Model chromatin as a chain of nucleosomes.
The nuc_chain package contains routines to calculate various configurational and dynamic properties of a model of chromatin that consists of wormlike-chains (linker DNA) connecting nucleosomes (approximately cylinders or spheres) at angles determined by the geometry of the entry/exit angles of DNA into the nucleosome crystal structure.
This package was developed to investigate the contributions of fluctuations in the linkers, heterogeneity in the linker length, and "breathing" (partial unwrapping of the DNA from the core particle) of nucleosomes to the physics governing chromatin fibers.
The eventual goal is to be able to output expected equilibrium structures (that can also be used for dynamic simulations) given an organism and a range of genomic coordinates.
This package can be pip installed
pip install nuc_chainFor detailed usage instructions, please see the docs.