Component
- class openff.evaluator.substances.Component(smiles=<openff.evaluator.attributes.attributes.UndefinedAttribute object>, role=Role.Solvent)[source]
Defines a single component in a chemical system, as well as it’s role within the system (if any).
- __init__(smiles=<openff.evaluator.attributes.attributes.UndefinedAttribute object>, role=Role.Solvent)[source]
Constructs a new Component object with either a label or a smiles string, but not both.
Notes
The label and smiles arguments are mutually exclusive, and only one can be passed while the other should be None.
- Parameters
smiles (str) – A SMILES descriptor of the component
role (Component.Role) – The role of this component in the system.
Methods
__init__
([smiles, role])Constructs a new Component object with either a label or a smiles string, but not both.
from_json
(file_path)Create this object from a JSON file.
get_attributes
([attribute_type])Returns all attributes of a specific attribute_type.
json
([file_path, format])Creates a JSON representation of this class.
parse_json
(string_contents)validate
([attribute_type])Validate the values of the attributes.
Attributes
A unique identifier for this component.
The role of this component in the system.
The SMILES pattern which describes this component.
- class Role(value)[source]
An enum which describes the role of a component in the system, such as whether the component is a solvent, a solute, a receptor etc.
These roles are mainly used by workflow to identify the correct species in a system, such as when doing docking or performing solvation free energy calculations.
- smiles
The SMILES pattern which describes this component. The default value of this attribute is not set and must be set by the user.. This attribute is read-only.
- Type
- role
The role of this component in the system. The default value of this attribute is
Role.Solvent
. This attribute is read-only.- Type
- classmethod from_json(file_path)
Create this object from a JSON file.
- Parameters
file_path (str) – The path to load the JSON from.
- Returns
The parsed class.
- Return type
cls
- classmethod get_attributes(attribute_type=None)
Returns all attributes of a specific attribute_type.
- Parameters
attribute_type (type of Attribute, optional) – The type of attribute to search for.
- Returns
The names of the attributes of the specified type.
- Return type
list of str
- json(file_path=None, format=False)
Creates a JSON representation of this class.
- validate(attribute_type=None)
Validate the values of the attributes. If attribute_type is set, only attributes of that type will be validated.
- Parameters
attribute_type (type of Attribute, optional) – The type of attribute to validate.
- Raises
ValueError or AssertionError –