Position single elements and reactions, not included to the first cascade reaction

[yauhen-karmyzau]

As a User, I want any reactions or elements in the RDF file that are not included in the reaction tree to be placed below the reaction tree on the canvas, so that I can view all the data from the RDF file in a structured and organized manner.

Acceptance Criteria:

1. The application should identify any reactions or elements in the loaded RDF file that are not included in the reaction tree.

2. Reactants and products without match should be understand as a separate reactions.

3. These identified reactions or elements should be placed on the canvas below the reaction tree. They should not overlap with the reaction tree or with each other.

4. Reactions not included to a pathway reaction, should be displayed as separate multi-tail reactions.

   • The case in RDF a+b->c, d+e->f, c+g->h. After loading we will have a pathway for a+b->c, c+g->h and another reaction separately d+e->f

5. Reactions with more than one product can be a part of pathway reaction if the match happens, they will be displayed without pluses, otherwise reactions will be displayed as separate ones with a multi-tail arrow when we have several reactants and with a single arrow when we have 1 reactant

6. TBD: Molecule with atoms that are placed on the same position can be loaded as reactants or products in pathway reaction - issues with existing behavior, defects are reported - "Convert error! metalayout: average bond length is too small" error appears when loading from RDF and RXN V2000/V3000 reactions with molecules with 0 coordinates #2431, Molecule with 0 coordinates in MOL V2000 is displayed incorrectly on Canvas after loading #2432

7. Reagents should be ignored (TBD - create a task for case where reagents can be recognized)

8. In case of empty RDF (no reactions, reactants or products), nothing should be added to the canvas.

9. In cases of one reactant or one product in pathway reaction, it should works as for single arrow in RXN

10. RDF file can be recognized if there are reactions, RDF file with molecules only can't be recognized - error is displayed

11. After loading from the RDF file, the ordering of separate cascade reactions on Canvas should be the same as in the RDF file

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13. The placement of these reactions or elements should be done in an organized manner, maintaining a clear separation between the reaction tree and the additional reactions or elements.
14. The user should be able to view and interact with these additional reactions or elements just like any other elements on the canvas.
15. The application should handle the display of multiple additional reactions or elements, ensuring that all are visible and distinguishable.

[ivanmaslow]

Exploratory testing is completed on RC Remote env:

• Ketcher [Version 2.26.0-rc.1] Build at 2024-10-04; 18:51:40
• Indigo Version 1.25.0-rc.1.0-g704673fcb-x86_64-linux-gnu-11.2.1
• Desktop, Windows 11 Enterprise
• Chrome Version 129.0.6668.90 (Official Build) (64-bit)

The feature includes different cases for loading from RDF (single reactions, cascade reactions), checks below are covered, tests are updated:

• Loading from RDF based on RXN V2000, V3000, examples of files with single and cascade reaction:
  rdf-rxn-v2000-single-reaction-3x1.zip:
  
  rdf-rxn-v3000-cascade-reaction-2-1-1.zip:
  
• Different types/combinations of single and cascade reactions can be loaded from RDF and saved to KET with correct positions:
  
• Reagents in RDF in reactions are ignored and not displayed on Canvas on loading;
• RDF file can't be loaded from Macro mode;
• Basic functionality is working properly for elements loaded from RDF: Undo/Redo of adding/deletion/movement/copying, Movement, Selection, Deletion (Erase/Clear Canvas), Zoom, Copy/Paste;

Detected and fixed defects:

• Preview: "Unordered_map::at: key not found" error is displayed after adding of specific reactions from the RDF file #2411

But there are some failed manual tests based on detected defects and the main scenario should be retested after fixes in the nearest releases 1.25.0-rc.2, 1.26.0-rc.1:

• The ordering of branches of cascade reactions and reactions themselves should be the same on Load/Save from/to RDF  #2407
• Not correct length of head arrow after loading from RDF or layout action #2453
• Not correct length of Multi-Tailed Arrow and Single arrow after loading from RDF or Layout action #2555
• Specific 1:1 reaction is added to Canvas from RXN with incorrect positions of elements #2531
• If the root reaction has similar reactants, a cascade reaction is built only to the first reactant and creates an additional reaction for the second reactant #2406
• An RDF cascade (pathway) reaction with the same reactant and product, when loaded from a saved RDF file, is missing arrows and shows only one duplicated element #2320
• Single arrow isn't displayed after loading from RDF reaction without reactants (0:1, 0:2...) #2414

This issue is added to refined backlog and will be fixed later:

• UI issues with displaying of chemical elements with abbreviation after loading from RDF #2408

Also, some unrelated issues were detected during exploratory testing:

• "Convert error! metalayout: average bond length is too small" error appears when loading from RDF and RXN V2000/V3000 reactions with molecules with 0 coordinates #2431
• Molecule with 0 coordinates in MOL V2000 is displayed incorrectly on Canvas after loading #2432

[ivanmaslow]

New defects related to length of arrows are detected:

• Not correct length of Multi-Tailed and Single arrows for reactions with atoms after loading from RDF or Layout actions #2583
• Arrows overlap atoms of chemical elements after save/load to/from RDF or layout actions #2586