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Adding titles to molecules in an sdf file using iBabel


The current COVID-19 pandemic has resulted in many groups sharing chemical structure files, however it is useful to understand the file format definition to do so accurately. There are many chemistry file formats, iBabel using the OpenBabel toolkit supports around 100 different file formats. One of the most popular is the sdf file format.

When handling, searching, combining sdf files it is often very useful to have a unique identifier to act as a key for each molecule, many software packages expect this to be the first line or title, unfortunately this line is often left blank and the unique identifier is held in a data field that might be called "ID", "IDNUMBER", "MOL", "molNAME"……..

iBabel can be used to generate the title in these cases, there is a detailed description of how to do this here.

You can download iBabel here.

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