YAML- and JSON-format input files

In its new input format, APBS accepts either JSON- or YAML-format input files.

These input files consist of the following keywords and objects:

• Data loading input file section (required)
  • Data loading input file API
• Calculation input file section (required)
  • Calculation types
    • Boundary-element Poisson-Boltzmann calculations
    • Finite-difference Poisson-Boltzmann calculations
    • Finite-element Poisson-Boltzmann calculations
    • Nonpolar grid-based calculations
  • Calculate API
• Results processing section (optional)
  • Data processing input file API

Input file class structure

The input file object parsing and validation follows the basic pattern implemented in apbs.input_file.InputFile (see below). This class should serve as a template for adding new input file sections.