Data processing input file API
These classes provide information about processing APBS output.
The top-level output summarizes or combines results from multiple calculations.
- class apbs.input_file.process.Element(dict_=None, yaml=None, json=None)[source]
Bases:
InputFile
Element of an arithmetic operation.
Objects can be initialized with dictionary/JSON/YAML data with a list of the following keys:
alias
: alias for quantity on which to operatecoefficient
: multiplicative coefficient for quantity (e.g., -1.0 to convert a sum to difference)
- property alias: str
Return alias for object to which this element refers.
- Raises:
TypeError – if alias is not a string.
- property coefficient: float
Return coefficient for this element.
- Raises:
TypeError – if not a number
- from_dict(input_)[source]
Load object contents from dictionary.
- Parameters:
input (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
- to_json() str
Produce JSON representation of self.
- to_yaml() str
Produce YAML representation of self.
- class apbs.input_file.process.Operation(dict_=None, yaml=None, json=None)[source]
Bases:
InputFile
Generic arithmetic operation.
Objects can be initialized with dictionary/JSON/YAML data with the following keys:
alias
: string for referring to the output of this operation elsewhereelements
: a list of elements for the operation; seeElement
for details
- property alias: str
String for referring to the output of this operation elsewhere.
- Raises:
TypeError – if alias is not a string
- property elements: list
List of
Element
objects for operation.- Raises:
TypeError – if list contains objects not
Element
- 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
- to_json() str
Produce JSON representation of self.
- to_yaml() str
Produce YAML representation of self.
- class apbs.input_file.process.Process(dict_=None, yaml=None, json=None)[source]
Bases:
InputFile
Arithmetic operations for output from APBS energy/force calculations.
Objects can be initialized with dictionary/JSON/YAML data with the following keys:
sums
: add elements together. This is a list ofOperation
objects.products
: multiply elements together. This is a list ofOperation
objects.exps
: element-wise exponentiation of elements. This is a list ofOperation
objects.
- property exps: list
List of exponential
Operation
objects.- Raises:
TypeError – if list contains something other than class:Operation objects
- from_dict(input_)[source]
Populate object from dictionary.
- Parameters:
input (dict) – input information
- Raises:
KeyError – if elements are missing from the input dictionary
- 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 products: list
List of product
Operation
objects.- Raises:
TypeError – if list contains something other than class:Operation objects
- property sums: list
List of sum
Operation
objects.- Raises:
TypeError – if list contains something other than class:Operation objects
- to_json() str
Produce JSON representation of self.
- to_yaml() str
Produce YAML representation of self.