Skip to content

Configuration

PDBFixer does not require a global configuration file or environment variables. Most behavior is controlled directly through PDBFixer constructor arguments and method parameters.

Environment variables

No environment variables are consumed by the library. If you rely on proxy settings for downloads, configure them at the system level (for example, HTTP_PROXY/HTTPS_PROXY).

Runtime parameters

  • Input source: choose one of filename, pdbfile, pdbxfile, url, or pdbid when creating PDBFixer.
  • Hydrogenation pH: pass pH to addMissingHydrogens().
  • Solvent box shape and ions: provide boxSize, padding, positiveIon, negativeIon, and ionicStrength to addSolvent().
  • Template resolution: supply custom templates with registerTemplate() or allow downloads via downloadTemplate().

Configuration files

No repository-level configuration files are required beyond the Python package itself. If you use OpenMM platform selection, pass an openmm.Platform instance to the PDBFixer constructor.