Zeobuilder is an extensible GUI-toolkit for molecular model construction.
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README

Zeobuilder is a user-friendly GUI toolkit for the construction of advanced
molecular models. The program contains several advanced tools to build, align,
manipulate and analyze molecular structures. Most of its novel functionality is
based on a hierarchical data-structure of reference frames to represent a
molecular structure. Furthermore, Zeobuilder is extensible. The core program is
compact and nearly all of the functionality is implemented through a plug-in
framework.

More information about Zeobuilder can be found on the CMM Software website:
http://molmod.ugent.be/software/

Zeobuilder is distributed as open source software under the conditions of the GPL
license version 3.  Read the file COPYING for more details, or visit
http://www.gnu.org/licenses/