Summary

Input data

Currently, ProLIF only accepts RDKit molecules as input and relies on MDAnalysis to convert input files for Molecular Dynamics simulations and docking experiments to this RDKit object. The documentation can be found in the Molecules section.

Residues

To decompose interactions by residue, ProLIF needs to split the prolif.molecule.Molecule component in residues. Information on how these residues are stored and accessed can be found in the Residues section.

Interaction fingerprint

An interaction fingerprint decomposes the interactions between two molecules in a binary vector. The interactions are detected by looking up predefined molecular patterns (using SMARTS queries in ProLIF) that satisfy geometrical constraints (distance, angle, dihedral…). To learn more on how these interactions are defined and how to use prolif to extract fingerprints, please refer to the Interaction fingerprint section.

Helper functions

ProLIF comes with a set of functions that should help users analyse the results produced by the package more easily. The documentation for these functions can be found in the Helper functions section. You can also find classes to plot the resulting interaction fingerprints in the Plotting section

Parallel processing

By default, ProLIF parallelizes the computation of interaction fingerprints using the multiprocess module. The number of parallel jobs can be controlled by the n_jobs parameter, which can be set to an integer or None to use the number of logical cores. For more information on the different strategies available and how to use them, please refer to the Parallel processing section.

Typing

Type aliases that are used throughout the code can be found in the Custom types section.