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/usr/share/doc/chemtool/TODO is in chemtool 1.6.14-2.

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 - more demo structures / templates
 - better documentation
 - combining mark and move modes without losing functionality
 - grouping (conceptually similar to xfig's compound objects) and automatic alignment
 - add option for drawing "background" rectangle if format does not support setting 
   the background color)
 - support user-defined colors
 - rewrite on-screen sub/superscript text rendering using pango markup