Due to the strong relationship to informatics this program belongs more to the category cheminformatics than to molecular modelling. It is available for Windows, Unix, Linux, macOS, and Android. It is free and open-source software released under a GNU General Public License (GPL) 2.0.
We discuss, for the first time, Open Babel, an open-source chemical toolbox that speaks the many languages of chemical data. Open Babel version 2.3 interconverts over 110 formats. The need to represent such a wide variety of chemical and molecular data requires a library that implements a wide range of cheminformatics algorithms, from partial charge assignment and aromaticity detection, to bond order perception and canonicalization. We detail the implementation of Open Babel, describe key advances in the 2.3 release, and outline a variety of uses both in terms of software products and scientific research, including applications far beyond simple format interconversion.
Open Babel 3.1.1 Download
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Open Babel presents a solution to the proliferation of multiple chemical file formats. In addition, it provides a variety of useful utilities from conformer searching and 2D depiction, to filtering, batch conversion, and substructure and similarity searching. For developers, it can be used as a programming library to handle chemical data in areas such as organic chemistry, drug design, materials science, and computational chemistry. It is freely available under an open-source license from
We outline for the first time, the development and use of the Open Babel project, a full-featured open chemical toolbox, designed to "speak" the many different representations of chemical data. It allows anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas. It provides both ready-to-use programs as well as a complete, extensible programmer's toolkit for developing cheminformatics software. It can handle reading, writing, and interconverting over 110 chemical file formats, supports filtering and searching molecule files using Daylight SMARTS pattern matching [7] and other methods, and provides extensible fingerprinting and molecular mechanics frameworks. We will discuss the frameworks for file format interconversion, fingerprinting, fast molecular searching, bond perception and atom typing, canonical numbering of molecular structures and fragments, molecular mechanics force fields, and the extensible interfaces provided by the software library to enable further chemistry software development.
Open Babel has its origin in a version of OELib released as open-source software by OpenEye Scientific under the GPL (GNU Public License). In 2001, OpenEye decided to rewrite OELib in-house as the proprietary OEChem library, so the existing code from OELib was spun out into the new Open Babel project. Since 2001, Open Babel has been developed and substantially extended as an international collaborative project using an open-source development model [8]. It has over 160,000 downloads, over 400 citations [9], is used by over 40 software projects [10], and is freely available from the Open Babel website [11].
Open Babel is implemented in standards-compliant C++. This ensures support for a wide variety of C++ compilers (MSVC, GCC, Intel Compiler, MinGW, Clang), operating systems (Windows, Mac OS X, Linux, BSD, Windows/Cygwin) and platforms (32-bit, 64-bit). Since version 2.3, it is compiled using the CMake build system [37, 38]. This is an open-source cross-platform build system with advanced features for dependency analysis. The build system has an associated unit test framework CTest, which allows nightly builds to be compiled and tested automatically with the results collated and displayed on a centralized dashboard [39].
Open Babel is open-source software, which offers end users and third-party developers a range of additional rights not granted by proprietary chemistry software. Open-source software, at its most basic level, grants users the rights to study how their software works, to adapt it for any purpose or otherwise modify it, and to share the software and their modifications with others. In this sense, Open Source functions in similar ways to the processes of open peer review, publication, and citation in science. The rights granted by open source licenses largely coincide with the norms of scientific ethics to enable verifiability, repeatability, and building on previous results and theories.
Beyond these rights, Open Babel (like most other open-source projects) offers open development -- that is, all development occurs in public forums and with public code repositories. This results in greater input from the community as any user can easily submit bug reports or feature suggestions, get involved in discussions on the future direction of Open Babel or even become a developer him/herself. In practice, the number of active contributors has increased over time through this level of open, public development (Figure 3). Moreover, it means that the development of the code is completely transparent and the quality of the software is available for public scrutiny. Indeed, since its inception, over 658 bugs have been submitted to the public tracker and fixed [41].
The Open Babel package is composed of a set of user applications as well as a programming library. The main command line application provided is obabel (a small upgrade on the earlier babel), which facilitates file format conversion, filtering (by SMARTS, title, descriptor value, or property field), 3D or 2D structure generation, conversion of hydrogens from implicit to explicit (and vice versa), and removal of small fragments or of duplicate structures. A number of features are provided to handle multi-molecule file formats (such as SDF or MOL2) and to use or manipulate the information in property fields and molecule titles. Here is an example of using obabel to convert from SDF format to SMILES:
The Open Babel graphical user interface (GUI) provides the same functionality. Figure 6 is a screenshot of the GUI carrying out the same filtering operation described in the obabel example above. The left panel deals with setting up the input file, the right panel handles the output and the central panel is for setting conversion options. Depending on whether a particular option requires a parameter, the available options are displayed either as check boxes or as text entry boxes. These interface elements are generated dynamically directly from the text description and help text provided by each format plugin.
Open Babel has already been referenced over 400 times for various uses. The most common use of Open Babel is through the obabel command line application (or the corresponding graphical user interface) for the interconversion of chemical file formats. Such conversions may also involve the calculation or inference of additional molecular information or application of a filter. Some published examples of these include the following:
Open Access This is an open access article distributed under the terms of the Creative Commons Attribution Noncommercial License ( -nc/2.0 ), which permits any noncommercial use, distribution, and reproduction in any medium, provided the original author(s) and source are credited.
Results:Ā We discuss, for the first time, Open Babel, an open-source chemical toolbox that speaks the many languages of chemical data. Open Babel version 2.3 interconverts over 110 formats. The need to represent such a wide variety of chemical and molecular data requires a library that implements a wide range of cheminformatics algorithms, from partial charge assignment and aromaticity detection, to bond order perception and canonicalization. We detail the implementation of Open Babel, describe key advances in the 2.3 release, and outline a variety of uses both in terms of software products and scientific research, including applications far beyond simple format interconversion.
Conclusions:Ā Open Babel presents a solution to the proliferation of multiple chemical file formats. In addition, it provides a variety of useful utilities from conformer searching and 2D depiction, to filtering, batch conversion, and substructure and similarity searching. For developers, it can be used as a programming library to handle chemical data in areas such as organic chemistry, drug design, materials science, and computational chemistry. It is freely available under an open-source license from
Due to some circumstances, I was ask to develop a page that uses Process in .Net C# to call the function through command prompt. The code works perfectly Fine on visual studio, but when deployed on an IIS server. the Process doesn't seems to work, I've debugged and find out the process itself works. but the open Babel command doesn't work, i did double check and the identity i supply with should be alright, i did even supply it with admin privilege but still doesn't work. it doesn't even pop or error, it just simply ignored it and go through the commands. I put the command into a .bat file, with some extra command to test if the .bat works. everything is fine until the command with open babel, then process just doesn't seem react with the command.
this is the command i supply it with, %1 is the input file while %2 is the output file name. A very simple conversion. Note: everything is fine, just only the open babel command got ignored in the entire file. and I've tried to supply it with admin privilege, still doesn't work. the open babel can be used if directly used with command prompt on the server, or through visual studio. but it doesn't work if i deployed it through IIS server.
Can anyone suggest please?
I have downloaded from Release Avogadro 1.97.0Ā OpenChemistry/avogadrolibsĀ GitHub the version Avogadro2-x86_64.AppImage on my Linux Ubuntu 20.04.3 LTS. I have then given the executable permission to this Appimage file. After this when I try to open a .cif file I get the following error: OpenBabel error: conversion failed. 2351a5e196
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