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:
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:
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:
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:
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:
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.