Welcome to Kartograf’s documentation!#

Kartograf is a packgage for atom mappings focussing on 3D geometries. This package can for example be used to generate hybrid topology systems, where an atom mapping is required to determine the core region of the approach. But of course, there exist also other use cases for this package. The atom mapper takes two sets of coordinates of molecules as input. Optionally those sets of coordinates can be aligned onto each other, checkout the atom_aligner module functions of Kartograf that offer a shape alignment implementation and an MCS-skeleton alignment. The atom_mapper can be used to generate the 3D geometry-focused atom mapping, the algorithm is described in the related publication of Kartograf (see reference). Additionally, rule-based filter functions can be provided to demap atoms, that do not fulfill the desired criteria, see filters. Several mapping scoring metrics are provided, that evaluate geometric properties of your mapping, from atom_mapping_scorer, which might be useful for checking the quality of your mappings. Finally, there is a visualization function display_mappings_3d that can be used to check out the mappings with a Jupyter Notebook widget.

You can find our Preprint on Ries, B.; Alibay, I.; Swenson, D. W. H; Baumann, H. M.; Henry, M. M.; Eastwood, J. R. B.; Gowers, R. J. - Kartograf: An Accurate Geometry-Based Atom Mapper for Hybrid Topology Relative Free Energy Calculations, Chemrxiv (2023)