Skip to content

Debugging and Improvements for `visualize_indigo`

R requested to merge visualize_indigo_debug into visualize_indigo

This merge request addresses the following bugs and (minor) improvements:

  • Prevent label merge errors using angle constraints; wedge hash spacing increased
  • Added area threshold for solid wedge labeling (before MST)
    • Addresses bug where very short lines were being interpreted as wedges
  • Repaired PDF debug image generation
  • Fixed character order for new sequence label nodes (LabelDisplay attribute)
  • Corrected font size for new node types (e.g., OH)
  • Using merged parallel line vertices in create_final_graph, code clean-up

Testing From the directory graphics_recognition:

  • git pull; git checkout visualize_indigo_debug
  • make chem-v2-all-test

Check CDXML

  • Check the file outputs/All/generated_cdxmls/or100.09.tables_full_cdxml/or100.09.tables_allpages.cdxml in ChemDraw, checking structures against the standard 24-page test file

Check SMILES

  • cp outputs/All/generated_smiles/or100.09.tables/smiles_out.txt ./smiles_test_NEW.txt
  • git checkout visualize_indigo
  • make chem-v2-all-test
  • diff outputs/All/generated_smiles/or100.09.tables/smiles_out.txt ./smiles_test_NEW.txt

Merge request reports