gufe.settings.models¶

Pydantic models used for storing settings.

Classes

`BaseForceFieldSettings`()	Base class for ForceFieldSettings objects
`OpenMMSystemGeneratorFFSettings`(*, ...)	Parameters to set up the force field with OpenMM ForceFields
`Settings`(*, forcefield_settings, thermo_settings)	Container for all settings needed by a protocol
`SettingsBaseModel`()	Settings and modifications we want for all settings classes.
`ThermoSettings`(*, temperature, FieldInfo, ...)	Settings for thermodynamic parameters.

class gufe.settings.models.SettingsBaseModel¶

Settings and modifications we want for all settings classes.

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

model_config = {'arbitrary_types_allowed': True, 'extra': 'forbid', 'validate_assignment': True, 'validate_default': True}¶: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

frozen_copy()¶

A copy of this Settings object which cannot be modified

This is intended to be used by Protocols to make their stored Settings read-only

unfrozen_copy()¶

A copy of this Settings object, which can be modified

Settings objects become frozen when within a Protocol. If you really need to reverse this, this method is how.

property is_frozen¶: If this Settings object is frozen and cannot be modified

classmethod construct(_fields_set: set[str] | None = None, **values: Any) → Self¶

Returns a copy of the model.

!!! warning “Deprecated”: This method is now deprecated; use model_copy instead.

If you need include or exclude, use:

`python {test="skip" lint="skip"} data = self.model_dump(include=include, exclude=exclude, round_trip=True) data = {**data, **(update or {})} copied = self.model_validate(data) `

Parameters:

include – Optional set or mapping specifying which fields to include in the copied model.
exclude – Optional set or mapping specifying which fields to exclude in the copied model.
update – Optional dictionary of field-value pairs to override field values in the copied model.
deep – If True, the values of fields that are Pydantic models will be deep-copied.

Returns:

A copy of the model with included, excluded and updated fields as specified.

dict(*, include: set[int] | set[str] | Mapping[int, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | Mapping[str, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | None = None, exclude: set[int] | set[str] | Mapping[int, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | Mapping[str, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | None = None, by_alias: bool = False, exclude_unset: bool = False, exclude_defaults: bool = False, exclude_none: bool = False) → Dict[str, Any]¶

classmethod from_orm(obj: Any) → Self¶

json(*, include: set[int] | set[str] | Mapping[int, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | Mapping[str, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | None = None, exclude: set[int] | set[str] | Mapping[int, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | Mapping[str, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | None = None, by_alias: bool = False, exclude_unset: bool = False, exclude_defaults: bool = False, exclude_none: bool = False, encoder: Callable[[Any], Any] | None = PydanticUndefined, models_as_dict: bool = PydanticUndefined, **dumps_kwargs: Any) → str¶

model_computed_fields = {}¶

classmethod model_construct(_fields_set: set[str] | None = None, **values: Any) → Self¶

Creates a new instance of the Model class with validated data.

Creates a new model setting __dict__ and __pydantic_fields_set__ from trusted or pre-validated data. Default values are respected, but no other validation is performed.

!!! note: model_construct() generally respects the model_config.extra setting on the provided model. That is, if model_config.extra == ‘allow’, then all extra passed values are added to the model instance’s __dict__ and __pydantic_extra__ fields. If model_config.extra == ‘ignore’ (the default), then all extra passed values are ignored. Because no validation is performed with a call to model_construct(), having model_config.extra == ‘forbid’ does not result in an error if extra values are passed, but they will be ignored.

Parameters:

_fields_set – A set of field names that were originally explicitly set during instantiation. If provided, this is directly used for the [model_fields_set][pydantic.BaseModel.model_fields_set] attribute. Otherwise, the field names from the values argument will be used.
values – Trusted or pre-validated data dictionary.

Returns:

A new instance of the Model class with validated data.

model_copy(*, update: Mapping[str, Any] | None = None, deep: bool = False) → Self¶

!!! abstract “Usage Documentation”: [model_copy](../concepts/serialization.md#model_copy)

Returns a copy of the model.

!!! note: The underlying instance’s [__dict__][object.__dict__] attribute is copied. This might have unexpected side effects if you store anything in it, on top of the model fields (e.g. the value of [cached properties][functools.cached_property]).

Parameters:

update – Values to change/add in the new model. Note: the data is not validated before creating the new model. You should trust this data.
deep – Set to True to make a deep copy of the model.

Returns:

New model instance.

model_dump(**kwargs) → dict[str, Any]¶

!!! abstract “Usage Documentation”: [model_dump](../concepts/serialization.md#modelmodel_dump)

Generate a dictionary representation of the model, optionally specifying which fields to include or exclude.

Parameters:

mode – The mode in which to_python should run. If mode is ‘json’, the output will only contain JSON serializable types. If mode is ‘python’, the output may contain non-JSON-serializable Python objects.
include – A set of fields to include in the output.
exclude – A set of fields to exclude from the output.
context – Additional context to pass to the serializer.
by_alias – Whether to use the field’s alias in the dictionary key if defined.
exclude_unset – Whether to exclude fields that have not been explicitly set.
exclude_defaults – Whether to exclude fields that are set to their default value.
exclude_none – Whether to exclude fields that have a value of None.
round_trip – If True, dumped values should be valid as input for non-idempotent types such as Json[T].
warnings – How to handle serialization errors. False/”none” ignores them, True/”warn” logs errors, “error” raises a [PydanticSerializationError][pydantic_core.PydanticSerializationError].
fallback – A function to call when an unknown value is encountered. If not provided, a [PydanticSerializationError][pydantic_core.PydanticSerializationError] error is raised.
serialize_as_any – Whether to serialize fields with duck-typing serialization behavior.

Returns:

A dictionary representation of the model.

model_dump_json(**kwargs) → str¶

!!! abstract “Usage Documentation”: [model_dump_json](../concepts/serialization.md#modelmodel_dump_json)

Generates a JSON representation of the model using Pydantic’s to_json method.

Parameters:

indent – Indentation to use in the JSON output. If None is passed, the output will be compact.
include – Field(s) to include in the JSON output.
exclude – Field(s) to exclude from the JSON output.
context – Additional context to pass to the serializer.
by_alias – Whether to serialize using field aliases.
exclude_unset – Whether to exclude fields that have not been explicitly set.
exclude_defaults – Whether to exclude fields that are set to their default value.
exclude_none – Whether to exclude fields that have a value of None.
round_trip – If True, dumped values should be valid as input for non-idempotent types such as Json[T].
warnings – How to handle serialization errors. False/”none” ignores them, True/”warn” logs errors, “error” raises a [PydanticSerializationError][pydantic_core.PydanticSerializationError].
fallback – A function to call when an unknown value is encountered. If not provided, a [PydanticSerializationError][pydantic_core.PydanticSerializationError] error is raised.
serialize_as_any – Whether to serialize fields with duck-typing serialization behavior.

Returns:

A JSON string representation of the model.

property model_extra: dict[str, Any] | None¶

Get extra fields set during validation.

Returns:: A dictionary of extra fields, or None if config.extra is not set to “allow”.

model_fields = {}¶

property model_fields_set: set[str]¶

Returns the set of fields that have been explicitly set on this model instance.

Returns:

A set of strings representing the fields that have been set,: i.e. that were not filled from defaults.

classmethod model_json_schema(by_alias: bool = True, ref_template: str = '#/$defs/{model}', schema_generator: type[GenerateJsonSchema] = <class 'pydantic.json_schema.GenerateJsonSchema'>, mode: Literal['validation', 'serialization']='validation') → dict[str, Any]¶

Generates a JSON schema for a model class.

Parameters:

by_alias – Whether to use attribute aliases or not.
ref_template – The reference template.
schema_generator – To override the logic used to generate the JSON schema, as a subclass of GenerateJsonSchema with your desired modifications
mode – The mode in which to generate the schema.

Returns:

The JSON schema for the given model class.

classmethod model_parametrized_name(params: tuple[type[Any], ...]) → str¶

Compute the class name for parametrizations of generic classes.

This method can be overridden to achieve a custom naming scheme for generic BaseModels.

Parameters:: params – Tuple of types of the class. Given a generic class Model with 2 type variables and a concrete model Model[str, int], the value (str, int) would be passed to params.
Returns:: String representing the new class where params are passed to cls as type variables.
Raises:: TypeError – Raised when trying to generate concrete names for non-generic models.

model_post_init(context: Any, /) → None¶

This function is meant to behave like a BaseModel method to initialise private attributes.

It takes context as an argument since that’s what pydantic-core passes when calling it.

Parameters:

self – The BaseModel instance.
context – The context.

classmethod model_rebuild(*, force: bool = False, raise_errors: bool = True, _parent_namespace_depth: int = 2, _types_namespace: MappingNamespace | None = None) → bool | None¶

Try to rebuild the pydantic-core schema for the model.

This may be necessary when one of the annotations is a ForwardRef which could not be resolved during the initial attempt to build the schema, and automatic rebuilding fails.

Parameters:

force – Whether to force the rebuilding of the model schema, defaults to False.
raise_errors – Whether to raise errors, defaults to True.
_parent_namespace_depth – The depth level of the parent namespace, defaults to 2.
_types_namespace – The types namespace, defaults to None.

Returns:

Returns None if the schema is already “complete” and rebuilding was not required. If rebuilding _was_ required, returns True if rebuilding was successful, otherwise False.

Validate a pydantic model instance.

Parameters:

obj – The object to validate.
strict – Whether to enforce types strictly.
from_attributes – Whether to extract data from object attributes.
context – Additional context to pass to the validator.
by_alias – Whether to use the field’s alias when validating against the provided input data.
by_name – Whether to use the field’s name when validating against the provided input data.

Raises:

ValidationError – If the object could not be validated.

Returns:

The validated model instance.

!!! abstract “Usage Documentation”: [JSON Parsing](../concepts/json.md#json-parsing)

Validate the given JSON data against the Pydantic model.

Parameters:

json_data – The JSON data to validate.
strict – Whether to enforce types strictly.
context – Extra variables to pass to the validator.
by_alias – Whether to use the field’s alias when validating against the provided input data.
by_name – Whether to use the field’s name when validating against the provided input data.

Returns:

The validated Pydantic model.

Raises:

ValidationError – If json_data is not a JSON string or the object could not be validated.

classmethod model_validate_strings(obj: Any, *, strict: bool | None = None, context: Any | None = None, by_alias: bool | None = None, by_name: bool | None = None) → Self¶

Validate the given object with string data against the Pydantic model.

Parameters:

obj – The object containing string data to validate.
strict – Whether to enforce types strictly.
context – Extra variables to pass to the validator.
by_alias – Whether to use the field’s alias when validating against the provided input data.
by_name – Whether to use the field’s name when validating against the provided input data.

Returns:

The validated Pydantic model.

classmethod parse_file(path: str | Path, *, content_type: str | None = None, encoding: str = 'utf8', proto: DeprecatedParseProtocol | None = None, allow_pickle: bool = False) → Self¶

classmethod parse_obj(obj: Any) → Self¶

classmethod parse_raw(b: str | bytes, *, content_type: str | None = None, encoding: str = 'utf8', proto: DeprecatedParseProtocol | None = None, allow_pickle: bool = False) → Self¶

classmethod schema(by_alias: bool = True, ref_template: str = '#/$defs/{model}') → Dict[str, Any]¶

classmethod schema_json(*, by_alias: bool = True, ref_template: str = '#/$defs/{model}', **dumps_kwargs: Any) → str¶

classmethod update_forward_refs(**localns: Any) → None¶

classmethod validate(value: Any) → Self¶

class gufe.settings.models.ThermoSettings(*, temperature: Quantity, FieldInfo(annotation=NoneType, required=True, validate_default=True), ~pydantic.functional_validators.PlainValidator(func=~gufe.settings.typing._plain_quantity_validator, json_schema_input_type=~typing.Any), ~pydantic.json_schema.WithJsonSchema(json_schema={'type': 'number'}, mode=None), ~pydantic.functional_serializers.PlainSerializer(func=~gufe.settings.typing._plain_quantity_serializer, return_type=PydanticUndefined, when_used=always), ~pydantic.functional_validators.AfterValidator(func=functools.partial(<function _has_compatible_dimensionality at 0x7add3b477ba0>, unit='kelvin', convert=True))] | None = None, pressure: Quantity, FieldInfo(annotation=NoneType, required=True, validate_default=True), ~pydantic.functional_validators.PlainValidator(func=~gufe.settings.typing._plain_quantity_validator, json_schema_input_type=~typing.Any), ~pydantic.json_schema.WithJsonSchema(json_schema={'type': 'number'}, mode=None), ~pydantic.functional_serializers.PlainSerializer(func=~gufe.settings.typing._plain_quantity_serializer, return_type=PydanticUndefined, when_used=always), ~pydantic.functional_validators.AfterValidator(func=functools.partial(<function _has_compatible_dimensionality at 0x7add3b477ba0>, unit='bar', convert=True))] | None = None, ph: Annotated[float, ~annotated_types.Gt(gt=0)] | None = None, redox_potential: Quantity, FieldInfo(annotation=NoneType, required=True, validate_default=True), ~pydantic.functional_validators.PlainValidator(func=~gufe.settings.typing._plain_quantity_validator, json_schema_input_type=~typing.Any), ~pydantic.json_schema.WithJsonSchema(json_schema={'type': 'number'}, mode=None), ~pydantic.functional_serializers.PlainSerializer(func=~gufe.settings.typing._plain_quantity_serializer, return_type=PydanticUndefined, when_used=always), ~pydantic.functional_validators.AfterValidator(func=functools.partial(<function _has_compatible_dimensionality at 0x7add3b477ba0>, unit='volts', convert=True))] | None = None)¶

Settings for thermodynamic parameters.

Note

No checking is done to ensure a valid thermodynamic ensemble is possible.

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

temperature: KelvinQuantity | None¶

pressure: BarQuantity | None¶

ph: PositiveFloat | None¶

redox_potential: VoltsQuantity | None¶

classmethod construct(_fields_set: set[str] | None = None, **values: Any) → Self¶

Returns a copy of the model.

!!! warning “Deprecated”: This method is now deprecated; use model_copy instead.

If you need include or exclude, use:

`python {test="skip" lint="skip"} data = self.model_dump(include=include, exclude=exclude, round_trip=True) data = {**data, **(update or {})} copied = self.model_validate(data) `

Parameters:

include – Optional set or mapping specifying which fields to include in the copied model.
exclude – Optional set or mapping specifying which fields to exclude in the copied model.
update – Optional dictionary of field-value pairs to override field values in the copied model.
deep – If True, the values of fields that are Pydantic models will be deep-copied.

Returns:

A copy of the model with included, excluded and updated fields as specified.

dict(*, include: set[int] | set[str] | Mapping[int, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | Mapping[str, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | None = None, exclude: set[int] | set[str] | Mapping[int, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | Mapping[str, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | None = None, by_alias: bool = False, exclude_unset: bool = False, exclude_defaults: bool = False, exclude_none: bool = False) → Dict[str, Any]¶

classmethod from_orm(obj: Any) → Self¶

frozen_copy()¶

A copy of this Settings object which cannot be modified

This is intended to be used by Protocols to make their stored Settings read-only

property is_frozen¶: If this Settings object is frozen and cannot be modified

json(*, include: set[int] | set[str] | Mapping[int, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | Mapping[str, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | None = None, exclude: set[int] | set[str] | Mapping[int, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | Mapping[str, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | None = None, by_alias: bool = False, exclude_unset: bool = False, exclude_defaults: bool = False, exclude_none: bool = False, encoder: Callable[[Any], Any] | None = PydanticUndefined, models_as_dict: bool = PydanticUndefined, **dumps_kwargs: Any) → str¶

model_computed_fields = {}¶

model_config = {'arbitrary_types_allowed': True, 'extra': 'forbid', 'validate_assignment': True, 'validate_default': True}¶: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

classmethod model_construct(_fields_set: set[str] | None = None, **values: Any) → Self¶

Creates a new instance of the Model class with validated data.

Creates a new model setting __dict__ and __pydantic_fields_set__ from trusted or pre-validated data. Default values are respected, but no other validation is performed.

!!! note: model_construct() generally respects the model_config.extra setting on the provided model. That is, if model_config.extra == ‘allow’, then all extra passed values are added to the model instance’s __dict__ and __pydantic_extra__ fields. If model_config.extra == ‘ignore’ (the default), then all extra passed values are ignored. Because no validation is performed with a call to model_construct(), having model_config.extra == ‘forbid’ does not result in an error if extra values are passed, but they will be ignored.

Parameters:

_fields_set – A set of field names that were originally explicitly set during instantiation. If provided, this is directly used for the [model_fields_set][pydantic.BaseModel.model_fields_set] attribute. Otherwise, the field names from the values argument will be used.
values – Trusted or pre-validated data dictionary.

Returns:

A new instance of the Model class with validated data.

model_copy(*, update: Mapping[str, Any] | None = None, deep: bool = False) → Self¶

!!! abstract “Usage Documentation”: [model_copy](../concepts/serialization.md#model_copy)

Returns a copy of the model.

!!! note: The underlying instance’s [__dict__][object.__dict__] attribute is copied. This might have unexpected side effects if you store anything in it, on top of the model fields (e.g. the value of [cached properties][functools.cached_property]).

Parameters:

update – Values to change/add in the new model. Note: the data is not validated before creating the new model. You should trust this data.
deep – Set to True to make a deep copy of the model.

Returns:

New model instance.

model_dump(**kwargs) → dict[str, Any]¶

!!! abstract “Usage Documentation”: [model_dump](../concepts/serialization.md#modelmodel_dump)

Generate a dictionary representation of the model, optionally specifying which fields to include or exclude.

Parameters:

mode – The mode in which to_python should run. If mode is ‘json’, the output will only contain JSON serializable types. If mode is ‘python’, the output may contain non-JSON-serializable Python objects.
include – A set of fields to include in the output.
exclude – A set of fields to exclude from the output.
context – Additional context to pass to the serializer.
by_alias – Whether to use the field’s alias in the dictionary key if defined.
exclude_unset – Whether to exclude fields that have not been explicitly set.
exclude_defaults – Whether to exclude fields that are set to their default value.
exclude_none – Whether to exclude fields that have a value of None.
round_trip – If True, dumped values should be valid as input for non-idempotent types such as Json[T].
warnings – How to handle serialization errors. False/”none” ignores them, True/”warn” logs errors, “error” raises a [PydanticSerializationError][pydantic_core.PydanticSerializationError].
fallback – A function to call when an unknown value is encountered. If not provided, a [PydanticSerializationError][pydantic_core.PydanticSerializationError] error is raised.
serialize_as_any – Whether to serialize fields with duck-typing serialization behavior.

Returns:

A dictionary representation of the model.

model_dump_json(**kwargs) → str¶

!!! abstract “Usage Documentation”: [model_dump_json](../concepts/serialization.md#modelmodel_dump_json)

Generates a JSON representation of the model using Pydantic’s to_json method.

Parameters:

indent – Indentation to use in the JSON output. If None is passed, the output will be compact.
include – Field(s) to include in the JSON output.
exclude – Field(s) to exclude from the JSON output.
context – Additional context to pass to the serializer.
by_alias – Whether to serialize using field aliases.
exclude_unset – Whether to exclude fields that have not been explicitly set.
exclude_defaults – Whether to exclude fields that are set to their default value.
exclude_none – Whether to exclude fields that have a value of None.
round_trip – If True, dumped values should be valid as input for non-idempotent types such as Json[T].
warnings – How to handle serialization errors. False/”none” ignores them, True/”warn” logs errors, “error” raises a [PydanticSerializationError][pydantic_core.PydanticSerializationError].
fallback – A function to call when an unknown value is encountered. If not provided, a [PydanticSerializationError][pydantic_core.PydanticSerializationError] error is raised.
serialize_as_any – Whether to serialize fields with duck-typing serialization behavior.

Returns:

A JSON string representation of the model.

property model_extra: dict[str, Any] | None¶

Get extra fields set during validation.

Returns:: A dictionary of extra fields, or None if config.extra is not set to “allow”.

model_fields = {'ph': FieldInfo(annotation=Union[Annotated[float, Gt], NoneType], required=False, default=None, description='Simulation pH.'), 'pressure': FieldInfo(annotation=Union[Annotated[Quantity, FieldInfo(annotation=NoneType, required=True, validate_default=True), PlainValidator, WithJsonSchema, PlainSerializer, AfterValidator], NoneType], required=False, default=None, description='Simulation pressure in bar. Compatible units will be converted to bar.'), 'redox_potential': FieldInfo(annotation=Union[Annotated[Quantity, FieldInfo(annotation=NoneType, required=True, validate_default=True), PlainValidator, WithJsonSchema, PlainSerializer, AfterValidator], NoneType], required=False, default=None, description='Simulation redox potential in millivolts (mV). Compatible units will be converted to mV.'), 'temperature': FieldInfo(annotation=Union[Annotated[Quantity, FieldInfo(annotation=NoneType, required=True, validate_default=True), PlainValidator, WithJsonSchema, PlainSerializer, AfterValidator], NoneType], required=False, default=None, description="Simulation temperature in Kelvin. Compatible units will be converted to Kelvin. NOTE: celsius must be input as ``Quantity(<magnitude>, 'celsius')``. See https://pint.readthedocs.io/en/stable/user/nonmult.html for more information.")}¶

property model_fields_set: set[str]¶

Returns the set of fields that have been explicitly set on this model instance.

Returns:

A set of strings representing the fields that have been set,: i.e. that were not filled from defaults.

Generates a JSON schema for a model class.

Parameters:

by_alias – Whether to use attribute aliases or not.
ref_template – The reference template.
schema_generator – To override the logic used to generate the JSON schema, as a subclass of GenerateJsonSchema with your desired modifications
mode – The mode in which to generate the schema.

Returns:

The JSON schema for the given model class.

classmethod model_parametrized_name(params: tuple[type[Any], ...]) → str¶

Compute the class name for parametrizations of generic classes.

This method can be overridden to achieve a custom naming scheme for generic BaseModels.

Parameters:: params – Tuple of types of the class. Given a generic class Model with 2 type variables and a concrete model Model[str, int], the value (str, int) would be passed to params.
Returns:: String representing the new class where params are passed to cls as type variables.
Raises:: TypeError – Raised when trying to generate concrete names for non-generic models.

model_post_init(context: Any, /) → None¶

This function is meant to behave like a BaseModel method to initialise private attributes.

It takes context as an argument since that’s what pydantic-core passes when calling it.

Parameters:

self – The BaseModel instance.
context – The context.

classmethod model_rebuild(*, force: bool = False, raise_errors: bool = True, _parent_namespace_depth: int = 2, _types_namespace: MappingNamespace | None = None) → bool | None¶

Try to rebuild the pydantic-core schema for the model.

This may be necessary when one of the annotations is a ForwardRef which could not be resolved during the initial attempt to build the schema, and automatic rebuilding fails.

Parameters:

force – Whether to force the rebuilding of the model schema, defaults to False.
raise_errors – Whether to raise errors, defaults to True.
_parent_namespace_depth – The depth level of the parent namespace, defaults to 2.
_types_namespace – The types namespace, defaults to None.

Returns:

Returns None if the schema is already “complete” and rebuilding was not required. If rebuilding _was_ required, returns True if rebuilding was successful, otherwise False.

Validate a pydantic model instance.

Parameters:

obj – The object to validate.
strict – Whether to enforce types strictly.
from_attributes – Whether to extract data from object attributes.
context – Additional context to pass to the validator.
by_alias – Whether to use the field’s alias when validating against the provided input data.
by_name – Whether to use the field’s name when validating against the provided input data.

Raises:

ValidationError – If the object could not be validated.

Returns:

The validated model instance.

!!! abstract “Usage Documentation”: [JSON Parsing](../concepts/json.md#json-parsing)

Validate the given JSON data against the Pydantic model.

Parameters:

json_data – The JSON data to validate.
strict – Whether to enforce types strictly.
context – Extra variables to pass to the validator.
by_alias – Whether to use the field’s alias when validating against the provided input data.
by_name – Whether to use the field’s name when validating against the provided input data.

Returns:

The validated Pydantic model.

Raises:

ValidationError – If json_data is not a JSON string or the object could not be validated.

classmethod model_validate_strings(obj: Any, *, strict: bool | None = None, context: Any | None = None, by_alias: bool | None = None, by_name: bool | None = None) → Self¶

Validate the given object with string data against the Pydantic model.

Parameters:

obj – The object containing string data to validate.
strict – Whether to enforce types strictly.
context – Extra variables to pass to the validator.
by_alias – Whether to use the field’s alias when validating against the provided input data.
by_name – Whether to use the field’s name when validating against the provided input data.

Returns:

The validated Pydantic model.

classmethod parse_file(path: str | Path, *, content_type: str | None = None, encoding: str = 'utf8', proto: DeprecatedParseProtocol | None = None, allow_pickle: bool = False) → Self¶

classmethod parse_obj(obj: Any) → Self¶

classmethod parse_raw(b: str | bytes, *, content_type: str | None = None, encoding: str = 'utf8', proto: DeprecatedParseProtocol | None = None, allow_pickle: bool = False) → Self¶

classmethod schema(by_alias: bool = True, ref_template: str = '#/$defs/{model}') → Dict[str, Any]¶

classmethod schema_json(*, by_alias: bool = True, ref_template: str = '#/$defs/{model}', **dumps_kwargs: Any) → str¶

unfrozen_copy()¶

A copy of this Settings object, which can be modified

Settings objects become frozen when within a Protocol. If you really need to reverse this, this method is how.

classmethod update_forward_refs(**localns: Any) → None¶

classmethod validate(value: Any) → Self¶

class gufe.settings.models.BaseForceFieldSettings¶

Base class for ForceFieldSettings objects

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

classmethod construct(_fields_set: set[str] | None = None, **values: Any) → Self¶

Returns a copy of the model.

!!! warning “Deprecated”: This method is now deprecated; use model_copy instead.

If you need include or exclude, use:

`python {test="skip" lint="skip"} data = self.model_dump(include=include, exclude=exclude, round_trip=True) data = {**data, **(update or {})} copied = self.model_validate(data) `

Parameters:

include – Optional set or mapping specifying which fields to include in the copied model.
exclude – Optional set or mapping specifying which fields to exclude in the copied model.
update – Optional dictionary of field-value pairs to override field values in the copied model.
deep – If True, the values of fields that are Pydantic models will be deep-copied.

Returns:

A copy of the model with included, excluded and updated fields as specified.

dict(*, include: set[int] | set[str] | Mapping[int, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | Mapping[str, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | None = None, exclude: set[int] | set[str] | Mapping[int, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | Mapping[str, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | None = None, by_alias: bool = False, exclude_unset: bool = False, exclude_defaults: bool = False, exclude_none: bool = False) → Dict[str, Any]¶

classmethod from_orm(obj: Any) → Self¶

frozen_copy()¶

A copy of this Settings object which cannot be modified

This is intended to be used by Protocols to make their stored Settings read-only

property is_frozen¶: If this Settings object is frozen and cannot be modified

json(*, include: set[int] | set[str] | Mapping[int, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | Mapping[str, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | None = None, exclude: set[int] | set[str] | Mapping[int, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | Mapping[str, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | None = None, by_alias: bool = False, exclude_unset: bool = False, exclude_defaults: bool = False, exclude_none: bool = False, encoder: Callable[[Any], Any] | None = PydanticUndefined, models_as_dict: bool = PydanticUndefined, **dumps_kwargs: Any) → str¶

model_computed_fields = {}¶

model_config = {'arbitrary_types_allowed': True, 'extra': 'forbid', 'validate_assignment': True, 'validate_default': True}¶: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

classmethod model_construct(_fields_set: set[str] | None = None, **values: Any) → Self¶

Creates a new instance of the Model class with validated data.

Creates a new model setting __dict__ and __pydantic_fields_set__ from trusted or pre-validated data. Default values are respected, but no other validation is performed.

!!! note: model_construct() generally respects the model_config.extra setting on the provided model. That is, if model_config.extra == ‘allow’, then all extra passed values are added to the model instance’s __dict__ and __pydantic_extra__ fields. If model_config.extra == ‘ignore’ (the default), then all extra passed values are ignored. Because no validation is performed with a call to model_construct(), having model_config.extra == ‘forbid’ does not result in an error if extra values are passed, but they will be ignored.

Parameters:

_fields_set – A set of field names that were originally explicitly set during instantiation. If provided, this is directly used for the [model_fields_set][pydantic.BaseModel.model_fields_set] attribute. Otherwise, the field names from the values argument will be used.
values – Trusted or pre-validated data dictionary.

Returns:

A new instance of the Model class with validated data.

model_copy(*, update: Mapping[str, Any] | None = None, deep: bool = False) → Self¶

!!! abstract “Usage Documentation”: [model_copy](../concepts/serialization.md#model_copy)

Returns a copy of the model.

!!! note: The underlying instance’s [__dict__][object.__dict__] attribute is copied. This might have unexpected side effects if you store anything in it, on top of the model fields (e.g. the value of [cached properties][functools.cached_property]).

Parameters:

update – Values to change/add in the new model. Note: the data is not validated before creating the new model. You should trust this data.
deep – Set to True to make a deep copy of the model.

Returns:

New model instance.

model_dump(**kwargs) → dict[str, Any]¶

!!! abstract “Usage Documentation”: [model_dump](../concepts/serialization.md#modelmodel_dump)

Generate a dictionary representation of the model, optionally specifying which fields to include or exclude.

Parameters:

mode – The mode in which to_python should run. If mode is ‘json’, the output will only contain JSON serializable types. If mode is ‘python’, the output may contain non-JSON-serializable Python objects.
include – A set of fields to include in the output.
exclude – A set of fields to exclude from the output.
context – Additional context to pass to the serializer.
by_alias – Whether to use the field’s alias in the dictionary key if defined.
exclude_unset – Whether to exclude fields that have not been explicitly set.
exclude_defaults – Whether to exclude fields that are set to their default value.
exclude_none – Whether to exclude fields that have a value of None.
round_trip – If True, dumped values should be valid as input for non-idempotent types such as Json[T].
warnings – How to handle serialization errors. False/”none” ignores them, True/”warn” logs errors, “error” raises a [PydanticSerializationError][pydantic_core.PydanticSerializationError].
fallback – A function to call when an unknown value is encountered. If not provided, a [PydanticSerializationError][pydantic_core.PydanticSerializationError] error is raised.
serialize_as_any – Whether to serialize fields with duck-typing serialization behavior.

Returns:

A dictionary representation of the model.

model_dump_json(**kwargs) → str¶

!!! abstract “Usage Documentation”: [model_dump_json](../concepts/serialization.md#modelmodel_dump_json)

Generates a JSON representation of the model using Pydantic’s to_json method.

Parameters:

indent – Indentation to use in the JSON output. If None is passed, the output will be compact.
include – Field(s) to include in the JSON output.
exclude – Field(s) to exclude from the JSON output.
context – Additional context to pass to the serializer.
by_alias – Whether to serialize using field aliases.
exclude_unset – Whether to exclude fields that have not been explicitly set.
exclude_defaults – Whether to exclude fields that are set to their default value.
exclude_none – Whether to exclude fields that have a value of None.
round_trip – If True, dumped values should be valid as input for non-idempotent types such as Json[T].
warnings – How to handle serialization errors. False/”none” ignores them, True/”warn” logs errors, “error” raises a [PydanticSerializationError][pydantic_core.PydanticSerializationError].
fallback – A function to call when an unknown value is encountered. If not provided, a [PydanticSerializationError][pydantic_core.PydanticSerializationError] error is raised.
serialize_as_any – Whether to serialize fields with duck-typing serialization behavior.

Returns:

A JSON string representation of the model.

property model_extra: dict[str, Any] | None¶

Get extra fields set during validation.

Returns:: A dictionary of extra fields, or None if config.extra is not set to “allow”.

model_fields = {}¶

property model_fields_set: set[str]¶

Returns the set of fields that have been explicitly set on this model instance.

Returns:

A set of strings representing the fields that have been set,: i.e. that were not filled from defaults.

Generates a JSON schema for a model class.

Parameters:

by_alias – Whether to use attribute aliases or not.
ref_template – The reference template.
schema_generator – To override the logic used to generate the JSON schema, as a subclass of GenerateJsonSchema with your desired modifications
mode – The mode in which to generate the schema.

Returns:

The JSON schema for the given model class.

classmethod model_parametrized_name(params: tuple[type[Any], ...]) → str¶

Compute the class name for parametrizations of generic classes.

This method can be overridden to achieve a custom naming scheme for generic BaseModels.

Parameters:: params – Tuple of types of the class. Given a generic class Model with 2 type variables and a concrete model Model[str, int], the value (str, int) would be passed to params.
Returns:: String representing the new class where params are passed to cls as type variables.
Raises:: TypeError – Raised when trying to generate concrete names for non-generic models.

model_post_init(context: Any, /) → None¶

This function is meant to behave like a BaseModel method to initialise private attributes.

It takes context as an argument since that’s what pydantic-core passes when calling it.

Parameters:

self – The BaseModel instance.
context – The context.

classmethod model_rebuild(*, force: bool = False, raise_errors: bool = True, _parent_namespace_depth: int = 2, _types_namespace: MappingNamespace | None = None) → bool | None¶

Try to rebuild the pydantic-core schema for the model.

This may be necessary when one of the annotations is a ForwardRef which could not be resolved during the initial attempt to build the schema, and automatic rebuilding fails.

Parameters:

force – Whether to force the rebuilding of the model schema, defaults to False.
raise_errors – Whether to raise errors, defaults to True.
_parent_namespace_depth – The depth level of the parent namespace, defaults to 2.
_types_namespace – The types namespace, defaults to None.

Returns:

Returns None if the schema is already “complete” and rebuilding was not required. If rebuilding _was_ required, returns True if rebuilding was successful, otherwise False.

Validate a pydantic model instance.

Parameters:

obj – The object to validate.
strict – Whether to enforce types strictly.
from_attributes – Whether to extract data from object attributes.
context – Additional context to pass to the validator.
by_alias – Whether to use the field’s alias when validating against the provided input data.
by_name – Whether to use the field’s name when validating against the provided input data.

Raises:

ValidationError – If the object could not be validated.

Returns:

The validated model instance.

!!! abstract “Usage Documentation”: [JSON Parsing](../concepts/json.md#json-parsing)

Validate the given JSON data against the Pydantic model.

Parameters:

json_data – The JSON data to validate.
strict – Whether to enforce types strictly.
context – Extra variables to pass to the validator.
by_alias – Whether to use the field’s alias when validating against the provided input data.
by_name – Whether to use the field’s name when validating against the provided input data.

Returns:

The validated Pydantic model.

Raises:

ValidationError – If json_data is not a JSON string or the object could not be validated.

classmethod model_validate_strings(obj: Any, *, strict: bool | None = None, context: Any | None = None, by_alias: bool | None = None, by_name: bool | None = None) → Self¶

Validate the given object with string data against the Pydantic model.

Parameters:

obj – The object containing string data to validate.
strict – Whether to enforce types strictly.
context – Extra variables to pass to the validator.
by_alias – Whether to use the field’s alias when validating against the provided input data.
by_name – Whether to use the field’s name when validating against the provided input data.

Returns:

The validated Pydantic model.

classmethod parse_file(path: str | Path, *, content_type: str | None = None, encoding: str = 'utf8', proto: DeprecatedParseProtocol | None = None, allow_pickle: bool = False) → Self¶

classmethod parse_obj(obj: Any) → Self¶

classmethod parse_raw(b: str | bytes, *, content_type: str | None = None, encoding: str = 'utf8', proto: DeprecatedParseProtocol | None = None, allow_pickle: bool = False) → Self¶

classmethod schema(by_alias: bool = True, ref_template: str = '#/$defs/{model}') → Dict[str, Any]¶

classmethod schema_json(*, by_alias: bool = True, ref_template: str = '#/$defs/{model}', **dumps_kwargs: Any) → str¶

unfrozen_copy()¶

A copy of this Settings object, which can be modified

Settings objects become frozen when within a Protocol. If you really need to reverse this, this method is how.

classmethod update_forward_refs(**localns: Any) → None¶

classmethod validate(value: Any) → Self¶

class gufe.settings.models.OpenMMSystemGeneratorFFSettings(*, constraints: ~typing.Annotated[~typing.Literal['hbonds', 'allbonds', 'hangles'], ~pydantic.functional_validators.BeforeValidator(func=~gufe.settings.models._to_lowercase, json_schema_input_type=PydanticUndefined)] | None = 'hbonds', rigid_water: bool = True, hydrogen_mass: float = 3.0, forcefields: list[str] = ['amber/ff14SB.xml', 'amber/tip3p_standard.xml', 'amber/tip3p_HFE_multivalent.xml', 'amber/phosaa10.xml', 'amber/lipid17_merged.xml'], small_molecule_forcefield: str = 'openff-2.2.1', nonbonded_method: str = 'PME', nonbonded_cutoff: ~typing.Annotated[~pint.Quantity, ~pydantic.functional_validators.PlainValidator(func=~gufe.settings.typing._plain_quantity_validator, json_schema_input_type=~typing.Any), ~pydantic.json_schema.WithJsonSchema(json_schema={'type': 'number'}, mode=None), ~pydantic.functional_serializers.PlainSerializer(func=~gufe.settings.typing._plain_quantity_serializer, return_type=PydanticUndefined, when_used=always), ~pydantic.functional_validators.AfterValidator(func=functools.partial(<function _has_compatible_dimensionality at 0x7add3b477ba0>, unit='nanometer', convert=True)), ~annotated_types.Ge(ge=0)] = <Quantity(0.9, 'nanometer')>)¶

Parameters to set up the force field with OpenMM ForceFields

Note

Currently, this stores what is needed for the openmmforcefields.system_generators.SystemGenerator signature. See the OpenMMForceField SystemGenerator documentation for more details.

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

constraints: Annotated[Literal['hbonds', 'allbonds', 'hangles'], BeforeValidator(_to_lowercase)] | None¶: Constraints to be applied to system. One of ‘hbonds’, ‘allbonds’, ‘hangles’ or None, default ‘hbonds’

rigid_water: bool¶: Whether to use a rigid water model. Default True

hydrogen_mass: float¶: Mass to be repartitioned to hydrogens from neighbouring heavy atoms (in amu), default 3.0

forcefields: list[str]¶: List of force field paths for all components except SmallMoleculeComponent

small_molecule_forcefield: str¶: Name of the force field to be used for SmallMoleculeComponent

nonbonded_method: str¶: Method for treating nonbonded interactions, options are currently “CutoffNonPeriodic”, “CutoffPeriodic”, “Ewald”, “LJPME”, “NoCutoff”, “PME”. Default PME.

classmethod construct(_fields_set: set[str] | None = None, **values: Any) → Self¶

Returns a copy of the model.

!!! warning “Deprecated”: This method is now deprecated; use model_copy instead.

If you need include or exclude, use:

`python {test="skip" lint="skip"} data = self.model_dump(include=include, exclude=exclude, round_trip=True) data = {**data, **(update or {})} copied = self.model_validate(data) `

Parameters:

include – Optional set or mapping specifying which fields to include in the copied model.
exclude – Optional set or mapping specifying which fields to exclude in the copied model.
update – Optional dictionary of field-value pairs to override field values in the copied model.
deep – If True, the values of fields that are Pydantic models will be deep-copied.

Returns:

A copy of the model with included, excluded and updated fields as specified.

dict(*, include: set[int] | set[str] | Mapping[int, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | Mapping[str, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | None = None, exclude: set[int] | set[str] | Mapping[int, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | Mapping[str, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | None = None, by_alias: bool = False, exclude_unset: bool = False, exclude_defaults: bool = False, exclude_none: bool = False) → Dict[str, Any]¶

classmethod from_orm(obj: Any) → Self¶

frozen_copy()¶

A copy of this Settings object which cannot be modified

This is intended to be used by Protocols to make their stored Settings read-only

property is_frozen¶: If this Settings object is frozen and cannot be modified

json(*, include: set[int] | set[str] | Mapping[int, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | Mapping[str, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | None = None, exclude: set[int] | set[str] | Mapping[int, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | Mapping[str, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | None = None, by_alias: bool = False, exclude_unset: bool = False, exclude_defaults: bool = False, exclude_none: bool = False, encoder: Callable[[Any], Any] | None = PydanticUndefined, models_as_dict: bool = PydanticUndefined, **dumps_kwargs: Any) → str¶

model_computed_fields = {}¶

model_config = {'arbitrary_types_allowed': True, 'extra': 'forbid', 'validate_assignment': True, 'validate_default': True}¶: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

classmethod model_construct(_fields_set: set[str] | None = None, **values: Any) → Self¶

Creates a new instance of the Model class with validated data.

Creates a new model setting __dict__ and __pydantic_fields_set__ from trusted or pre-validated data. Default values are respected, but no other validation is performed.

!!! note: model_construct() generally respects the model_config.extra setting on the provided model. That is, if model_config.extra == ‘allow’, then all extra passed values are added to the model instance’s __dict__ and __pydantic_extra__ fields. If model_config.extra == ‘ignore’ (the default), then all extra passed values are ignored. Because no validation is performed with a call to model_construct(), having model_config.extra == ‘forbid’ does not result in an error if extra values are passed, but they will be ignored.

Parameters:

_fields_set – A set of field names that were originally explicitly set during instantiation. If provided, this is directly used for the [model_fields_set][pydantic.BaseModel.model_fields_set] attribute. Otherwise, the field names from the values argument will be used.
values – Trusted or pre-validated data dictionary.

Returns:

A new instance of the Model class with validated data.

model_copy(*, update: Mapping[str, Any] | None = None, deep: bool = False) → Self¶

!!! abstract “Usage Documentation”: [model_copy](../concepts/serialization.md#model_copy)

Returns a copy of the model.

!!! note: The underlying instance’s [__dict__][object.__dict__] attribute is copied. This might have unexpected side effects if you store anything in it, on top of the model fields (e.g. the value of [cached properties][functools.cached_property]).

Parameters:

update – Values to change/add in the new model. Note: the data is not validated before creating the new model. You should trust this data.
deep – Set to True to make a deep copy of the model.

Returns:

New model instance.

model_dump(**kwargs) → dict[str, Any]¶

!!! abstract “Usage Documentation”: [model_dump](../concepts/serialization.md#modelmodel_dump)

Generate a dictionary representation of the model, optionally specifying which fields to include or exclude.

Parameters:

mode – The mode in which to_python should run. If mode is ‘json’, the output will only contain JSON serializable types. If mode is ‘python’, the output may contain non-JSON-serializable Python objects.
include – A set of fields to include in the output.
exclude – A set of fields to exclude from the output.
context – Additional context to pass to the serializer.
by_alias – Whether to use the field’s alias in the dictionary key if defined.
exclude_unset – Whether to exclude fields that have not been explicitly set.
exclude_defaults – Whether to exclude fields that are set to their default value.
exclude_none – Whether to exclude fields that have a value of None.
round_trip – If True, dumped values should be valid as input for non-idempotent types such as Json[T].
warnings – How to handle serialization errors. False/”none” ignores them, True/”warn” logs errors, “error” raises a [PydanticSerializationError][pydantic_core.PydanticSerializationError].
fallback – A function to call when an unknown value is encountered. If not provided, a [PydanticSerializationError][pydantic_core.PydanticSerializationError] error is raised.
serialize_as_any – Whether to serialize fields with duck-typing serialization behavior.

Returns:

A dictionary representation of the model.

model_dump_json(**kwargs) → str¶

!!! abstract “Usage Documentation”: [model_dump_json](../concepts/serialization.md#modelmodel_dump_json)

Generates a JSON representation of the model using Pydantic’s to_json method.

Parameters:

indent – Indentation to use in the JSON output. If None is passed, the output will be compact.
include – Field(s) to include in the JSON output.
exclude – Field(s) to exclude from the JSON output.
context – Additional context to pass to the serializer.
by_alias – Whether to serialize using field aliases.
exclude_unset – Whether to exclude fields that have not been explicitly set.
exclude_defaults – Whether to exclude fields that are set to their default value.
exclude_none – Whether to exclude fields that have a value of None.
round_trip – If True, dumped values should be valid as input for non-idempotent types such as Json[T].
warnings – How to handle serialization errors. False/”none” ignores them, True/”warn” logs errors, “error” raises a [PydanticSerializationError][pydantic_core.PydanticSerializationError].
fallback – A function to call when an unknown value is encountered. If not provided, a [PydanticSerializationError][pydantic_core.PydanticSerializationError] error is raised.
serialize_as_any – Whether to serialize fields with duck-typing serialization behavior.

Returns:

A JSON string representation of the model.

property model_extra: dict[str, Any] | None¶

Get extra fields set during validation.

Returns:: A dictionary of extra fields, or None if config.extra is not set to “allow”.

model_fields = {'constraints': FieldInfo(annotation=Union[Annotated[Literal['hbonds', 'allbonds', 'hangles'], BeforeValidator], NoneType], required=False, default='hbonds'), 'forcefields': FieldInfo(annotation=list[str], required=False, default=['amber/ff14SB.xml', 'amber/tip3p_standard.xml', 'amber/tip3p_HFE_multivalent.xml', 'amber/phosaa10.xml', 'amber/lipid17_merged.xml']), 'hydrogen_mass': FieldInfo(annotation=float, required=False, default=3.0), 'nonbonded_cutoff': FieldInfo(annotation=Quantity, required=False, default=<Quantity(0.9, 'nanometer')>, description='Cutoff value for short range nonbonded interactions in nm. Compatible units will be converted to nm.', validate_default=True, metadata=[PlainValidator(func=<function _plain_quantity_validator>, json_schema_input_type=typing.Any), WithJsonSchema(json_schema={'type': 'number'}, mode=None), PlainSerializer(func=<function _plain_quantity_serializer>, return_type=PydanticUndefined, when_used='always'), AfterValidator(func=functools.partial(<function _has_compatible_dimensionality>, unit='nanometer', convert=True)), Ge(ge=0)]), 'nonbonded_method': FieldInfo(annotation=str, required=False, default='PME'), 'rigid_water': FieldInfo(annotation=bool, required=False, default=True), 'small_molecule_forcefield': FieldInfo(annotation=str, required=False, default='openff-2.2.1')}¶

property model_fields_set: set[str]¶

Returns the set of fields that have been explicitly set on this model instance.

Returns:

A set of strings representing the fields that have been set,: i.e. that were not filled from defaults.

Generates a JSON schema for a model class.

Parameters:

by_alias – Whether to use attribute aliases or not.
ref_template – The reference template.
schema_generator – To override the logic used to generate the JSON schema, as a subclass of GenerateJsonSchema with your desired modifications
mode – The mode in which to generate the schema.

Returns:

The JSON schema for the given model class.

classmethod model_parametrized_name(params: tuple[type[Any], ...]) → str¶

Compute the class name for parametrizations of generic classes.

This method can be overridden to achieve a custom naming scheme for generic BaseModels.

Parameters:: params – Tuple of types of the class. Given a generic class Model with 2 type variables and a concrete model Model[str, int], the value (str, int) would be passed to params.
Returns:: String representing the new class where params are passed to cls as type variables.
Raises:: TypeError – Raised when trying to generate concrete names for non-generic models.

model_post_init(context: Any, /) → None¶

This function is meant to behave like a BaseModel method to initialise private attributes.

It takes context as an argument since that’s what pydantic-core passes when calling it.

Parameters:

self – The BaseModel instance.
context – The context.

classmethod model_rebuild(*, force: bool = False, raise_errors: bool = True, _parent_namespace_depth: int = 2, _types_namespace: MappingNamespace | None = None) → bool | None¶

Try to rebuild the pydantic-core schema for the model.

This may be necessary when one of the annotations is a ForwardRef which could not be resolved during the initial attempt to build the schema, and automatic rebuilding fails.

Parameters:

force – Whether to force the rebuilding of the model schema, defaults to False.
raise_errors – Whether to raise errors, defaults to True.
_parent_namespace_depth – The depth level of the parent namespace, defaults to 2.
_types_namespace – The types namespace, defaults to None.

Returns:

Returns None if the schema is already “complete” and rebuilding was not required. If rebuilding _was_ required, returns True if rebuilding was successful, otherwise False.

Validate a pydantic model instance.

Parameters:

obj – The object to validate.
strict – Whether to enforce types strictly.
from_attributes – Whether to extract data from object attributes.
context – Additional context to pass to the validator.
by_alias – Whether to use the field’s alias when validating against the provided input data.
by_name – Whether to use the field’s name when validating against the provided input data.

Raises:

ValidationError – If the object could not be validated.

Returns:

The validated model instance.

!!! abstract “Usage Documentation”: [JSON Parsing](../concepts/json.md#json-parsing)

Validate the given JSON data against the Pydantic model.

Parameters:

json_data – The JSON data to validate.
strict – Whether to enforce types strictly.
context – Extra variables to pass to the validator.
by_alias – Whether to use the field’s alias when validating against the provided input data.
by_name – Whether to use the field’s name when validating against the provided input data.

Returns:

The validated Pydantic model.

Raises:

ValidationError – If json_data is not a JSON string or the object could not be validated.

classmethod model_validate_strings(obj: Any, *, strict: bool | None = None, context: Any | None = None, by_alias: bool | None = None, by_name: bool | None = None) → Self¶

Validate the given object with string data against the Pydantic model.

Parameters:

obj – The object containing string data to validate.
strict – Whether to enforce types strictly.
context – Extra variables to pass to the validator.
by_alias – Whether to use the field’s alias when validating against the provided input data.
by_name – Whether to use the field’s name when validating against the provided input data.

Returns:

The validated Pydantic model.

classmethod parse_file(path: str | Path, *, content_type: str | None = None, encoding: str = 'utf8', proto: DeprecatedParseProtocol | None = None, allow_pickle: bool = False) → Self¶

classmethod parse_obj(obj: Any) → Self¶

classmethod parse_raw(b: str | bytes, *, content_type: str | None = None, encoding: str = 'utf8', proto: DeprecatedParseProtocol | None = None, allow_pickle: bool = False) → Self¶

classmethod schema(by_alias: bool = True, ref_template: str = '#/$defs/{model}') → Dict[str, Any]¶

classmethod schema_json(*, by_alias: bool = True, ref_template: str = '#/$defs/{model}', **dumps_kwargs: Any) → str¶

unfrozen_copy()¶

A copy of this Settings object, which can be modified

Settings objects become frozen when within a Protocol. If you really need to reverse this, this method is how.

classmethod update_forward_refs(**localns: Any) → None¶

classmethod validate(value: Any) → Self¶

nonbonded_cutoff: Annotated[NanometerQuantity, Ge(0)]¶

classmethod allowed_nonbonded_methods(v)¶

class gufe.settings.models.Settings(*, forcefield_settings: Annotated[BaseForceFieldSettings, InstanceOf()], thermo_settings: Annotated[ThermoSettings, InstanceOf()])¶

Container for all settings needed by a protocol

This represents the minimal surface that all settings objects will have.

Protocols can subclass this to extend this to cater for their additional settings.

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

classmethod construct(_fields_set: set[str] | None = None, **values: Any) → Self¶

Returns a copy of the model.

!!! warning “Deprecated”: This method is now deprecated; use model_copy instead.

If you need include or exclude, use:

`python {test="skip" lint="skip"} data = self.model_dump(include=include, exclude=exclude, round_trip=True) data = {**data, **(update or {})} copied = self.model_validate(data) `

Parameters:

include – Optional set or mapping specifying which fields to include in the copied model.
exclude – Optional set or mapping specifying which fields to exclude in the copied model.
update – Optional dictionary of field-value pairs to override field values in the copied model.
deep – If True, the values of fields that are Pydantic models will be deep-copied.

Returns:

A copy of the model with included, excluded and updated fields as specified.

dict(*, include: set[int] | set[str] | Mapping[int, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | Mapping[str, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | None = None, exclude: set[int] | set[str] | Mapping[int, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | Mapping[str, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | None = None, by_alias: bool = False, exclude_unset: bool = False, exclude_defaults: bool = False, exclude_none: bool = False) → Dict[str, Any]¶

classmethod from_orm(obj: Any) → Self¶

frozen_copy()¶

A copy of this Settings object which cannot be modified

This is intended to be used by Protocols to make their stored Settings read-only

property is_frozen¶: If this Settings object is frozen and cannot be modified

json(*, include: set[int] | set[str] | Mapping[int, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | Mapping[str, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | None = None, exclude: set[int] | set[str] | Mapping[int, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | Mapping[str, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | None = None, by_alias: bool = False, exclude_unset: bool = False, exclude_defaults: bool = False, exclude_none: bool = False, encoder: Callable[[Any], Any] | None = PydanticUndefined, models_as_dict: bool = PydanticUndefined, **dumps_kwargs: Any) → str¶

model_computed_fields = {}¶

model_config = {'arbitrary_types_allowed': True, 'extra': 'forbid', 'validate_assignment': True, 'validate_default': True}¶: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

classmethod model_construct(_fields_set: set[str] | None = None, **values: Any) → Self¶

Creates a new instance of the Model class with validated data.

Creates a new model setting __dict__ and __pydantic_fields_set__ from trusted or pre-validated data. Default values are respected, but no other validation is performed.

!!! note: model_construct() generally respects the model_config.extra setting on the provided model. That is, if model_config.extra == ‘allow’, then all extra passed values are added to the model instance’s __dict__ and __pydantic_extra__ fields. If model_config.extra == ‘ignore’ (the default), then all extra passed values are ignored. Because no validation is performed with a call to model_construct(), having model_config.extra == ‘forbid’ does not result in an error if extra values are passed, but they will be ignored.

Parameters:

_fields_set – A set of field names that were originally explicitly set during instantiation. If provided, this is directly used for the [model_fields_set][pydantic.BaseModel.model_fields_set] attribute. Otherwise, the field names from the values argument will be used.
values – Trusted or pre-validated data dictionary.

Returns:

A new instance of the Model class with validated data.

model_copy(*, update: Mapping[str, Any] | None = None, deep: bool = False) → Self¶

!!! abstract “Usage Documentation”: [model_copy](../concepts/serialization.md#model_copy)

Returns a copy of the model.

!!! note: The underlying instance’s [__dict__][object.__dict__] attribute is copied. This might have unexpected side effects if you store anything in it, on top of the model fields (e.g. the value of [cached properties][functools.cached_property]).

Parameters:

update – Values to change/add in the new model. Note: the data is not validated before creating the new model. You should trust this data.
deep – Set to True to make a deep copy of the model.

Returns:

New model instance.

model_dump(**kwargs) → dict[str, Any]¶

!!! abstract “Usage Documentation”: [model_dump](../concepts/serialization.md#modelmodel_dump)

Generate a dictionary representation of the model, optionally specifying which fields to include or exclude.

Parameters:

mode – The mode in which to_python should run. If mode is ‘json’, the output will only contain JSON serializable types. If mode is ‘python’, the output may contain non-JSON-serializable Python objects.
include – A set of fields to include in the output.
exclude – A set of fields to exclude from the output.
context – Additional context to pass to the serializer.
by_alias – Whether to use the field’s alias in the dictionary key if defined.
exclude_unset – Whether to exclude fields that have not been explicitly set.
exclude_defaults – Whether to exclude fields that are set to their default value.
exclude_none – Whether to exclude fields that have a value of None.
round_trip – If True, dumped values should be valid as input for non-idempotent types such as Json[T].
warnings – How to handle serialization errors. False/”none” ignores them, True/”warn” logs errors, “error” raises a [PydanticSerializationError][pydantic_core.PydanticSerializationError].
fallback – A function to call when an unknown value is encountered. If not provided, a [PydanticSerializationError][pydantic_core.PydanticSerializationError] error is raised.
serialize_as_any – Whether to serialize fields with duck-typing serialization behavior.

Returns:

A dictionary representation of the model.

model_dump_json(**kwargs) → str¶

!!! abstract “Usage Documentation”: [model_dump_json](../concepts/serialization.md#modelmodel_dump_json)

Generates a JSON representation of the model using Pydantic’s to_json method.

Parameters:

indent – Indentation to use in the JSON output. If None is passed, the output will be compact.
include – Field(s) to include in the JSON output.
exclude – Field(s) to exclude from the JSON output.
context – Additional context to pass to the serializer.
by_alias – Whether to serialize using field aliases.
exclude_unset – Whether to exclude fields that have not been explicitly set.
exclude_defaults – Whether to exclude fields that are set to their default value.
exclude_none – Whether to exclude fields that have a value of None.
round_trip – If True, dumped values should be valid as input for non-idempotent types such as Json[T].
warnings – How to handle serialization errors. False/”none” ignores them, True/”warn” logs errors, “error” raises a [PydanticSerializationError][pydantic_core.PydanticSerializationError].
fallback – A function to call when an unknown value is encountered. If not provided, a [PydanticSerializationError][pydantic_core.PydanticSerializationError] error is raised.
serialize_as_any – Whether to serialize fields with duck-typing serialization behavior.

Returns:

A JSON string representation of the model.

property model_extra: dict[str, Any] | None¶

Get extra fields set during validation.

Returns:: A dictionary of extra fields, or None if config.extra is not set to “allow”.

model_fields = {'forcefield_settings': FieldInfo(annotation=BaseForceFieldSettings, required=True, metadata=[InstanceOf()]), 'thermo_settings': FieldInfo(annotation=ThermoSettings, required=True, metadata=[InstanceOf()])}¶

property model_fields_set: set[str]¶

Returns the set of fields that have been explicitly set on this model instance.

Returns:

A set of strings representing the fields that have been set,: i.e. that were not filled from defaults.

Generates a JSON schema for a model class.

Parameters:

by_alias – Whether to use attribute aliases or not.
ref_template – The reference template.
schema_generator – To override the logic used to generate the JSON schema, as a subclass of GenerateJsonSchema with your desired modifications
mode – The mode in which to generate the schema.

Returns:

The JSON schema for the given model class.

classmethod model_parametrized_name(params: tuple[type[Any], ...]) → str¶

Compute the class name for parametrizations of generic classes.

This method can be overridden to achieve a custom naming scheme for generic BaseModels.

Parameters:: params – Tuple of types of the class. Given a generic class Model with 2 type variables and a concrete model Model[str, int], the value (str, int) would be passed to params.
Returns:: String representing the new class where params are passed to cls as type variables.
Raises:: TypeError – Raised when trying to generate concrete names for non-generic models.

model_post_init(context: Any, /) → None¶

This function is meant to behave like a BaseModel method to initialise private attributes.

It takes context as an argument since that’s what pydantic-core passes when calling it.

Parameters:

self – The BaseModel instance.
context – The context.

classmethod model_rebuild(*, force: bool = False, raise_errors: bool = True, _parent_namespace_depth: int = 2, _types_namespace: MappingNamespace | None = None) → bool | None¶

Try to rebuild the pydantic-core schema for the model.

This may be necessary when one of the annotations is a ForwardRef which could not be resolved during the initial attempt to build the schema, and automatic rebuilding fails.

Parameters:

force – Whether to force the rebuilding of the model schema, defaults to False.
raise_errors – Whether to raise errors, defaults to True.
_parent_namespace_depth – The depth level of the parent namespace, defaults to 2.
_types_namespace – The types namespace, defaults to None.

Returns:

Returns None if the schema is already “complete” and rebuilding was not required. If rebuilding _was_ required, returns True if rebuilding was successful, otherwise False.

Validate a pydantic model instance.

Parameters:

obj – The object to validate.
strict – Whether to enforce types strictly.
from_attributes – Whether to extract data from object attributes.
context – Additional context to pass to the validator.
by_alias – Whether to use the field’s alias when validating against the provided input data.
by_name – Whether to use the field’s name when validating against the provided input data.

Raises:

ValidationError – If the object could not be validated.

Returns:

The validated model instance.

!!! abstract “Usage Documentation”: [JSON Parsing](../concepts/json.md#json-parsing)

Validate the given JSON data against the Pydantic model.

Parameters:

json_data – The JSON data to validate.
strict – Whether to enforce types strictly.
context – Extra variables to pass to the validator.
by_alias – Whether to use the field’s alias when validating against the provided input data.
by_name – Whether to use the field’s name when validating against the provided input data.

Returns:

The validated Pydantic model.

Raises:

ValidationError – If json_data is not a JSON string or the object could not be validated.

classmethod model_validate_strings(obj: Any, *, strict: bool | None = None, context: Any | None = None, by_alias: bool | None = None, by_name: bool | None = None) → Self¶

Validate the given object with string data against the Pydantic model.

Parameters:

obj – The object containing string data to validate.
strict – Whether to enforce types strictly.
context – Extra variables to pass to the validator.
by_alias – Whether to use the field’s alias when validating against the provided input data.
by_name – Whether to use the field’s name when validating against the provided input data.

Returns:

The validated Pydantic model.

classmethod parse_file(path: str | Path, *, content_type: str | None = None, encoding: str = 'utf8', proto: DeprecatedParseProtocol | None = None, allow_pickle: bool = False) → Self¶

classmethod parse_obj(obj: Any) → Self¶

classmethod parse_raw(b: str | bytes, *, content_type: str | None = None, encoding: str = 'utf8', proto: DeprecatedParseProtocol | None = None, allow_pickle: bool = False) → Self¶

classmethod schema(by_alias: bool = True, ref_template: str = '#/$defs/{model}') → Dict[str, Any]¶

classmethod schema_json(*, by_alias: bool = True, ref_template: str = '#/$defs/{model}', **dumps_kwargs: Any) → str¶

unfrozen_copy()¶

A copy of this Settings object, which can be modified

Settings objects become frozen when within a Protocol. If you really need to reverse this, this method is how.

classmethod update_forward_refs(**localns: Any) → None¶

classmethod validate(value: Any) → Self¶

forcefield_settings: InstanceOf[BaseForceFieldSettings]¶

thermo_settings: InstanceOf[ThermoSettings]¶

classmethod get_defaults()¶