Cinfony – combining Open Source cheminformatics toolkits behind a common interface

By Noel M. O'Boyle, Geoffrey R. Hutchison. 2008

48 citations recorded by the source corpus.

BackgroundOpen Source cheminformatics toolkits such as OpenBabel, the CDK and the RDKit share the same core functionality but support different sets of file formats and forcefields, and calculate different fingerprints and descriptors. Despite their complementary features, using these toolkits in the same program is difficult as they are implemented in different languages (C++ versus Java), have different underlying chemical models and have different application programming interfaces (APIs).ResultsWe 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.ConclusionBy providing a simplified interface and improving interoperability, Cinfony makes it easy to combine complementary features of OpenBabel, the CDK and the RDKit.

Subfields: Computational Theory and Mathematics, Materials Chemistry, Molecular Biology

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Citations in the corpus

Mordred: a molecular descriptor calculator (2018, methodology): “Although both open-source and proprietary software have been developed for calculating molecular descrip-tors—such as PaDEL-Descriptor [6], BlueDesc [7], Che-moPy [8], PyDPI [9], Rcpi [10], cinfony [11], and Dragon [12]—they each have advantages and disadvantages (Table 1).”
Molecular fingerprint similarity search in virtual screening. (2015, methodology): “• Cinfony [40,48]: Cinfony is not a toolkit in itself and does not implement any fingerprint, but it gives the user access to several toolkits (OpenBabel, RDKit, CDK, JChem, and Indigo) through a common API in Python and to some extent in Jython (JVM) and IronPython (.”
Chemception: A Deep Neural Network with Minimal Chemistry Knowledge Matches the Performance of Expert-developed QSAR/QSPR Models (2017, methodology): “Data preparation was performed using Python, utilizing script bindings to open-source cheminformatics software, including OpenBabel(33), Pybel(34) and RDKit(35) through the Cinfony interface.(36) Chemicals in the databases are stored as SMILES strings,(37-38) which are compact string”
The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching (2017, methodology): “Use of the CDK ranges from inclusion of CDK functionality in wrapper platforms such as Cinfony [5], incorporation within the R environment (rcdk [6]), and as plugins for Taverna [7], KNIME [8], Cytoscape (ChemViz2 [9]), and for Microsoft Excel (LICSS [10]).”
ChemoPy: freely available python package for computational biology and chemoinformatics (2013, methodology): “We chose to use python because it is open source, and there already exist packages to handle small molecules [e.g. Pybel (O’Boyle et al ., 2008b), PyMol and Cinfony (O’Boyle et al ., 2008a)].”
Rcpi: R/Bioconductor package to generate various descriptors of proteins, compounds and their interactions (2015, unknown): “…such as TOPS-MODE, Cinfony, Dragon, CODESSA, PROFEAT, BioJava, BioPython, PseAAC, ProPy, etc (Cao et al., 2013a, c; Cock et al., 2009; Du et al., 2012; Holland et al., 2008; Katritzky et al., 1994; Li et al., 2006; O'Boyle et al., 2008; P erez-Gonz alez et al., 2003; Todeschini et al., 2010).”