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, pressure, ...])	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 if the input data cannot be parsed to form a valid model.

class Config¶

Noindex:

extra = 'forbid'¶

arbitrary_types_allowed = False¶

smart_union = True¶

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: SetStr | None = None, **values: Any) → Model¶: Creates a new model setting __dict__ and __fields_set__ from trusted or pre-validated data. Default values are respected, but no other validation is performed. Behaves as if Config.extra = ‘allow’ was set since it adds all passed values

Duplicate a model, optionally choose which fields to include, exclude and change.

Parameters:

include – fields to include in new model
exclude – fields to exclude from new model, as with values this takes precedence over include
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

dict(*, include: AbstractSetIntStr | MappingIntStrAny | None = None, exclude: AbstractSetIntStr | MappingIntStrAny | None = None, by_alias: bool = False, skip_defaults: bool | None = None, exclude_unset: bool = False, exclude_defaults: bool = False, exclude_none: bool = False) → DictStrAny¶: Generate a dictionary representation of the model, optionally specifying which fields to include or exclude.

classmethod from_orm(obj: Any) → Model¶

json(*, include: AbstractSetIntStr | MappingIntStrAny | None = None, exclude: AbstractSetIntStr | MappingIntStrAny | None = None, by_alias: bool = False, skip_defaults: bool | None = None, exclude_unset: bool = False, exclude_defaults: bool = False, exclude_none: bool = False, encoder: Callable[[Any], Any] | None = None, models_as_dict: bool = True, **dumps_kwargs: Any) → str¶

Generate a JSON representation of the model, include and exclude arguments as per dict().

encoder is an optional function to supply as default to json.dumps(), other arguments as per json.dumps().

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

classmethod parse_obj(obj: Any) → Model¶

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

classmethod schema(by_alias: bool = True, ref_template: str = '#/definitions/{model}') → DictStrAny¶

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

classmethod update_forward_refs(**localns: Any) → None¶: Try to update ForwardRefs on fields based on this Model, globalns and localns.

classmethod validate(value: Any) → Model¶

class gufe.settings.models.ThermoSettings(*, temperature: FloatQuantity = None, pressure: FloatQuantity = None, ph: PositiveFloat | None = None, redox_potential: float | 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 if the input data cannot be parsed to form a valid model.

temperature: FloatQuantity¶

pressure: FloatQuantity¶

ph: PositiveFloat | None¶

redox_potential: float | None¶

class Config¶

Noindex:

arbitrary_types_allowed = False¶

extra = 'forbid'¶

smart_union = True¶

classmethod construct(_fields_set: SetStr | None = None, **values: Any) → Model¶: Creates a new model setting __dict__ and __fields_set__ from trusted or pre-validated data. Default values are respected, but no other validation is performed. Behaves as if Config.extra = ‘allow’ was set since it adds all passed values

Duplicate a model, optionally choose which fields to include, exclude and change.

Parameters:

include – fields to include in new model
exclude – fields to exclude from new model, as with values this takes precedence over include
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

dict(*, include: AbstractSetIntStr | MappingIntStrAny | None = None, exclude: AbstractSetIntStr | MappingIntStrAny | None = None, by_alias: bool = False, skip_defaults: bool | None = None, exclude_unset: bool = False, exclude_defaults: bool = False, exclude_none: bool = False) → DictStrAny¶: Generate a dictionary representation of the model, optionally specifying which fields to include or exclude.

classmethod from_orm(obj: Any) → Model¶

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

Generate a JSON representation of the model, include and exclude arguments as per dict().

encoder is an optional function to supply as default to json.dumps(), other arguments as per json.dumps().

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

classmethod parse_obj(obj: Any) → Model¶

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

classmethod schema(by_alias: bool = True, ref_template: str = '#/definitions/{model}') → DictStrAny¶

classmethod schema_json(*, by_alias: bool = True, ref_template: str = '#/definitions/{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¶: Try to update ForwardRefs on fields based on this Model, globalns and localns.

classmethod validate(value: Any) → Model¶

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 if the input data cannot be parsed to form a valid model.

class Config¶

Noindex:

classmethod construct(_fields_set: SetStr | None = None, **values: Any) → Model¶: Creates a new model setting __dict__ and __fields_set__ from trusted or pre-validated data. Default values are respected, but no other validation is performed. Behaves as if Config.extra = ‘allow’ was set since it adds all passed values

Duplicate a model, optionally choose which fields to include, exclude and change.

Parameters:

include – fields to include in new model
exclude – fields to exclude from new model, as with values this takes precedence over include
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

dict(*, include: AbstractSetIntStr | MappingIntStrAny | None = None, exclude: AbstractSetIntStr | MappingIntStrAny | None = None, by_alias: bool = False, skip_defaults: bool | None = None, exclude_unset: bool = False, exclude_defaults: bool = False, exclude_none: bool = False) → DictStrAny¶: Generate a dictionary representation of the model, optionally specifying which fields to include or exclude.

classmethod from_orm(obj: Any) → Model¶

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

Generate a JSON representation of the model, include and exclude arguments as per dict().

encoder is an optional function to supply as default to json.dumps(), other arguments as per json.dumps().

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

classmethod parse_obj(obj: Any) → Model¶

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

classmethod schema(by_alias: bool = True, ref_template: str = '#/definitions/{model}') → DictStrAny¶

classmethod schema_json(*, by_alias: bool = True, ref_template: str = '#/definitions/{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¶: Try to update ForwardRefs on fields based on this Model, globalns and localns.

classmethod validate(value: Any) → Model¶

class gufe.settings.models.OpenMMSystemGeneratorFFSettings(*, constraints: str | 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'], small_molecule_forcefield: str = 'openff-2.1.1', nonbonded_cutoff: ~gufe.vendor.openff.models.types.FloatQuantity = <Quantity(1.0, 'nanometer')>, nonbonded_method: str = 'PME')¶

Parameters to set up the force field with OpenMM ForceFields

Note

Right now we just basically just grab what we need 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 if the input data cannot be parsed to form a valid model.

class Config¶

Noindex:

constraints: str | 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¶: Method for treating nonbonded interactions, currently only PME and NoCutoff are allowed. Default PME.

nonbonded_cutoff: FloatQuantity¶: Cutoff value for short range nonbonded interactions. Default 1.0 * unit.nanometer.

classmethod allowed_nonbonded(v)¶

classmethod construct(_fields_set: SetStr | None = None, **values: Any) → Model¶: Creates a new model setting __dict__ and __fields_set__ from trusted or pre-validated data. Default values are respected, but no other validation is performed. Behaves as if Config.extra = ‘allow’ was set since it adds all passed values

Duplicate a model, optionally choose which fields to include, exclude and change.

Parameters:

include – fields to include in new model
exclude – fields to exclude from new model, as with values this takes precedence over include
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

dict(*, include: AbstractSetIntStr | MappingIntStrAny | None = None, exclude: AbstractSetIntStr | MappingIntStrAny | None = None, by_alias: bool = False, skip_defaults: bool | None = None, exclude_unset: bool = False, exclude_defaults: bool = False, exclude_none: bool = False) → DictStrAny¶: Generate a dictionary representation of the model, optionally specifying which fields to include or exclude.

classmethod from_orm(obj: Any) → Model¶

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

Generate a JSON representation of the model, include and exclude arguments as per dict().

encoder is an optional function to supply as default to json.dumps(), other arguments as per json.dumps().

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

classmethod parse_obj(obj: Any) → Model¶

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

classmethod schema(by_alias: bool = True, ref_template: str = '#/definitions/{model}') → DictStrAny¶

classmethod schema_json(*, by_alias: bool = True, ref_template: str = '#/definitions/{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¶: Try to update ForwardRefs on fields based on this Model, globalns and localns.

classmethod validate(value: Any) → Model¶

classmethod is_positive_distance(v)¶

classmethod constraint_check(v)¶

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

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 if the input data cannot be parsed to form a valid model.

class Config¶

Noindex:

arbitrary_types_allowed = False¶

extra = 'forbid'¶

smart_union = True¶

classmethod construct(_fields_set: SetStr | None = None, **values: Any) → Model¶: Creates a new model setting __dict__ and __fields_set__ from trusted or pre-validated data. Default values are respected, but no other validation is performed. Behaves as if Config.extra = ‘allow’ was set since it adds all passed values

Duplicate a model, optionally choose which fields to include, exclude and change.

Parameters:

include – fields to include in new model
exclude – fields to exclude from new model, as with values this takes precedence over include
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

dict(*, include: AbstractSetIntStr | MappingIntStrAny | None = None, exclude: AbstractSetIntStr | MappingIntStrAny | None = None, by_alias: bool = False, skip_defaults: bool | None = None, exclude_unset: bool = False, exclude_defaults: bool = False, exclude_none: bool = False) → DictStrAny¶: Generate a dictionary representation of the model, optionally specifying which fields to include or exclude.

classmethod from_orm(obj: Any) → Model¶

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

Generate a JSON representation of the model, include and exclude arguments as per dict().

encoder is an optional function to supply as default to json.dumps(), other arguments as per json.dumps().

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

classmethod parse_obj(obj: Any) → Model¶

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

classmethod schema(by_alias: bool = True, ref_template: str = '#/definitions/{model}') → DictStrAny¶

classmethod schema_json(*, by_alias: bool = True, ref_template: str = '#/definitions/{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¶: Try to update ForwardRefs on fields based on this Model, globalns and localns.

classmethod validate(value: Any) → Model¶

forcefield_settings: BaseForceFieldSettings¶

thermo_settings: ThermoSettings¶

classmethod get_defaults()¶