bubblebuster 2.0

A Python Library for detecting water box bubbles in structural files used in molecular simulations.

Bubblebuster is a Python Library for detecting water box bubbles in structural files used in molecular simulations, by partitioning the system’s periodic box into a cubic grid. The atom density of each cube is compared against the periodic box’s atom density. If any cube has a density less than the periodic box atom density multiplied by the cutoff parameter (default is 0.5), the water box is deemed to likely have a bubble. The size of the cubes, along with the cutoff value, can be customized according to the system. However, this must be done with caution as a cutoff value that is to large/small can yield false positives/negatives.