polykit

Generic toolkit for polymer simulation setup and analysis

Installation

The renderers module for Jupyter-notebook-embedded visualization requires the fresnel library, which can be installed through conda:

conda install -c conda-forge fresnel

Usage

All functions within the analysis module should work as described in the Polychrom documentation, on condition that an appropriate load_function is provided to parse the required trajectory files. For HOOMD-blue's native GSD file format, the corresponding function takes the following form:

def load_gsd(URI):
    filename, group = URI.split("::")

    with gsd.hoomd.open(name=filename, mode="rb") as traj:
        return traj[int(group)].particles.position