MollyCule is described as 'completely free Open Source Chemistry visualisation program for MacOS, Linux and Windows. MollyCule is designed to be a nice, easy to use program to help ordinary people who want to explore Chemistry' and is an app in the Education & Reference category. There are four alternatives to MollyCule for Windows, Mac, Linux and Wine. The best alternative is Marvin, which is free. Other great apps like MollyCule are BKchem (Free, Open Source), ACD/ChemSketch (Free Personal) and ChemDraw (Paid).
Marvin suite is a chemically intelligent desktop toolkit built to help you draw, edit, publish, render, import and export your chemical structures and as well as allowing you to convert between various chemical and graphical file formats.
ACD/ChemSketch is a chemically intelligent drawing interface that allows you to draw almost any chemical structure including organics, organometallics, polymers, and Markush structures. Use it to produce professional looking structures and diagrams for reports and publications.