E-CAM polymer_data_analysis module¶
The polymer_data_analysis module provides functions to compute quantities like gyration radius, internal distances, contact maps, contact probabilities, etc. This module takes advantage of the Numba parallelisation implementation and JIT (just-in-time) compilation. It also uses Dask to deploy numerous data analysis on job queuing systems.
The module takes advantage of the Python language as well as Numpy to write simple scripts that run complete data analysis of polymer systems. It also uses Numba to perform fast computation and easily handle nested loops.
However, computation of quantities like contact maps or internal distances needs an algorithm that scales like the square of the system size. If computation cannot use Numba, the modules proposes to deploy data analysis on job queuing systems.
You can also compute quantities like twist and writhe to study bacteria conformation.
We would like to provide a pipeline to help biophysicist extract quantities from simulations.
The instructions to install, test and run the module can be find on the data analysis GitLab repository.