Data loading input file section (required)

This required section is denoted by the keyword read and is described in Read. The section includes objects indexed by the following keywords:

  • molecules: a list of molecule input objects of class Molecule

  • potential maps: a list of electrostatic potential map input objects of class Map

  • charge density maps: a list of charge density map input objects of class Map

  • ion accessibility maps: a list of ion accessibility map input objects of class Map

  • dielectric maps: a list of dielectric map input objects of class DielectricMapGroup

  • parameters: a list of parameter files of class Parameter


Data loading input file API

These classes provide information about data input for APBS.

class apbs.input_file.read.DielectricMapGroup(dict_=None, yaml=None, json=None)[source]

Bases: InputFile

Input class for a group of three dielectric maps.

These three maps represent the dielectric function mapped to three meshes, shifted by one-half grid spacing in the x, y, and z directions. The inputs are maps of dielectric variables between the solvent and biomolecular dielectric constants; these values are unitless.

Objects can be initialized with dictionary/JSON/YAML data with the following keys:

  • alias: see alias()

  • format: see format()

  • x-shifted path: string with path to x-shifted map (see paths())

  • y-shifted path: string with path to y-shifted map (see paths())

  • x-shifted path: string with path to z-shifted map (see paths())

More information about these properties is provided below.

property alias: str

String used to refer to these maps elsewhere in the input file.

Raises

TypeError – if value is not string

property format: str

Format for scalar input map.

One of:

Raises

ValueError – if assigned incorrect format value

from_dict(dict_)[source]

Load object contents from dictionary.

Parameters

dict (dict) – dictionary with object contents

Raises

KeyError – if dictionary elements 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

property paths: tuple

3-tuple of strings.

Tuple contains paths to the x-, y-, and z-shifted dielectric maps.

Raises
  • IndexError – if length of list is not 3

  • TypeError – if list does not contain strings

to_dict() dict[source]

Produce dictionary representation of self.

to_json() str

Produce JSON representation of self.

to_yaml() str

Produce YAML representation of self.

validate()[source]

Validate object.

Raises

ValueError – if object invalid

class apbs.input_file.read.Map(dict_=None, yaml=None, json=None)[source]

Bases: InputFile

Input class for scalar grid data input.

Objects can be initialized with dictionary/JSON/YAML data with the following keys:

property alias: str

String used to refer to this map elsewhere in the input file.

Raises

TypeError – if alias is not a string

property format: str

Format for scalar input map.

One of:

Raises

ValueError – if format is not one of allowed values

from_dict(input_)[source]

Load object contents from dictionary.

Parameters

input (dict) – input dictionary

Raises

KeyError – if input is missing keys

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

property path: str

Path for scalar input map.

Raises

TypeError – if path is not a string

to_dict() dict[source]

Produce dictionary representation of self.

to_json() str

Produce JSON representation of self.

to_yaml() str

Produce YAML representation of self.

validate()[source]

Validate the object.

Raises

ValueError – if object is not valid

class apbs.input_file.read.Molecule(dict_=None, yaml=None, json=None)[source]

Bases: InputFile

Input class for molecule input.

Objects can be initialized with dictionary/JSON/YAML data with the following keys:

property alias: str

String used to refer to this map elsewhere in the input file.

Raises

TypeError – if alias is not string

property format: str

Format of molecule input.

One of:

Raises

ValueError – if format is not one of the above

from_dict(input_)[source]

Load object contents from dictionary.

Parameters

input (dict) – input dictionary

Raises

KeyError – if input is missing keys

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

property path: str

Path of molecule input.

Raises

TypeError – if path is not string

to_dict() dict[source]

Produce dictionary representation of self.

to_json() str

Produce JSON representation of self.

to_yaml() str

Produce YAML representation of self.

validate()[source]

Validate the object.

Raises

ValueError – if object is not valid

class apbs.input_file.read.Parameter(dict_=None, yaml=None, json=None)[source]

Bases: InputFile

Input class for parameter file input.

Objects can be initialized with dictionary/JSON/YAML data with the following keys:

property alias: str

String used to refer to this map elsewhere in the input file.

Raises

TypeError – if not a string

property format: str

Format of the parameter file.

One of:

Raises

ValueError – if given invalid format

from_dict(input_)[source]

Load object contents from dictionary.

Parameters

input (dict) – input dictionary

Raises

KeyError – if dictionary elements 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

property path: str

Path to the parameter file.

Raises

TypeError – if not a string

to_dict() dict[source]

Produce dictionary representation of self.

to_json() str

Produce JSON representation of self.

to_yaml() str

Produce YAML representation of self.

validate()[source]

Validate this object.

Raises

ValueError – if object is invalid

class apbs.input_file.read.Read(dict_=None, yaml=None, json=None)[source]

Bases: InputFile

Class for information about data to be loaded into APBS.

Objects can be initialized with dictionary/JSON/YAML data with the following keys:

  • molecules: a list of molecule input objects (see Molecule)

  • potential maps: a list of electrostatic potential map input objects (see Map)

  • charge density maps: a list of charge density map input objects (see Map)

  • ion accessibility maps: a list of ion accessibility map input objects (see Map)

  • dielectric maps: a list of dielectric map input objects (see DielectricMapGroup)

  • parameters: a list of parameter files

property charge_density_maps: list

List of charge density Map objects..

These maps can be used to provide charge density (source term) distributions outside of the normal atom-based charge distribution obtained from a molecular structure.

Units of charge density are \(e_c Å^{-3}\).

Raises

TypeError – if something other than Map in list

property dielectric_maps: list

List of DielectricMapGroup objects.

These 3-tuples represent the dielectric function mapped to 3 meshes, shifted by one-half grid spacing in the x, y, and z directions. The inputs are maps of dielectric variables between the solvent and biomolecular dielectric constants; these values are unitless.

Raises

TypeError – if something other than DielectricMapGroup in list

from_dict(input_)[source]

Load object contents from dictionary.

Parameters

input (dict) – input dictionary

Raises

KeyError – if input is missing keys

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

property ion_accessibility_maps: list

List of ion accessibility Map objects..

The maps specify ion accessibility values which range between 0 (inaccessible) and the value of the Debye-Hückel screening parameter; these values have units of \(Å^{-2}\).

Raises

TypeError – if something other than Map in list

property molecules: list

List of Molecule objects.

Raises

TypeError – if something other than Molecule in list

property potential_maps: list

List of electrostatic potential Map objects.”.

These maps can be used to set the electrostatic potential at the boundary to values outside of the traditional mappings.

Units of electrostatic potential are \(k_b T e_c^{-1}\).

Raises

TypeError – if something other than Map in list

to_dict() dict[source]

Produce dictionary representation of self.

to_json() str

Produce JSON representation of self.

to_yaml() str

Produce YAML representation of self.

validate()[source]

Validate this input object.

Raises

ValueError – if invalid