epam / epam/Indigo

Intermediate reaction products can't be recognized on Save to RDF/Layout if there are more than one product

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Cascade reactions MMPK Priority: Medium
Dominant language
C++
Stars
406
Forks
134
Avg merge
2d 11h
Merged PRs (30d)
24

Description

**Steps to Reproduce**
1. Add to Canvas 2:2:1 reaction from the RDF file:
[rdf-rxn-v3000-pathway-reaction-2-2-1.zip](https://github.com/user-attachments/files/17075447/rdf-rxn-v3000-pathway-reaction-2-2-1.zip)
![image](https://github.com/user-attachments/assets/f5d2a1ba-216d-447e-a814-af2785888608)
2. Click on Save to RDF - the similar issue as in https://github.com/epam/Indigo/issues/2412:
![image](https://github.com/user-attachments/assets/33dea389-86ea-4b12-afd0-4969f643ece2)
- When this part is fixed this case will work
3. Move up the second product to be intersected by the continuation of the single arrow:
![image](https://github.com/user-attachments/assets/3c01a8e3-f0dc-45f6-8732-c7939bc3b2bc)
4. Click on Save to RDF
5. Load from saved RDF file

**Actual Result**
- Reactions are displayed as separate:
![image](https://github.com/user-attachments/assets/08ca19e5-849d-40cf-b3f8-5f6f570d886c)

**Expected Result**
- TBD - need to be clarified with @AlexanderSavelyev and @vanoprenko;
- They should be displayed as one cascade;

**Workarounds to save this reaction to RDF as cascade reaction**
- Add a plus between elements:
![image](https://github.com/user-attachments/assets/9e8ba598-1f35-4d15-b014-05689dd7397b)
- Move element to not be intersected by arrow/tail - it will work after https://github.com/epam/Indigo/issues/2412:
![image](https://github.com/user-attachments/assets/ce853985-a13d-47c4-8345-83beb807d6e1)

**Environment details**
- Tested on CI-CD 2237-detect-pathway SA environment
- Ketcher [Version 2.25.0-rc.2] Build at 2024-09-20; 03:00:51
- Indigo Version 1.25.0-dev.1.57-gdf86cde5-wasm32-wasm-clang-12.0.0
- Windows 11 Enterprise
- Chrome Version 129.0.6668.59 (Official Build) (64-bit)

**Notes**
- Tests are added in xls and have to be automated after fix
- Issue is detected during exploratory testing of Save to RDF feature for cascade reactions - https://github.com/epam/Indigo/issues/2237

Contributor guide

No contributing guide indexed for this repository

Research direction

Reproduce the case with rdf-rxn-v3000-pathway-reaction-2-2-1.zip and the Save to RDF flow, comparing it with issue #2412. Review the existing XLS tests for cascade reactions and clarify the expected single-cascade result with the named contacts. Once the behavior is defined and fixed, automate the reported case and verify that the saved RDF reloads as one cascade.

Written by the indexing model from the issue text.

Assessment

Tech stack
cpp
Domain
data
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
35/100

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