Debugging and Improvements for `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