There are faster libraries to make queries in a DataFrame

[dprada]

There are faster libraries than Pandas. The concept of having the topology and the bonds as DataFrames is useful since we can, at any time, try other libraries such as Vaex, PySpark, Dask, ..., which seems to be more efficient than Pandas. We have to implement the fastest one doing queries in large systems. This is one of the strongest points of MolSysMT, the possibility to be the fastest library loading molecular systems and doing atoms selections (in small and very large systems); together with the fact that the topology is in a standard type of object used by many libraries.

[dprada]

Modin could be an easy implementation since its syntaxis is exactly the same as Pandas. Modin can be implemented in just one line.

[dprada]

Other options to be evaluated is working with SQL APIs like SQLite through Pandas. See: https://datacarpentry.org/python-ecology-lesson/09-working-with-sql/index.html or https://blog.thedataincubator.com/2018/05/sqlite-vs-pandas-performance-benchmarks/