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 five alternatives to MollyCule for Windows, Mac, Linux, BSD and Wine. The best MollyCule alternative is Chemaxon Marvin, which is free. Other great apps like MollyCule are Molsketch, ChemDraw, ACD/ChemSketch and BKchem.
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.
A 2D molecular editing tool for GNU/Linux, Mac OS X and Windows. Its goal is to help you draw molecules quick and easily. Of course your creations can be exported afterwards in high quality in a number of vector and bitmap formats.
ChemDraw is a communication suite for managing, reporting and presenting Chemistry research. Produce precise chemical structures with our premier chemical drawing solution.
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.
BKChem is a free (as in free software :o) chemical drawing program. It was conceived and written by Beda Kosata and is currently maintained by Reinis Danne.
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