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mol2ps is a freely available command-line utility program which reads molecular structure files in different formats (see below) and generates Postscript output for 2D display. The Postscript file can then be used e.g. for creating a bitmap file, using a Postscript interpreter like Ghostscript.

As an example, the following 2D representation of caffeine in PNG (Portable Network Graphics) format was created from the corresponding MDL molfile (PubChem CID 2519), using mol2ps in combination with Ghostscript:

Caffeine 2D structure

As input files, MDL molfiles and SD files (*.mol, *.sdf; 2D and 3D), Alchemy molfiles (*.mol), and Sybyl mol2 files (*.mol2) are accepted by mol2ps, the preferred format is the MDL molfile format. At present, it is not intended to extend the number of supported input file formats, as there are powerful file format converters available, such as OpenBabel.

The main purpose of mol2ps is to create small, but high-quality 2D pictures of molecules for display on web pages. Especially for web-based molecular structure databases it is quite useful to have pre-built pictures for display in hitlists instead of invoking browser plugins, Java applets, or server-side programs for display of the individual structures. A description of how such structure databases can be created with free software is given here.


mol2ps is freely available under the terms of the GNU General Public License (GPL), for a detailed description of this license, please visit
It is written in Pascal and it was compiled with the Free Pascal compiler for the following platforms: Linux i386, FreeBSD i386, Windows (Win32 console application). You may use it on your own risk, there is no warranty for anything.


source code: mol2ps.pas (approx. 139 KB)
Linux (i386) executable: mol2ps-latest-linux-i386.gz (approx. 81 KB)
FreeBSD (i386) executable: mol2ps-latest-freebsd-i386.gz (approx. 114 KB)
Win32 console application: (approx. 62 KB)
example color definition file: color.conf
posted on 2009-11-20 15:26 周锐 阅读(379) 评论(0)  编辑  收藏 所属分类: ChemistryOpenbabel