![]() ![]() ![]() ![]() It can read 82 formats and write 85 formats. With the release of Open Babel 2.3, Open Babel supports 111 chemical file formats in total. It has over 160,000 downloads, over 400 citations, is used by over 40 software projects, and is freely available from the Open Babel website. Since 2001, Open Babel has been developed and substantially extended as an international collaborative project using an open-source development model. 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. Open Babel has its origin in a version of OELib released as open-source software by OpenEye Scientific under the GPL (GNU Public License). 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. It can handle reading, writing, and interconverting over 110 chemical file formats, supports filtering and searching molecule files using Daylight SMARTS pattern matching and other methods, and provides extensible fingerprinting and molecular mechanics frameworks. It provides both ready-to-use programs as well as a complete, extensible programmer's toolkit for developing cheminformatics software. It allows anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas. 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. Consequently, a frequent problem in computational modeling is the interconversion of molecular structures between different formats, a process that involves extraction and interpretation of their chemical data and semantics. While attempts have been made to provide a standard format for storing chemical data, including most notably the development of Chemical Markup Language (CML), an XML dialect, such formats have not yet achieved widespread use. ![]() Other types of representations require specification of atom types on the basis of a specific valence bond model, inclusion of computed partial charges, indication of biomolecular residues, or multiple conformations. Hydrogen atoms are frequently omitted from x-ray crystallography due to the difficulty in establishing coordinates, and are often ignored by some file formats as the "implicit valence" of heavy atoms that indicates their presence. For example, line notations like Daylight SMILES do not offer coordinate information, while crystallographic or quantum mechanical formats frequently do not store chemical bonding data. Such representations focus on specific atomic or molecular information and may not attempt to store all possible chemical data. The history of chemical informatics has included a huge variety of textual and computer representations of molecular data. ![]()
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