Overview#
Improved features#
The major changes in prolint2 compared to the old version that allow them to overpass the previously mentioned limitations are the migration to the MDAnalysis ecosystem, the use of a Cython version of a cell list algorithm greatly inspired by the neighbors grid search implemented in GROMACS (including the capacity to handle PBC), and the use of highly optimized data structures (Scipy matrices and Pandas dataframes) to store the contacts.
Routine to calculate the distance-based contacts using a cell list fixed radius neighbors search algorithm.
It reads the frames of the trajectory completely on-the-fly, so it does not overload memory.
It takes into account the PBC in both orthorhombic and triclinic types of simulation boxes.
It automatically identifies the Protein and Lipid groups for the calculation of the contacts, so you do not need to make any previous cleaning steps in your system.
User-friendly, easy-to-install and well-documented tool, based on the actively-maintained MDAnalysis package.