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 classMolecule
potential maps
: a list of electrostatic potential map input objects of classMap
charge density maps
: a list of charge density map input objects of classMap
ion accessibility maps
: a list of ion accessibility map input objects of classMap
dielectric maps
: a list of dielectric map input objects of classDielectricMapGroup
parameters
: a list of parameter files of classParameter
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
: seealias()
format
: seeformat()
x-shifted path
: string with path to x-shifted map (seepaths()
)y-shifted path
: string with path to y-shifted map (seepaths()
)x-shifted path
: string with path to z-shifted map (seepaths()
)
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:
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
- 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_json() str
Produce JSON representation of self.
- to_yaml() str
Produce YAML representation of self.
- 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:
- 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:
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
- property path: str
Path for scalar input map.
- Raises
TypeError – if path is not a string
- to_json() str
Produce JSON representation of self.
- to_yaml() str
Produce YAML representation of self.
- 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:
- 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_json() str
Produce JSON representation of self.
- to_yaml() str
Produce YAML representation of self.
- 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:
- 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_json() str
Produce JSON representation of self.
- to_yaml() str
Produce YAML representation of self.
- 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 (seeMolecule
)potential maps
: a list of electrostatic potential map input objects (seeMap
)charge density maps
: a list of charge density map input objects (seeMap
)ion accessibility maps
: a list of ion accessibility map input objects (seeMap
)dielectric maps
: a list of dielectric map input objects (seeDielectricMapGroup
)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_json() str
Produce JSON representation of self.
- to_yaml() str
Produce YAML representation of self.