API Reference

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 project contains classes to work with CHARMM topology and parameter files, classes which represent CHARMM residues and patch residues, and convenience functions to load CHARMM data and generate molecules with arbitrary sequences. These molecules can be written out to PSF and PDB to run simulations.

Subpackages

• pygen_structures.mol_containers package
  • Submodules
    • pygen_structures.mol_containers.atom module
    • pygen_structures.mol_containers.molecule module
    • pygen_structures.mol_containers.structure module

Submodules

• pygen_structures.charmm_containers module
• pygen_structures.convenience_functions module