Open Access Software

mol2chemfig, a tool for rendering chemical structures from molfile or SMILES format to LATE X code

Eric K Brefo-Mensah and Michael Palmer*

Author Affiliations

Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada

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Journal of Cheminformatics 2012, 4:24  doi:10.1186/1758-2946-4-24

Published: 2 October 2012

Abstract

Displaying chemical structures in LATE X documents currently requires either hand-coding of the structures using one of several LATE X packages, or the inclusion of finished graphics files produced with an external drawing program. There is currently no software tool available to render the large number of structures available in molfile or SMILES format to LATE X source code. We here present mol2chemfig, a Python program that provides this capability. Its output is written in the syntax defined by the chemfig TE X package, which allows for the flexible and concise description of chemical structures and reaction mechanisms. The program is freely available both through a web interface and for local installation on the user’s computer. The code and accompanying documentation can be found at http://chimpsky.uwaterloo.ca/mol2chemfig webcite.

Keywords:
LATE X Chemfig; Molfile; SMILES; Molecular structures; Code generation