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.

Input file parsing classes.

class apbs.input_file.InputFile(dict_=None, yaml=None, json=None)

Bases: abc.ABC

Base class for input file classes.

from_dict(input_)

Parse dictionary-format input into this object.

Parameters:input (dict) – input dictionary Raises:KeyError – when input is missing

from_json(input_)

Parse JSON-format input string into this object.

Parameters:input (str) – JSON-format input string

from_yaml(input_)

Parse YAML-format input string into this object.

Parameters:input (str) – YAML-format input string

to_dict() → dict

Produce dictionary representation of self.

to_json() → str

Produce JSON representation of self.

to_yaml() → str

Produce YAML representation of self.

validate()

Validate the object.

Raises:ValueError – if object is not valid