Data in images: what tools for data visualization?

Free or open-source tools for chemistry

This is a non-exhaustive review of available tools, developed by the community or accessible free-of-charge for academics, for molecule editing and spectra visualization software. (1)

Focus on the ChemAxon suite

The software included in the ChemAxon suite are proprietary tools which can be made available free-of-charge to researchers and students with an academic license. A similar model exists for Chemsketch. This concerns MarvinSketch, a very complete 2D/3D molecule editor, and Jchem, a plug-in compatible with Microsoft tools (Word, Excel, PowerPoint, Outlook).

MarvinSketch is compatible with many formats for import/export and calculates molecular properties. It has a prediction and visualization tool for NMR spectra. It also performs structure searches in the Reaxys and Chemicalize databases. Command lines can also be entered.

See all the Chemaxon tool documentation here

Selection of open source software

Logiciels Caractéristiques
JmolJmol is one of the most recognized molecular viewer tools. Available in 2D and 3D as well as spectra display. Jmol supports many file formats including standard .pdb, .mol and .xyz.
IQmolIQmol presents a sleek interface with many available functions. It is compatible with a variety of formats: xyz, cml, pdb, mol, fchk, cube data and Q-Chem. Extensive documentation is provided.
AvogadroAvogadro is compatible with nearly 80 file formats. 2D and 3D molecule editor and viewer.
MolviewMolview has the particularity of being a web application. Molecules can be edited in 2D and then converted to 3D. Export formats in png, .mol and jcamp. Searches can be made by chemical sub-structures from databases supported by Molview. Files cannot be imported.
JChempaintJChempaint is compatible with formats CML, MDL MOL, MDL SDF and exports to CML and MDL MOL formats. Structures are saved as images: BMP, JPEG, PNG, SVG.
BKChemBKChem is a simple 2D editor developed in Python that supports the CML, CML2 and Molfile formats and exports to SVG, OpenOffice, PDF and PNG formats for example.
GabeditSoftware developed by Abdul-Rahman Allouche, researcher at ILM (Lyon 1). It serves as a graphical interface for theoretical calculation software. It also allows molecules to be edited in 2D and 3D (Molecule Builder).
  • 1. This resource has been prepared with the assistance of Thierry Billard CNRS Director of Research at ICBMS (UMR CNRS 5246).