Skip to content

Fix character reversals and handling of '-' in Molconvert SVGs

R requested to merge cdxml_svg_fix into containerize

Addresses issue with SVG rendering shown below by:

  • Generating modified CDXML for SVG generation (no nested fragments; nicknames/fragments given type "Unknown")
  • Replacing '-' by '\-' in node labels (avoids superscript -- assuming we generally don't want charges there for now)

Testing:

  • git checkout cdxml_svg_fix
  • make clean-out; make chem-v2-all-test from top-level directory
  • Check that modified CDXMLs appear in outputs/All/generated_cdxmls/or100.09.tables_SVG with that associated svg images included in a svg/ subdirectory.
  • Check that the example below (Page 15 no 17) is correct in the generated SVG image.
  • Confirm that the full page CDXML file in the directory or100.09.tables_full_cdxml look correct.
  • Confirm that output at command line looks correct, and include this information on SMILES exact matches:
Exact matches: 141 243 Percent: 0.5802469135802469 
Eval Dir: outputs/All/eval_tsv/or100.09.tables_eval.tsv 
[ WRITING EVAL METRICS TO: outputs/All/eval_tsv... ]

image.png

Edited by R

Merge request reports