SMARTS tools


... is an extremely important concept for defining patterns in molecules. Unfortunately the SMARTS-language[1] is quite complex and the description of a pattern easily becomes quite complex. Here we introduce two tools developed by Karen Schomburg and Lars Wetzer at the Center for Bioinformatics at the University of Hamburg that make life easier when working with SMARTS. Temporary licenses are granted for free.

As examples see below a number of patterns illustrating the SMARTSviewer visualization concept along with its dynamic legend, which describes each distinct atom and bond in natural language. For more examples including the so-called Pan Assay Interference Compounds (PAINS) patterns please visit the gallery website of our collaborators.

SMARTS pattern describing the reactive group of sulfuryl halogenides SMARTS describing a pattern with an azo group SMARTS pattern matching a non-aromatic nitrogen bound to an aromatic carbon SMARTS pattern describing a reactive sulfur group SMARTS pattern describing an aromatic ring containing a nitrogen SMARTS pattern describing sulfur- or phosphornitride oxide SMARTS pattern describing one form of a sulfonamide


  • instant SMARTS pattern visualizations
  • graphical interface
  • dynamic human-readable legend

SMARTSviewer automatically generates high-quality 2D structure-diagrams of molecular patterns given in form of a SMARTS. It also allows you to interactively manipulate the pattern in a graphical user interface. This way you may for example jump-start from a SMILES definition of a substructure and tweak it such that it ultimately describes the pattern that you have in mind.

Take a look at the
SMARTSviewer tutorial movie.

You may also want to read the original publication[2] and try out the SMARTSviewer web-interface[4].

If you are interested, grab a free copy from this download mirror[5]. The package contains executables for Windows, Linux and MacOS. Please note that with the download you accept our terms and conditions*.

download SMARTSviewer


  • draw molecule patterns
  • develop SMARTS interactively
  • recursions and pre-defined patterns

SMARTSeditor is an interactive GUI application that lets you draw substructure patterns. Jump-starting from a molecule you may develop a SMARTS in a quite intuitive fashion by editing the topology and properties. Using pre-defined patterns for common functional groups lets you quickly reach your goal. SMARTSeditor supports recursions, allowing you to go to any level of complexity without getting lost.

Take a look at the
SMARTSeditor tutorial movie.

Interested? Then go ahead and download a free copy to try it out yourself. The package contains executables for Windows, Linux and MacOS. Please note that with the download you accept our terms and conditions*.

download SMARTSeditor
* Terms and conditions:
The SMARTS tools are prototypes developed by our academic partner at the Center for Bioinformatics (ZBH) of the University of Hamburg.
The SMARTS tools may be used free of charge for academic research or evaluation purposes.
No support is granted any warranty or liability is hereby expressly excluded. You use SMARTS tools at your own risk!
Any publication in reference to SMARTS tools must cite the original publication: SMARTSviewer[2], SMARTSeditor[3].
Please provide us your feedback. Also, if you are interested in a longer-term use or running the SMARTS tools on other operating systems, please let us know.
[1]C. A. James and D. Weininger
Daylight Theory Manual
Daylight Chemical Information Systems, Inc: 27401 Los Altos, 2006
[2]K. Schomburg, H.-C. Ehrlich, K. Stierand, M.Rarey
From Structure Diagrams to Visual Chemical Patterns
J. Chem. Inf. Model., 2010, 50 (9), pp 1529-1535
[3]K. Schomburg, L. Wetzer, M. Rarey
Interactive Design of generic chemical patterns
Drug Discov Today (2013)
[4]SMARTSviewer web-interface:
[5]This is a download mirror. The respective packages may also be obtained here.


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