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Improving Molconvert SVG Rendering

R requested to merge SVG_fix into containerize

Minor changes, to force CDXML font sizes to have 'pt' at the end (e.g., size="6pt" rather than size="6")

  • Causes molconvert to complain (Java exception), but then render text much more readably
  • Also increased default render scale to 20 (%?) so that it is easier to read when loaded in a browser
  • Added flag for command-line SVG render when building files
  • Makefile rule chem-v2-all-test now includes the --svg flag to force SVG generation
  • Forced bracketed groups to be 'SRU' rather than 'MultipleGroup' (avoids molconvert adding 'ht' in SVGs)
  • No other changes to parsing/pipeline.

To test, run make clean-out; make chem-v2-all-test.

  • Confirm that the final CDXML file still looks okay (outputs/All/generated_cdxmls/or100.09.tables_full_cdxml/or100.09.tables.cdxml)
  • Look at SVG renders that will appear in the individual molecule CDXML directory: outputs/All/generated_cdxmls/or100.09.tables/. Confirm that text is more readable (use a web browser to view easily)
Edited by R

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