This article is cited by 29 publications. It is freely available under an open-source license from. 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. In addition, it provides a variety of useful utilities from conformer searching and 2D depiction, to filtering, batch conversion, and substructure and similarity searching. CONCLUSIONS: Open Babel presents a solution to the proliferation of multiple chemical file formats. 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. 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. Open Babel version 2.3 interconverts over 110 formats. RESULTS: We discuss, for the first time, Open Babel, an open-source chemical toolbox that speaks the many languages of chemical data. While standard interchange formats exist (for example, Chemical Markup Language) and de facto standards have arisen (for example, SMILES format), the need to interconvert formats is a continuing problem due to the multitude of different application areas for chemistry data, differences in the data stored by different formats (0D versus 3D, for example), and competition between software along with a lack of vendor-neutral formats. (3)īACKGROUND: A frequent problem in computational modeling is the interconversion of chemical structures between different formats. Or an instructor might ask more open-ended questions such as build a molecule with an unusually long C–C single bond. For example, an instructor might ask students to compute the effect of a substituent on a particular vibration and then rationalize the effect using molecular orbitals. Similar to a pocket calculator or a symbolic math program (such as Mathematica or MAPLE), MolCalc allows an instructor to assign higher-level chemical problems that are not practically possible to solve otherwise. The idea was to have students develop a chemical intuition about how molecular structure affects molecular properties, without performing the underlying calculations by hand (which would be nearly impossible for all but the simplest chemical systems). MolCalc was designed to run fast, and therefore, the estimated molecular properties will not match experimental values exactly and, in some cases, will be quite different. MolCalc was designed to be used for teaching and for assignments in which the students build their own molecules and estimate the molecular properties, as opposed to reading from tables in textbooks.
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