Author Topic: SketchEl is a Chemical structure sketching tool for viewing & creating MOL files  (Read 2158 times)

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SketchEl is a Cross Platform chemical structure sketching tool for viewing, creating and editing MDL MOL files.



Chemical structure sketching tool, for use with various cheminformatics applications. Convenient to use and moderately sophisticated. Suitable for viewing, creating and editing MDL MOL files.

Chemistry, Molecular Science


    chemical diagram drawing
    molecular datasheet editing
    import/export MDL MOL, MDL SDF, CML
    export raster graphics (PNG)
    export vector graphics (SVG, OpenDocument)

SketchEl is an interactive chemical molecule sketching tool, and molecular spreadsheet data entry application. The feature set provided by the molecular sketcher is largely limited to the minimum features required to conveniently edit diagram representations of small molecule structures. Toolbars, templates, mouse gestures, keyboard shortcuts, utility commands and several view modes are offered in order to make this as convenient as possible. Molecules can be easily interconverted with the ubiquitous MDL MOL file format, though not not necessarily without information loss. Molecule diagrams are rendered interactively in high quality, and can also be exported as SVG graphics.

The newer datasheet feature of SketchEl allows viewing and editing of simple tables of data, for which each column is a common scalar type (string, int, real, boolean) or a molecule. Editing and viewing of molecules is linked to the molecule sketching tool. The datasheet editing is intended to be convenient for entering numeric property and identification data, alongside the molecular structures of interest. The native format is XML based, with features for interconverting with MDL SD files.

All of the SketchEl features are written and compiled with Java 1.5, and make full use of the features available in the default libraries. There are no additional dependencies. The code is most extensively tested on Linux platforms, frequently on Windows, and occasionally on Mac OS X. The single-molecule editing feature can be run as a Java Applet within a web page, and the underlying molecule contents can be manipulated by JavaScript programs.


Feature-complete. Version 1.00 provided all of the baseline features for single-molecule sketching. Subsequent improvements include the datasheet editor and SVG export, as well as regular bug fixes and minor improvements. Most recent files often contain experimental features which may not have been tested extensively. Consult changelogs for more information.

    Easy to use interactive tools for placing atoms and bonds.

    Tools are multipurposed in order to provide convenient access to necessary drawing modes, and to operate with either fine-control or generally reasonable assumptions.

    Automatic or manual control over creation, calculation and rendering of hydrogen atoms.

    Built-in structure templates.

    Aesthetically pleasant output, using anti-aliased rendering and arbitrary size scaling.

    Molecules can be exported as SVG (Scalable Vector Graphics) pictures for external use.

    More recently, pictures can be exported as ODG (OpenDocument Graphics) pictures, which can be used within the OpenOffice suite, among others.

    Reads and writes industry standard MDL MOL files, a flavour of CML XML, as well as its own format.

    Provides a datasheet editor, which allows tables of data with molecular structures to be edited alongside accompanying data.

    Datasheets use an XML format, and can be interconverted with MDL SD files.

    Platform independent and open source; uses Java 1.5, Swing with no further dependencies. All source code is copyrighted by the author, and made available under the GPL v2.0.

    Applet mode can be used for embedding molecular sketching in a web page.



No official user documentation exists at the present time, though the menu entries, toolbar icons and popup help should be largely self-explanatory, given a modicum of experimentation. The most uptodate description of the molecule file format is provided on the Molecular Materials Informatics website.


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