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: apbs.input_file.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.

alias¶

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

Raises:	TypeError – if value is not string

format¶

Format for scalar input map.

One of:

dx: OpenDX scalar data format
dx.gz: GZip-compressed OpenDX scalar data format

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

paths¶

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: apbs.input_file.InputFile

Input class for scalar grid data input.

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

alias: see alias()
format: see format()
path: see path()

alias¶

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

Raises:	TypeError – if alias is not a string

format¶

Format for scalar input map.

One of:

dx: OpenDX scalar data format
dx.gz: GZip-compressed OpenDX scalar data format

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

path¶

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: apbs.input_file.InputFile

Input class for molecule input.

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

alias: see alias()
format: see format()
path: see path()

alias¶

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

Raises:	TypeError – if alias is not string

format¶

Format of molecule input.

One of:

pdb: PDB molecular structure format
pqr: PQR molecular structure format

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

path¶

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: apbs.input_file.InputFile

Input class for parameter file input.

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

alias: see alias()
format: see format()
path: see path()

alias¶

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

Raises:	TypeError – if not a string

format¶

Format of the parameter file.

One of:

flat: APBS flat-file parameter format
xml: APBS XML parameter format

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

path¶

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: apbs.input_file.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

charge_density_maps¶

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

dielectric_maps¶

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

ion_accessibility_maps¶

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

molecules¶

List of Molecule objects.

Raises:	TypeError – if something other than `Molecule` in list

potential_maps¶

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