BKChem

BKChem is a vector graphics application, developed on Python, that lets you create a schematic representation of a chemical compound by hand.

Editing compounds is really easy, thanks to bond-by-bond drawing and restrictions in their length and angle. It supports linear formulas, charges, and radicals.

You don't need to draw every single compound by hand; BKChem includes default models for benzene, purine, cyclopentadiene, cyclopentane, and cycloheptane.

The models you create with BKChem can be exported into a wide range of formats, such as SVG, OpenOffice Draw, ODF, PDF, PNG, CML, CML2, Molfies, SMILES, and Encapsulated PostScript.