epub version 3 supports math equations and symbols and svg graphs and fonts with symbols but there is not a tool to do automatic conversions with a decent formatting of the equations since the format of those publications is veryplex I may be wrong but I think that indesign or quark can import the PDFs and then after re-formating the changes you can export to epub would be a lot easier if you have the source file of those PDFs but still will need the human touch always does not matter what tool you choice there is always some level of manual formatting involve to get the right format and proper TOCs