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Error returned when try to convert structure with custom query for bond into SMARTS format #1351

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urszula-gawlowska opened this issue Oct 19, 2023 · 0 comments · Fixed by #1353
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@urszula-gawlowska
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Steps to reproduction
Put anything at custom query for bond (e.g. '-' or '=') and try to convert it into SMARTS format

Expected behavior
Structure should be converted without error

Actual behavior
Error at response:

{
    "error": "struct data not recognized as molecule, query, reaction or reaction query"
}

Technical details
Method:
v2/indigo/convert

Payload options:

{
  "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
}

Payload struct:
bond_custom_query_bug.zip

Indigo/Bingo version
Version 1.15.0-dev.3.0-g530e55f33-x86_64-linux-gnu-11.2.1
Version 1.15.0-dev.4.0-g4bfe0976e-x86_64-linux-gnu-11.2.1

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