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Abstract Background Open 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). Results 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. Conclusion By providing a simplified interface and improving interoperability, Cinfony makes it easy to combine complementary features of OpenBabel, the CDK and the RDKit.

Abstract Background We present a novel feature selection algorithm, Winnowing Artificial Ant Colony (WAAC), that performs simultaneous feature selection and model parameter optimisation for the development of predictive quantitative structure-property relationship (QSPR) models. The WAAC algorithm is an extension of the modified ant colony algorithm of Shen et al. (J Chem Inf Model 2005, 45: 1024–1029). We test the ability of the algorithm to develop a predictive partial least squares model for the Karthikeyan dataset (J Chem Inf Model 2005, 45: 581–590) of melting point values. We also test its ability to perform feature selection on a support vector machine model for the same dataset. Results Starting from an initial set of 203 descriptors, the WAAC algorithm selected a PLS model with 68 descriptors which has an RMSE on an external test set of 46.6°C and R2 of 0.51. The number of components chosen for the model was 49, which was close to optimal for this feature selection. The selected SVM model has 28 descriptors (cost of 5, ε of 0.21) and an RMSE of 45.1°C and R2 of 0.54. This model outperforms a kNN model (RMSE of 48.3°C, R2 of 0.47) for the same data and has similar performance to a Random Forest model (RMSE of 44.5°C, R2 of 0.55). However it is much less prone to bias at the extremes of the range of melting points as shown by the slope of the line through the residuals: -0.43 for WAAC/SVM, -0.53 for Random Forest. Conclusion With a careful choice of objective function, the WAAC algorithm can be used to optimise machine learning and regression models that suffer from overfitting. Where model parameters also need to be tuned, as is the case with support vector machine and partial least squares models, it can optimise these simultaneously. The moving probabilities used by the algorithm are easily interpreted in terms of the best and current models of the ants, and the winnowing procedure promotes the removal of irrelevant descriptors.

Abstract Background Scripting languages such as Python are ideally suited to common programming tasks in cheminformatics such as data analysis and parsing information from files. However, for reasons of efficiency, cheminformatics toolkits such as the OpenBabel toolkit are often implemented in compiled languages such as C++. We describe Pybel, a Python module that provides access to the OpenBabel toolkit. Results Pybel wraps the direct toolkit bindings to simplify common tasks such as reading and writing molecular files and calculating fingerprints. Extensive use is made of Python iterators to simplify loops such as that over all the molecules in a file. A Pybel Molecule can be easily interconverted to an OpenBabel OBMol to access those methods or attributes not wrapped by Pybel. Conclusion Pybel allows cheminformaticians to rapidly develop Python scripts that manipulate chemical information. It is open source, available cross-platform, and offers the power of the OpenBabel toolkit to Python programmers.

Abstract Background The web has seen an explosion of chemistry and biology related resources in the last 15 years: thousands of scientific journals, databases, wikis, blogs and resources are available with a wide variety of types of information. There is a huge need to aggregate and organise this information. However, the sheer number of resources makes it unrealistic to link them all in a centralised manner. Instead, search engines to find information in those resources flourish, and formal languages like Resource Description Framework and Web Ontology Language are increasingly used to allow linking of resources. A recent development is the use of userscripts to change the appearance of web pages, by on-the-fly modification of the web content. This opens possibilities to aggregate information and computational results from different web resources into the web page of one of those resources. Results Several userscripts are presented that enrich biology and chemistry related web resources by incorporating or linking to other computational or data sources on the web. The scripts make use of Greasemonkey-like plugins for web browsers and are written in JavaScript. Information from third-party resources are extracted using open Application Programming Interfaces, while common Universal Resource Locator schemes are used to make deep links to related information in that external resource. The userscripts presented here use a variety of techniques and resources, and show the potential of such scripts. Conclusion This paper discusses a number of userscripts that aggregate information from two or more web resources. Examples are shown that enrich web pages with information from other resources, and show how information from web pages can be used to link to, search, and process information in other resources. Due to the nature of userscripts, scientists are able to select those scripts they find useful on a daily basis, as the scripts run directly in their own web browser rather than on the web server. This flexibility allows the scientists to tune the features of web resources to optimise their productivity.

A density functional theory (DFT) study was carried out of an osmium polypyridyl complex adsorbed on Au(111). The results showed that the coupling between the immobilized complex and the gold surface involves electronic polarization at the adsorbate/substrate interface rather than the formation of a covalent bond.

The synthesis, characterization and electrochemical, photophysical and photocvhemical properties of the binuclear compounds [(Ru(H8-bpy)(sub 2))(sub 2)(Metr)(sub 2)Pz)](PF6)(sub 2) and [(Ru(D8-bpy)(sub 2))(sub 2)(Metr)(Sub 2)Pz)](PF6)(sub 2) where bpy is 2,2'-bipyridine and H2(Metr)(sub 2)Pz is the planar ligand 2,5-bis(5'-methyl-4'H-[1,2,4]triaz-3'-yl)-pyrazine are reported. Resonance Raman, transient and time-resolved spectroscopies enable a detailed assignment to be made of the excited-state photophysical properties of the complexes.