Version 1.0, December 2018
Andrey Golov, Igor Karpukhin
This service provides determination of chemical bonds for given set of atoms in unit cell and output it into CIF file.
For determination of the net of bonds, we use the algorithm Domains based on geometrical criteria for assigning some type to the interatomic contact (valence, H-bonds, van der Waals interactions, Halogen bonds). The bonds will be written as an adjacency matrix (connectivity list) in accordance with extended CIF dictionary with special directory describing data on topology and topological properties of crystals.
All programs, databases, tools of crystal data processing must consider the format. They should be capable to save and exchange topological data. The modernized format can save a connectivity list(adjacency matrix) of a crystal structure that contains information about all topological properties. From the connectivity list, using ToposPro, it is possible to compute a variety of topological parameters (cycles, tiles, building units, migration pathways etc.).
The number of symmetry inequivalent atoms must be less than 1000.