Modern pharmaceutical companies have hundreds of information systems and applications for keeping track and processing of compounds. From registration systems, to electronic lab notebooks, to inventory management, to predictive chemistry applications such as ADMET QSAR modeling and virtual screening. The plumbing that holds these myriad systems together is the interchange of files encoding the connection table representations of molecules. Over the years a number of de facto standard file formats have gained, if not popularity, widespread usage between systems from multiple vendors. These include MDL's mol, SD, rxn and RD file formats, Daylight's SMILES strings, Tripos' Mol2 files, PDB files, ChemDraw and ISIS/Draw sketches etc.Curiously, the more widely used a molecular file format, the more misunderstood and maligned it becomes. Alas often poor reputations are not the fault of the file formats themselves (or their designers) but the inherent complexity of representing molecules in a computer, and ignorance of how to correctly interpret their content. If a file format were not fit for some purpose, it would not have become popular and would likely have been be displaced by a better competing representation.In this talk, I describe features of various popular file formats that solve important challenges in exchanging chemical information, but alas are often poorly or not widely implemented. Hopefully, raising awareness of such features may help them become more widely implemented and adopted.As one example, I shall present details of community-wide efforts to improve the handling of implicit hydrogen valence in MDL mol files. An experiment to compare the interpretation of MDL V2000 files across more than twenty cheminformatics tools revealed a significant number of differences in interpretation. As a result, many issues uncovered by this investigation have since been fixed by vendors and software developmers, including RDKit, OpenBabel, Optibrium, CACTVS, NAOMI and MayaChemTools.

Reading and writing molecular file formats for data exchange of small molecules, biopolymers, and reactions

246th National Meeting (2013)

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