"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

[ivanmaslow]

Steps to Reproduce Case 1 - Reactions

1. Add to Canvas a reaction:
   
2. Save reaction to RXN V2000 or V3000
3. Open RXN document and manually change coordinates to 0.0000:
   
   Example of files with changed coordinates for RXN V2000, V3000:
   !rxn-v2000-0-coordinates.zip
   !rxn-v3000-0-coordinates.zip
4. Add RXN files to Canvas

Actual behavior

• Error "Convert error! metalayout: average bond length is too small" appears for RXN V2000/V3000:
  

Expected behavior

• 1:1 reaction is added to Canvas without errors;

Environment details

• Tested on RC SA env
• Ketcher [Version 2.25.0-rc.5] Build at 2024-09-24; 18:17:25
• Indigo Version Version 1.24.0-rc.4.0-gdf51dc428-wasm32-wasm-clang-19.0.0
• Desktop Windows 11 Enterprise
• Chrome Version 129.0.6668.70 (Official Build) (64-bit)

Notes

• The fix also should be tested for RDF - to load as RDF, add $RDFILE to the top line of RXN document with reaction;
• Issue can be related to this defect - Molecule with 0 coordinates in MOL V2000 is displayed incorrectly on Canvas after loading #2432
• Issue is detected during exploratory testing of Load from RDF feature, but it's an existing issue and not related to new changes - Position single elements and reactions, not included to the first cascade reaction #2102