-2452.zip

The third case is fixed: