Evan Hepler-Smith, Harvard University
Leah R. McEwen, Cornell University
- Understand the principles behind connection table representation of chemical structures
- Translate structural formulas into simplified connection tables and vice-versa
- Recognize the parts of a MOL file, a common connection table file format
- Map the correspondence between features of a structural formula and entries in a MOL file
- Adjust connection tables to make simple modifications to chemical structures
- Track how changes in a chemical sketch program and the underlying connection table data relate to each other.
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Connection tables are a cluster of related file formats specifically designed to render chemical structure in machine-readable form. No matter what form of input and output a computer program uses, anytime a computer does any analysis on chemical structure, it most likely makes use of connection tables. Connection tables are typically employed behind the scenes of chemical computer programs, out of the user’s view. Whether you are involved in sophisticated cheminformatics analysis of chemical structure data or you just want to be able to search chemical databases confidently, it’s important to have a general idea of how connection tables work.
Like structural formulas, connection tables represent the basic building blocks of structural organic chemistry: atoms and bonds. They encode information and rules about chemical structures in the form of a table that a computer algorithm can parse. A program can then use this information in many ways, to present a visual image to a user, to compare structural features among many compounds and associated data, to provide a link between chemical records in different databases, and much more. Connection tables enable chemical structure information to be programmatically accessible and are the key to most cheminformatics applications.
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