https://github.com/open2c/polykit

https://github.com/open2c/polykit

Last synced: 3 months ago
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• Host: GitHub
• URL: https://github.com/open2c/polykit
• Owner: open2c
• License: mit
• Created: 2023-03-27T20:36:09.000Z (about 3 years ago)
• Default Branch: main
• Last Pushed: 2025-08-13T01:35:52.000Z (10 months ago)
• Last Synced: 2025-08-13T02:36:12.946Z (10 months ago)
• Language: Python
• Homepage:
• Size: 4.77 MB
• Stars: 6
• Watchers: 8
• Forks: 3
• Open Issues: 2
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

          
# polykit

Generic toolkit for polymer simulation setup and analysis

## Installation

The `renderers` module for Jupyter-notebook-embedded visualization requires the [**`fresnel`**](https://fresnel.readthedocs.io/en/v0.13.5/) library, which can be installed through conda:

~~~shell

conda install -c conda-forge fresnel

~~~

## Usage

All functions within the `analysis` module should work as described in the [**Polychrom**](https://polychrom.readthedocs.io/en/latest/index.html) documentation, on condition that an appropriate [**`load_function`**](https://polychrom.readthedocs.io/en/latest/polychrom.hdf5_format.html#polychrom.hdf5_format.load_URI) is provided to parse the required trajectory files. For [**HOOMD-blue**](https://glotzerlab.engin.umich.edu/hoomd-blue/)'s native [**GSD**](https://gsd.readthedocs.io/en/stable/index.html) file format, the corresponding function takes the following form:

~~~python

def load_gsd(URI):

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

    with gsd.hoomd.open(name=filename, mode="rb") as traj:

        return traj[int(group)].particles.position

~~~