Conformational Searching using Python

This is the first of a series examining the use of python to generate candidate structures of molecules. These conformations may serve a variety of functions, though our particular purpose is to identify candidates for additional optimization and ultimate use in ion mobility modeling experiments. After considering a range of tools (e.g. Avogadro or ChemDraw), it was apparent that a more automated, open-source work-flow was needed. In full disclosure, there are surely other mechanisms to make this happen but the following jupyter notebook is a reasonable approach. Visualization of the conformers can be accomplished using pymol if you that module is installed and a server instance running in the background (i.e. pymol -R).

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