pygen-structures: A Python package to generate 3D molecular structures for simulations using the CHARMM forcefield (Version 0.2.4)



pygen-structures (pigeon structures) is a Python utility which allows for the generation of 3 dimensional molecular structures which can be used in molecular dynamics or Monte Carlo simulations. Molecules are generated from a list of residues and patches in the format of the CHARMM forcefield, and can be written out as valid PSF and PDB files. The package can be used as a command line utility, or as a Python library.

pygen-structures can be installed using pip (pip install pygen-structures), but relies upon RDKit, which is not pip-installable. RDKit can be installed in many ways, but the easiest way is to use the conda package manager. numpy is an additional dependency. For full installation instructions, see Installation. Python 3.6 and 3.7 are supported. To run the tests, pytest and OpenMM are required.

The software is externally hosted in a Zenodo/Git-Hub integration
Date made available24 Apr 2020

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