HiCNet is an approach for establishing small-world networks for individual chromosomes using Hi-C data. It is a tool capable of converting Hi-C contacts to spatial distances. And it can also infer three-dimensional structures using spatial distances and multidimensional scaling methods.
Source code can be downloaded here.
Tong Liu and Zheng Wang. Reconstructing high-resolution chromosome three-dimensional structures by Hi-C complex networks. BMC Bioinformatics 2018, 19(17):496.