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 :ref:`source/modules/input:Molecules` section.
To decompose interactions by residue, ProLIF needs to split the :class:`prolif.molecule.Molecule` component in residues. Information on how these residues are stored and accessed can be found in the :ref:`source/modules/residues:Residues` section.
An interaction fingerprint decomposes the interactions between two molecules in a binary vector. The interactions are detected by looking up for predefined molecular patterns (like SMARTS queries) 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 :ref:`source/modules/interaction-fingerprint:Interaction fingerprint` section.
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 :ref:`source/modules/utils:Helper functions` section. You can also find classes to plot the resulting interaction fingerprints in the :ref:`source/modules/plotting:Plotting` section