Representing paint molecules with JChemPaint

Importing and Exporting

JChemPaint supports several common formats that let you save drawings for processing in other programs. It is a good idea to save the drawing itself as Chemical Markup Language (CML) [4], an XML-compliant schema for the chemistry field, or MDL MOL, a text-based file format for chemical information ending in the abbreviation .mol [5]. For final or term papers, you can export the drawings as PNG, BMP, or SVG graphics by selecting File | Save as Image. Alternatively, you can output SMILES strings of the drawings by selecting Tools | Create SMILES. This means that you can carry on processing the chemical compound represented with various online services such as Molinspiration [6].

JChemPaint can import files in Structure Data File (SDF) format [7], a common file format ending in .sdf for exchanging chemical information. Various chemistry websites also present compounds in the IUPAC International Chemical Identifier (InChI) notation [8], which shows the molecule as a string (unlike SMILES, InChI is a free format under the LGPL), or as a Chemical Abstracts Service (CAS) Registry Number [9], which is a unique number for each molecule managed in a database by the American Chemical Society. Both notations compete with the SMILES notation.


JChemPaint is unique in that there are currently no better alternatives on Linux or as free software in general. It supports common formats that let you retrieve information for the drawings in other programs or from online services. But note that the program is still at an early stage of development. In our lab, it was not possible to draw rings with circles inside. These structures are available as templates, though. In addition, various actions result in nasty Java exceptions due to errors not being fielded. Having said this, JChemPaint is a very useful editor that lets users generate attractive 2D views of chemical compounds.

The Author

Anzela Minosi offers various IT services on Fiverr under the pczoneminosi nickname. This includes gigs for cleaning up, analyzing, and visualizing data.

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