There’s a utility in MS Visualizer for preliminary optimization of the geometry of a given structure in focus, the “Clean” tool. However, this nice tool processes the structure under focus, only. How would one automate the “cleaning’ process for a large number of structures?

The script (attached) addresses the above challenge, by reading in the user-specified trajectory file (that contains the structures to be cleaned), calculating bonds and cleaning individual structures, then outputting the cleaned structures into a new trajectory collection.

Note: Collections of structures in, e.g., SD format will turn into trajectory collections when loaded into MS Visualizer. See for example, “Where are my structures in a .sdf file when imported into Materials Studio?”

------------------

Disclaimer: This script is shared "as is" and is NOT supported by DS nor is it warranted for any purpose whatsoever. The user assumes responsibility for any malfunctions or bugs.

------------------