MaAg-bel

This is MaAg-bel, a reduced fork of the Open Babel chemical toolbox desiged to work with the tools distributed as Manipulate Aggregates. It is meant to be used only as a Python package. Its functionality is reduced to that needed by Manipulate Aggregates.

Notable changes

Most notable changes with respect to the Open Babel base are:

• one library containing all the functionality instead of multiple ones
• standalone ops removed
• eigen3 added as a hard dependency
• removed cmake as dependency
• XML and ZLIB functionality removed
• inchi, smiles and cml formats removed (the latter 2 depend on inchi to some degree)
• more formats removed:
  • JOSN-based
  • XML-based
• Windows compatibility removed (use the WSL is you need to use Windows)
• MacOS compatibility removed

Installation

Make sure that eigen version 3 is installed. Afterwards, run pip install maagbel. If you are using conda, run conda install eigen to install it. Most likely, you want to install this as a dependency of ManipulateAggregates.

More information regarding Open Babel

Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It's an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas.

• Ready-to-use programs, and complete programmer's toolkit
• Read, write and convert over 90 chemical file formats
• Filter and search molecular files using SMARTS and other methods
• Generate 2D and 3D coordinates for SMILES and other formats
• Supports molecular modeling, cheminformatics, bioinformatics, organic chemistry, inorganic chemistry, solid-state materials, nuclear chemistry...

Open Babel is distributed under the GNU General Public License (GPL). This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation version 2 of the License. Full details can be found in the file "COPYING" which should be included in your distribution.

For more information, check the [Open Babel website]( <http://openbabel.org/).