Disease predicting software for small molecules
Do you mean predicting health effects/toxicity of a given chemical? I haven't seen such software and I doubt it exists. Much easier problem (predict optimal synthetic route to compound X remains unsolved.   

By hand your best way is to check toxicity of related compounds. A program that can predict health effects of compounds will revolutionize drug design (and cause job loss for 99% of RnD chemists in pharma).