Cinfony – combining Open Source cheminformatics toolkits behind a common interface

We describe Cinfony, a Python module that presents a common interface to all three of these toolkits, allowing the user to easily combine methods and results from any of the toolkits. In general, the run time of the Cinfony modules is almost as fast as accessing the underlying toolkits directly from C++ or Java, but Cinfony makes it much easier to carry out common tasks in cheminformatics such as reading file formats and calculating descriptors.By providing a simplified interface and improving interoperability, Cinfony makes it easy to combine complementary features of OpenBabel, the CDK and the RDKit.Cheminformatics toolkits are essential to the day-to-day work of the practising cheminformatician. They enable the user to deal with such tasks as handling different chemistry file formats, substructure searching, calculation of molecular fingerprints, and structure diagram generation. The main Open Source cheminformatics libraries under active development are OpenBabel [1], the Chemistry Development Kit (CDK) [2], and the RDKit [3]. OpenBabel is a C++ toolkit with bindings in Perl, Python, Ruby and Java, the CDK is a Java toolkit, while the RDKit is another C++ toolkit with Python bindings. While the CDK has its origins in academia, both OpenBabel and the RDKit originated in companies (OpenEye and Rational Discovery, respectively) and have subsequently been developed by the community under Open Source licenses.In general, all of these toolkits share the same core functionality although the implementation details and underlying chemical model may differ. However, as a result of their independent development and history, each has functionality specific to itself and each toolkit supports different sets of file formats and forcefields, and can calculate different molecular fingerprints and molecular descriptors (Table 1). Despite the diversity of these toolkits and the potential benefits in being able to access all of them at the same time, there has been little work on