Ketcher sends different set of parameters to indigo in case of Copy/Paste and Layout operation

[AlexeyGirin]

Steps to Reproduce

1. Go to Micro
2. Load to canvas following reaction using paste from clipboard way: [#15]1-[#6]=[#6]-[#6]=[#6]-1>Br.Br>[#8]

Actual behavior
Reaction layout is wrong

This is because ketcher sends different set of parameters to indigo:
Paste operation:

{
  "smart-layout": true,
  "ignore-stereochemistry-errors": true,
  "mass-skip-error-on-pseudoatoms": false,
  "gross-formula-add-rsites": true,
  "aromatize-skip-superatoms": true,
  "dearomatize-on-load": false,
  "ignore-no-chiral-flag": false,
  "gross-formula-add-isotopes": true,
  "bond-length-unit": "px",
  "bond-length": 40,
  "reaction-component-margin-size-unit": "px",
  "reaction-component-margin-size": 20,
  "image-resolution": 72
}

Layout operation:

{
  "smart-layout": true,
  "ignore-stereochemistry-errors": true,
  "mass-skip-error-on-pseudoatoms": false,
  "gross-formula-add-rsites": true,
  "aromatize-skip-superatoms": true,
  "dearomatize-on-load": false,
  "ignore-no-chiral-flag": false,
  "gross-formula-add-isotopes": true,
  "render-label-mode": "terminal-hetero",
  "render-font-size": 13,
  "render-font-size-unit": "px",
  "render-font-size-sub": 13,
  "render-font-size-sub-unit": "px",
  "output-content-type": "application/json",
  "bond-length-unit": "px",
  "bond-length": 40,
  "reaction-component-margin-size-unit": "px",
  "reaction-component-margin-size": 20,
  "image-resolution": 72
}

Expected behavior
Reaction layout is correct

Versions

• Ketcher Version 2.28.0-dev.1 Build at 2024-11-28; 06:41:11
• Version 1.27.0-dev.3.0-g62217e49f-wasm32-wasm-clang-19.0.0
• Chrome Version 131.0.6778.86 (Official Build) (64-bit)
• Win10

Issue found while testing - epam/ketcher#5152

[AliaksandrDziarkach]

Reproduced only with SMARTS .

[AlexeyGirin]

Works wrong only for SMARTS
Problem is on Indigo side