aiida_gromacs.data package¶
Submodules¶
aiida_gromacs.data.editconf module¶
Data types provided by plugin
Register data types via the “aiida.data” entry point in setup.json.
- class aiida_gromacs.data.editconf.EditconfParameters(dict=None, **kwargs)[source]¶
Bases:
DictCommand line options for diff.
This class represents a python dictionary used to pass command line options to the executable.
- class AttributesModel(**data: Any)¶
Bases:
AttributesModel- __abstractmethods__ = frozenset({})¶
- __annotations__ = {}¶
- __class_vars__ = {}¶
The names of the class variables defined on the model.
- __dict__¶
- __module__ = 'aiida_gromacs.data.editconf'¶
- __private_attributes__ = {'_AIIDA_MINIMAL_MODEL': ModelPrivateAttr()}¶
Metadata about the private attributes of the model.
- __pydantic_complete__ = True¶
Whether model building is completed, or if there are still undefined fields.
- __pydantic_computed_fields__ = {}¶
A dictionary of computed field names and their corresponding [ComputedFieldInfo][pydantic.fields.ComputedFieldInfo] objects.
- __pydantic_core_schema__ = {'cls': <class 'aiida_gromacs.data.editconf.EditconfParameters.AttributesModel'>, 'config': {'extra_fields_behavior': 'allow', 'serialize_by_alias': True, 'title': 'EditconfParametersAttributesModel', 'validate_by_alias': True, 'validate_by_name': True}, 'custom_init': False, 'metadata': {'pydantic_js_functions': [<bound method BaseModel.__get_pydantic_json_schema__ of <class 'aiida_gromacs.data.editconf.EditconfParameters.AttributesModel'>>]}, 'post_init': 'model_post_init', 'ref': 'aiida_gromacs.data.editconf.EditconfParameters.AttributesModel:109607548146256', 'root_model': False, 'schema': {'computed_fields': [], 'fields': {'source': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'Source of the data'}}, 'schema': {'default': None, 'schema': {'schema': {'keys_schema': {'type': 'any'}, 'type': 'dict', 'values_schema': {'type': 'any'}}, 'type': 'nullable'}, 'type': 'default'}, 'type': 'model-field'}}, 'model_name': 'AttributesModel', 'type': 'model-fields'}, 'type': 'model'}¶
The core schema of the model.
- __pydantic_custom_init__ = False¶
Whether the model has a custom __init__ method.
- __pydantic_decorators__ = DecoratorInfos(validators={}, field_validators={}, root_validators={}, field_serializers={}, model_serializers={}, model_validators={}, computed_fields={})¶
Metadata containing the decorators defined on the model. This replaces Model.__validators__ and Model.__root_validators__ from Pydantic V1.
- __pydantic_extra__¶
A dictionary containing extra values, if [extra][pydantic.config.ConfigDict.extra] is set to ‘allow’.
- __pydantic_extra_info__ = None¶
A wrapper around the __pydantic_extra__ annotation, if explicitly annotated on a model.
This is a private attribute, not meant to be used outside Pydantic.
- __pydantic_fields__ = {'source': FieldInfo(annotation=Union[dict, NoneType], required=False, default=None, description='Source of the data', json_schema_extra={}, metadata=[{'priority': 0}, {'read_only': False}, {'write_only': False}, {'may_be_large': False}])}¶
A dictionary of field names and their corresponding [FieldInfo][pydantic.fields.FieldInfo] objects. This replaces Model.__fields__ from Pydantic V1.
- __pydantic_fields_set__¶
The names of fields explicitly set during instantiation.
- __pydantic_generic_metadata__ = {'args': (), 'origin': None, 'parameters': ()}¶
A dictionary containing metadata about generic Pydantic models.
The origin and args items map to the [__origin__][genericalias.__origin__] and [__args__][genericalias.__args__] attributes of [generic aliases][types-genericalias], and the parameter item maps to the __parameter__ attribute of generic classes.
- __pydantic_post_init__ = 'model_post_init'¶
The name of the post-init method for the model, if defined.
- __pydantic_private__¶
Values of private attributes set on the model instance.
- __pydantic_serializer__ = SchemaSerializer(serializer=PolymorphismTrampoline( PolymorphismTrampoline { class: Py( 0x000063affef8d250, ), serializer: PolymorphismTrampoline( PolymorphismTrampoline { class: Py( 0x000063affef8d250, ), serializer: Model( ModelSerializer { class: Py( 0x000063affef8d250, ), serializer: Fields( GeneralFieldsSerializer { fields: { "source": SerField { key: "source", alias: None, serializer: Some( WithDefault( WithDefaultSerializer { default: Default( Py( 0x00007310e7455800, ), ), serializer: Nullable( NullableSerializer { serializer: Dict( DictSerializer { key_serializer: Any( AnySerializer, ), value_serializer: Any( AnySerializer, ), filter: SchemaFilter { include: None, exclude: None, }, name: "dict[any, any]", }, ), }, ), }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, }, computed_fields: Some( ComputedFields( [], ), ), mode: ModelExtra, extra_serializer: None, filter: SchemaFilter { include: None, exclude: None, }, required_fields: 1, }, ), has_extra: true, root_model: false, name: "AttributesModel", }, ), enabled_from_config: false, }, ), enabled_from_config: false, }, ), definitions=[])¶
The pydantic-core SchemaSerializer used to dump instances of the model.
- __pydantic_setattr_handlers__ = {}¶
__setattr__ handlers. Memoizing the handlers leads to a dramatic performance improvement in __setattr__
- __pydantic_validator__ = SchemaValidator(title="EditconfParametersAttributesModel", validator=Model( ModelValidator { revalidate: Never, validator: ModelFields( ModelFieldsValidator { fields: [ Field { name: "source", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "source", ), rest: [], }, by_alias: [], }, validator: WithDefault( WithDefaultValidator { default: Default( Py( 0x00007310e7455800, ), ), on_error: Raise, validator: Nullable( NullableValidator { validator: Dict( DictValidator { strict: false, key_validator: Any( AnyValidator, ), value_validator: Any( AnyValidator, ), min_length: None, max_length: None, fail_fast: false, name: "dict[any,any]", }, ), name: "nullable[dict[any,any]]", }, ), validate_default: false, copy_default: false, name: "default[nullable[dict[any,any]]]", undefined: Py( 0x00007310e53bdb90, ), }, ), frozen: false, }, ], model_name: "AttributesModel", extra_behavior: Allow, extras_validator: None, extras_keys_validator: None, strict: false, from_attributes: false, loc_by_alias: true, lookup: LookupTree { inner: { PathItemString( "source", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 0, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, }, }, validate_by_alias: Some( true, ), validate_by_name: Some( true, ), }, ), class: Py( 0x000063affef8d250, ), generic_origin: None, post_init: Some( Py( 0x00007310e2571630, ), ), frozen: false, custom_init: false, root_model: false, undefined: Py( 0x00007310e53bdb90, ), name: "AttributesModel", }, ), definitions=[], cache_strings=True)¶
The pydantic-core SchemaValidator used to validate instances of the model.
- _abc_impl = <_abc._abc_data object>¶
- model_config = {'arbitrary_types_allowed': True, 'defer_build': True, 'extra': 'allow', 'json_encoders': {<class 'datetime.datetime'>: <function OrmModel.<lambda>>}, 'serialize_by_alias': True, 'title': 'EditconfParametersAttributesModel', 'validate_by_alias': True, 'validate_by_name': True}¶
Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].
- class ReadModel(**data: Any)¶
Bases:
ReadModel- __abstractmethods__ = frozenset({})¶
- __annotations__ = {'attributes': <class 'aiida_gromacs.data.editconf.EditconfParameters.AttributesModel'>, 'node_type': typing.Literal['data.gromacs.editconf.EditconfParameters.']}¶
- __class_vars__ = {}¶
The names of the class variables defined on the model.
- __dict__¶
- __module__ = 'aiida_gromacs.data.editconf'¶
- __private_attributes__ = {'_AIIDA_MINIMAL_MODEL': ModelPrivateAttr()}¶
Metadata about the private attributes of the model.
- __pydantic_complete__ = True¶
Whether model building is completed, or if there are still undefined fields.
- __pydantic_computed_fields__ = {}¶
A dictionary of computed field names and their corresponding [ComputedFieldInfo][pydantic.fields.ComputedFieldInfo] objects.
- __pydantic_core_schema__ = {'cls': <class 'aiida_gromacs.data.editconf.EditconfParameters.ReadModel'>, 'config': {'extra_fields_behavior': 'forbid', 'serialize_by_alias': True, 'title': 'EditconfParametersReadModel', 'validate_by_alias': True, 'validate_by_name': True}, 'custom_init': False, 'metadata': {'pydantic_js_functions': [<bound method BaseModel.__get_pydantic_json_schema__ of <class 'aiida_gromacs.data.editconf.EditconfParameters.ReadModel'>>]}, 'post_init': 'model_post_init', 'ref': 'aiida_gromacs.data.editconf.EditconfParameters.ReadModel:109607548156272', 'root_model': False, 'schema': {'computed_fields': [], 'fields': {'attributes': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'The node attributes', 'examples': [{'attr_key': 'attr_value'}]}}, 'schema': {'cls': <class 'aiida_gromacs.data.editconf.EditconfParameters.AttributesModel'>, 'config': {'extra_fields_behavior': 'allow', 'serialize_by_alias': True, 'title': 'EditconfParametersAttributesModel', 'validate_by_alias': True, 'validate_by_name': True}, 'custom_init': False, 'metadata': {'pydantic_js_functions': [<bound method BaseModel.__get_pydantic_json_schema__ of <class 'aiida_gromacs.data.editconf.EditconfParameters.AttributesModel'>>]}, 'post_init': 'model_post_init', 'ref': 'aiida_gromacs.data.editconf.EditconfParameters.AttributesModel:109607548146256', 'root_model': False, 'schema': {'computed_fields': [], 'fields': {'source': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'Source of the data'}}, 'schema': {'default': None, 'schema': {'schema': {'keys_schema': {'type': 'any'}, 'type': 'dict', 'values_schema': {'type': 'any'}}, 'type': 'nullable'}, 'type': 'default'}, 'type': 'model-field'}}, 'model_name': 'AttributesModel', 'type': 'model-fields'}, 'type': 'model'}, 'type': 'model-field'}, 'computer': {'metadata': {'pydantic_js_extra': {'readOnly': True}, 'pydantic_js_updates': {'description': 'The PK of the computer', 'examples': [42]}}, 'schema': {'default': None, 'schema': {'schema': {'type': 'int'}, 'type': 'nullable'}, 'type': 'default'}, 'type': 'model-field'}, 'ctime': {'metadata': {'pydantic_js_extra': {'readOnly': True}, 'pydantic_js_updates': {'description': 'The creation time of the node', 'examples': ['2024-01-01T12:00:00+00:00']}}, 'schema': {'microseconds_precision': 'truncate', 'serialization': {'function': <function OrmModel.<lambda>>, 'type': 'function-plain', 'when_used': 'json'}, 'type': 'datetime'}, 'type': 'model-field'}, 'description': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'The node description', 'examples': ['This is my node description.']}}, 'schema': {'default': '', 'schema': {'type': 'str'}, 'type': 'default'}, 'type': 'model-field'}, 'extras': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'The node extras', 'examples': [{'extra_key': 'extra_value'}]}}, 'schema': {'default_factory': <class 'dict'>, 'default_factory_takes_data': False, 'schema': {'keys_schema': {'type': 'str'}, 'type': 'dict', 'values_schema': {'type': 'any'}}, 'type': 'default'}, 'type': 'model-field'}, 'label': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'The node label', 'examples': ['my_node']}}, 'schema': {'default': '', 'schema': {'type': 'str'}, 'type': 'default'}, 'type': 'model-field'}, 'mtime': {'metadata': {'pydantic_js_extra': {'readOnly': True}, 'pydantic_js_updates': {'description': 'The modification time of the node', 'examples': ['2024-01-02T12:00:00+00:00']}}, 'schema': {'microseconds_precision': 'truncate', 'serialization': {'function': <function OrmModel.<lambda>>, 'type': 'function-plain', 'when_used': 'json'}, 'type': 'datetime'}, 'type': 'model-field'}, 'node_type': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'The type of the node.'}}, 'schema': {'expected': ['data.gromacs.editconf.EditconfParameters.'], 'type': 'literal'}, 'type': 'model-field'}, 'pk': {'metadata': {'pydantic_js_extra': {'readOnly': True}, 'pydantic_js_updates': {'description': 'The primary key of the entity', 'examples': [42]}}, 'schema': {'type': 'int'}, 'type': 'model-field'}, 'process_type': {'metadata': {'pydantic_js_extra': {'readOnly': True}, 'pydantic_js_updates': {'description': 'The process type of the node', 'examples': ['aiida.calculations:arithmetic.add.']}}, 'schema': {'default': None, 'schema': {'schema': {'type': 'str'}, 'type': 'nullable'}, 'type': 'default'}, 'type': 'model-field'}, 'repository_metadata': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'Virtual hierarchy of the file repository', 'examples': [{'o': {'file.txt': {'k': '<file_hash>'}}}]}}, 'schema': {'default_factory': <class 'dict'>, 'default_factory_takes_data': False, 'schema': {'keys_schema': {'type': 'str'}, 'type': 'dict', 'values_schema': {'type': 'any'}}, 'type': 'default'}, 'type': 'model-field'}, 'user': {'metadata': {'pydantic_js_extra': {'readOnly': True}, 'pydantic_js_updates': {'description': 'The PK of the user who owns the node', 'examples': [7]}}, 'schema': {'type': 'int'}, 'type': 'model-field'}, 'uuid': {'metadata': {'pydantic_js_extra': {'readOnly': True}, 'pydantic_js_updates': {'description': 'The UUID of the node', 'examples': ['123e4567-e89b-12d3-a456-426614174000']}}, 'schema': {'type': 'uuid'}, 'type': 'model-field'}}, 'model_name': 'ReadModel', 'type': 'model-fields'}, 'type': 'model'}¶
The core schema of the model.
- __pydantic_custom_init__ = False¶
Whether the model has a custom __init__ method.
- __pydantic_decorators__ = DecoratorInfos(validators={}, field_validators={}, root_validators={}, field_serializers={}, model_serializers={}, model_validators={}, computed_fields={})¶
Metadata containing the decorators defined on the model. This replaces Model.__validators__ and Model.__root_validators__ from Pydantic V1.
- __pydantic_extra__¶
A dictionary containing extra values, if [extra][pydantic.config.ConfigDict.extra] is set to ‘allow’.
- __pydantic_extra_info__ = None¶
A wrapper around the __pydantic_extra__ annotation, if explicitly annotated on a model.
This is a private attribute, not meant to be used outside Pydantic.
- __pydantic_fields__ = {'attributes': FieldInfo(annotation=EditconfParameters.AttributesModel, required=True, description='The node attributes', examples=[{'attr_key': 'attr_value'}], json_schema_extra={}, metadata=[{'priority': 0}, {'read_only': False}, {'write_only': False}, {'may_be_large': True}]), 'computer': FieldInfo(annotation=Union[int, NoneType], required=False, default=None, description='The PK of the computer', examples=[42], json_schema_extra={'readOnly': True}, metadata=[{'priority': 0}, {'read_only': True}, {'write_only': False}, {'may_be_large': False}, {'orm_class': <class 'aiida.orm.computers.Computer'>}, {'orm_to_model': <function Node.ReadModel.<lambda>>}]), 'ctime': FieldInfo(annotation=datetime, required=True, description='The creation time of the node', examples=['2024-01-01T12:00:00+00:00'], json_schema_extra={'readOnly': True}, metadata=[{'priority': 0}, {'read_only': True}, {'write_only': False}, {'may_be_large': False}]), 'description': FieldInfo(annotation=str, required=False, default='', description='The node description', examples=['This is my node description.'], json_schema_extra={}, metadata=[{'priority': 0}, {'read_only': False}, {'write_only': False}, {'may_be_large': False}]), 'extras': FieldInfo(annotation=dict[str, Any], required=False, default_factory=dict, description='The node extras', examples=[{'extra_key': 'extra_value'}], json_schema_extra={}, metadata=[{'priority': 0}, {'read_only': False}, {'write_only': False}, {'may_be_large': True}, {'orm_to_model': <function Node.MutableNodeFields.<lambda>>}]), 'label': FieldInfo(annotation=str, required=False, default='', description='The node label', examples=['my_node'], json_schema_extra={}, metadata=[{'priority': 0}, {'read_only': False}, {'write_only': False}, {'may_be_large': False}]), 'mtime': FieldInfo(annotation=datetime, required=True, description='The modification time of the node', examples=['2024-01-02T12:00:00+00:00'], json_schema_extra={'readOnly': True}, metadata=[{'priority': 0}, {'read_only': True}, {'write_only': False}, {'may_be_large': False}]), 'node_type': FieldInfo(annotation=Literal['data.gromacs.editconf.EditconfParameters.'], required=True, description='The type of the node.', json_schema_extra={}, metadata=[{'priority': 0}, {'read_only': False}, {'write_only': False}, {'may_be_large': False}]), 'pk': FieldInfo(annotation=int, required=True, description='The primary key of the entity', examples=[42], json_schema_extra={'readOnly': True}, metadata=[{'priority': 0}, {'read_only': True}, {'write_only': False}, {'may_be_large': False}]), 'process_type': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, description='The process type of the node', examples=['aiida.calculations:arithmetic.add.'], json_schema_extra={'readOnly': True}, metadata=[{'priority': 0}, {'read_only': True}, {'write_only': False}, {'may_be_large': False}]), 'repository_metadata': FieldInfo(annotation=dict[str, Any], required=False, default_factory=dict, description='Virtual hierarchy of the file repository', examples=[{'o': {'file.txt': {'k': '<file_hash>'}}}], json_schema_extra={}, metadata=[{'priority': 0}, {'read_only': False}, {'write_only': False}, {'may_be_large': True}, {'orm_to_model': <function Node.WritableFields.<lambda>>}]), 'user': FieldInfo(annotation=int, required=True, description='The PK of the user who owns the node', examples=[7], json_schema_extra={'readOnly': True}, metadata=[{'priority': 0}, {'read_only': True}, {'write_only': False}, {'may_be_large': False}, {'orm_class': <class 'aiida.orm.users.User'>}, {'orm_to_model': <function Node.ReadModel.<lambda>>}]), 'uuid': FieldInfo(annotation=UUID, required=True, description='The UUID of the node', examples=['123e4567-e89b-12d3-a456-426614174000'], json_schema_extra={'readOnly': True}, metadata=[{'priority': 0}, {'read_only': True}, {'write_only': False}, {'may_be_large': False}])}¶
A dictionary of field names and their corresponding [FieldInfo][pydantic.fields.FieldInfo] objects. This replaces Model.__fields__ from Pydantic V1.
- __pydantic_fields_set__¶
The names of fields explicitly set during instantiation.
- __pydantic_generic_metadata__ = {'args': (), 'origin': None, 'parameters': ()}¶
A dictionary containing metadata about generic Pydantic models.
The origin and args items map to the [__origin__][genericalias.__origin__] and [__args__][genericalias.__args__] attributes of [generic aliases][types-genericalias], and the parameter item maps to the __parameter__ attribute of generic classes.
- __pydantic_post_init__ = 'model_post_init'¶
The name of the post-init method for the model, if defined.
- __pydantic_private__¶
Values of private attributes set on the model instance.
- __pydantic_serializer__ = SchemaSerializer(serializer=PolymorphismTrampoline( PolymorphismTrampoline { class: Py( 0x000063affef8f970, ), serializer: PolymorphismTrampoline( PolymorphismTrampoline { class: Py( 0x000063affef8f970, ), serializer: Model( ModelSerializer { class: Py( 0x000063affef8f970, ), serializer: Fields( GeneralFieldsSerializer { fields: { "label": SerField { key: "label", alias: None, serializer: Some( WithDefault( WithDefaultSerializer { default: Default( Py( 0x00007310e7482e40, ), ), serializer: Str( StrSerializer, ), }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "node_type": SerField { key: "node_type", alias: None, serializer: Some( Literal( LiteralSerializer { expected_int: {}, expected_str: { "data.gromacs.editconf.EditconfParameters.", }, expected_py: None, name: "literal['data.gromacs.editconf.EditconfParameters.']", }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "repository_metadata": SerField { key: "repository_metadata", alias: None, serializer: Some( WithDefault( WithDefaultSerializer { default: DefaultFactory( Py( 0x00007310e74524a0, ), false, ), serializer: Dict( DictSerializer { key_serializer: Str( StrSerializer, ), value_serializer: Any( AnySerializer, ), filter: SchemaFilter { include: None, exclude: None, }, name: "dict[str, any]", }, ), }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "process_type": SerField { key: "process_type", alias: None, serializer: Some( WithDefault( WithDefaultSerializer { default: Default( Py( 0x00007310e7455800, ), ), serializer: Nullable( NullableSerializer { serializer: Str( StrSerializer, ), }, ), }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "ctime": SerField { key: "ctime", alias: None, serializer: Some( Function( FunctionPlainSerializer { func: Py( 0x00007310e2355c60, ), name: "plain_function[<lambda>]", function_name: "<lambda>", return_serializer: Any( AnySerializer, ), fallback_serializer: Some( Datetime( DatetimeSerializer { temporal_mode: Iso8601, }, ), ), when_used: Json, is_field_serializer: false, info_arg: false, }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "mtime": SerField { key: "mtime", alias: None, serializer: Some( Function( FunctionPlainSerializer { func: Py( 0x00007310e2355c60, ), name: "plain_function[<lambda>]", function_name: "<lambda>", return_serializer: Any( AnySerializer, ), fallback_serializer: Some( Datetime( DatetimeSerializer { temporal_mode: Iso8601, }, ), ), when_used: Json, is_field_serializer: false, info_arg: false, }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "computer": SerField { key: "computer", alias: None, serializer: Some( WithDefault( WithDefaultSerializer { default: Default( Py( 0x00007310e7455800, ), ), serializer: Nullable( NullableSerializer { serializer: Int( IntSerializer, ), }, ), }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "user": SerField { key: "user", alias: None, serializer: Some( Int( IntSerializer, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "attributes": SerField { key: "attributes", alias: None, serializer: Some( PolymorphismTrampoline( PolymorphismTrampoline { class: Py( 0x000063affef8d250, ), serializer: Prebuilt( PrebuiltSerializer { schema_serializer: Py( 0x00007310d2e456c0, ), }, ), enabled_from_config: false, }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "uuid": SerField { key: "uuid", alias: None, serializer: Some( Uuid( UuidSerializer, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "pk": SerField { key: "pk", alias: None, serializer: Some( Int( IntSerializer, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "extras": SerField { key: "extras", alias: None, serializer: Some( WithDefault( WithDefaultSerializer { default: DefaultFactory( Py( 0x00007310e74524a0, ), false, ), serializer: Dict( DictSerializer { key_serializer: Str( StrSerializer, ), value_serializer: Any( AnySerializer, ), filter: SchemaFilter { include: None, exclude: None, }, name: "dict[str, any]", }, ), }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "description": SerField { key: "description", alias: None, serializer: Some( WithDefault( WithDefaultSerializer { default: Default( Py( 0x00007310e7482e40, ), ), serializer: Str( StrSerializer, ), }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, }, computed_fields: Some( ComputedFields( [], ), ), mode: SimpleDict, extra_serializer: None, filter: SchemaFilter { include: None, exclude: None, }, required_fields: 13, }, ), has_extra: false, root_model: false, name: "ReadModel", }, ), enabled_from_config: false, }, ), enabled_from_config: false, }, ), definitions=[])¶
The pydantic-core SchemaSerializer used to dump instances of the model.
- __pydantic_setattr_handlers__ = {}¶
__setattr__ handlers. Memoizing the handlers leads to a dramatic performance improvement in __setattr__
- __pydantic_validator__ = SchemaValidator(title="EditconfParametersReadModel", validator=Model( ModelValidator { revalidate: Never, validator: ModelFields( ModelFieldsValidator { fields: [ Field { name: "pk", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "pk", ), rest: [], }, by_alias: [], }, validator: Int( IntValidator { strict: false, }, ), frozen: false, }, Field { name: "label", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "label", ), rest: [], }, by_alias: [], }, validator: WithDefault( WithDefaultValidator { default: Default( Py( 0x00007310e7482e40, ), ), on_error: Raise, validator: Str( StrValidator { strict: false, coerce_numbers_to_str: false, }, ), validate_default: false, copy_default: false, name: "default[str]", undefined: Py( 0x00007310e53bdb90, ), }, ), frozen: false, }, Field { name: "description", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "description", ), rest: [], }, by_alias: [], }, validator: WithDefault( WithDefaultValidator { default: Default( Py( 0x00007310e7482e40, ), ), on_error: Raise, validator: Str( StrValidator { strict: false, coerce_numbers_to_str: false, }, ), validate_default: false, copy_default: false, name: "default[str]", undefined: Py( 0x00007310e53bdb90, ), }, ), frozen: false, }, Field { name: "extras", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "extras", ), rest: [], }, by_alias: [], }, validator: WithDefault( WithDefaultValidator { default: DefaultFactory( Py( 0x00007310e74524a0, ), false, ), on_error: Raise, validator: Dict( DictValidator { strict: false, key_validator: Str( StrValidator { strict: false, coerce_numbers_to_str: false, }, ), value_validator: Any( AnyValidator, ), min_length: None, max_length: None, fail_fast: false, name: "dict[str,any]", }, ), validate_default: false, copy_default: false, name: "default[dict[str,any]]", undefined: Py( 0x00007310e53bdb90, ), }, ), frozen: false, }, Field { name: "node_type", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "node_type", ), rest: [], }, by_alias: [], }, validator: Literal( LiteralValidator { lookup: LiteralLookup { expected_bool: None, expected_int: None, expected_str: Some( { "data.gromacs.editconf.EditconfParameters.": 0, }, ), expected_py_dict: None, expected_py_values: None, expected_py_primitives: Some( Py( 0x00007310d2de1d40, ), ), values: [ Py( 0x00007310d9122a90, ), ], }, expected_repr: "'data.gromacs.editconf.EditconfParameters.'", name: "literal['data.gromacs.editconf.EditconfParameters.']", }, ), frozen: false, }, Field { name: "attributes", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "attributes", ), rest: [], }, by_alias: [], }, validator: Prebuilt( PrebuiltValidator { schema_validator: Py( 0x00007310d2e45360, ), }, ), frozen: false, }, Field { name: "repository_metadata", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "repository_metadata", ), rest: [], }, by_alias: [], }, validator: WithDefault( WithDefaultValidator { default: DefaultFactory( Py( 0x00007310e74524a0, ), false, ), on_error: Raise, validator: Dict( DictValidator { strict: false, key_validator: Str( StrValidator { strict: false, coerce_numbers_to_str: false, }, ), value_validator: Any( AnyValidator, ), min_length: None, max_length: None, fail_fast: false, name: "dict[str,any]", }, ), validate_default: false, copy_default: false, name: "default[dict[str,any]]", undefined: Py( 0x00007310e53bdb90, ), }, ), frozen: false, }, Field { name: "uuid", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "uuid", ), rest: [], }, by_alias: [], }, validator: Uuid( UuidValidator { strict: false, version: None, }, ), frozen: false, }, Field { name: "process_type", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "process_type", ), rest: [], }, by_alias: [], }, validator: WithDefault( WithDefaultValidator { default: Default( Py( 0x00007310e7455800, ), ), on_error: Raise, validator: Nullable( NullableValidator { validator: Str( StrValidator { strict: false, coerce_numbers_to_str: false, }, ), name: "nullable[str]", }, ), validate_default: false, copy_default: false, name: "default[nullable[str]]", undefined: Py( 0x00007310e53bdb90, ), }, ), frozen: false, }, Field { name: "ctime", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "ctime", ), rest: [], }, by_alias: [], }, validator: Datetime( DateTimeValidator { strict: false, constraints: None, microseconds_precision: Truncate, val_temporal_unit: Infer, }, ), frozen: false, }, Field { name: "mtime", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "mtime", ), rest: [], }, by_alias: [], }, validator: Datetime( DateTimeValidator { strict: false, constraints: None, microseconds_precision: Truncate, val_temporal_unit: Infer, }, ), frozen: false, }, Field { name: "computer", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "computer", ), rest: [], }, by_alias: [], }, validator: WithDefault( WithDefaultValidator { default: Default( Py( 0x00007310e7455800, ), ), on_error: Raise, validator: Nullable( NullableValidator { validator: Int( IntValidator { strict: false, }, ), name: "nullable[int]", }, ), validate_default: false, copy_default: false, name: "default[nullable[int]]", undefined: Py( 0x00007310e53bdb90, ), }, ), frozen: false, }, Field { name: "user", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "user", ), rest: [], }, by_alias: [], }, validator: Int( IntValidator { strict: false, }, ), frozen: false, }, ], model_name: "ReadModel", extra_behavior: Forbid, extras_validator: None, extras_keys_validator: None, strict: false, from_attributes: false, loc_by_alias: true, lookup: LookupTree { inner: { PathItemString( "label", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 1, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "node_type", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 4, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "pk", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 0, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "extras", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 3, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "attributes", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 5, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "repository_metadata", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 6, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "process_type", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 8, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "ctime", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 9, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "description", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 2, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "mtime", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 10, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "user", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 12, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "computer", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 11, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "uuid", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 7, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, }, }, validate_by_alias: Some( true, ), validate_by_name: Some( true, ), }, ), class: Py( 0x000063affef8f970, ), generic_origin: None, post_init: Some( Py( 0x00007310e2571630, ), ), frozen: false, custom_init: false, root_model: false, undefined: Py( 0x00007310e53bdb90, ), name: "ReadModel", }, ), definitions=[], cache_strings=True)¶
The pydantic-core SchemaValidator used to validate instances of the model.
- _abc_impl = <_abc._abc_data object>¶
- attributes: AttributesModel¶
- model_config = {'defer_build': True, 'extra': 'forbid', 'json_encoders': {<class 'datetime.datetime'>: <function OrmModel.<lambda>>}, 'serialize_by_alias': True, 'title': 'EditconfParametersReadModel', 'validate_by_alias': True, 'validate_by_name': True}¶
Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].
- class WriteModel(**data: Any)¶
Bases:
WriteModel- __abstractmethods__ = frozenset({})¶
- __annotations__ = {'attributes': <class 'aiida_gromacs.data.editconf.EditconfParameters.AttributesWriteModel'>, 'description': <class 'str'>, 'extras': dict[str, typing.Any], 'label': <class 'str'>, 'node_type': typing.Literal['data.gromacs.editconf.EditconfParameters.'], 'repository_metadata': dict[str, typing.Any]}¶
- __class_vars__ = {}¶
The names of the class variables defined on the model.
- __dict__¶
- __module__ = 'aiida_gromacs.data.editconf'¶
- __private_attributes__ = {'_AIIDA_MINIMAL_MODEL': ModelPrivateAttr()}¶
Metadata about the private attributes of the model.
- __pydantic_complete__ = True¶
Whether model building is completed, or if there are still undefined fields.
- __pydantic_computed_fields__ = {}¶
A dictionary of computed field names and their corresponding [ComputedFieldInfo][pydantic.fields.ComputedFieldInfo] objects.
- __pydantic_core_schema__ = {'cls': <class 'aiida_gromacs.data.editconf.EditconfParameters.WriteModel'>, 'config': {'extra_fields_behavior': 'forbid', 'serialize_by_alias': True, 'title': 'EditconfParametersWriteModel', 'validate_by_alias': True, 'validate_by_name': True}, 'custom_init': False, 'metadata': {'pydantic_js_functions': [<bound method BaseModel.__get_pydantic_json_schema__ of <class 'aiida_gromacs.data.editconf.EditconfParameters.WriteModel'>>]}, 'post_init': 'model_post_init', 'ref': 'aiida_gromacs.data.editconf.EditconfParameters.WriteModel:109607548158592', 'root_model': False, 'schema': {'computed_fields': [], 'fields': {'attributes': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'The node attributes', 'examples': [{'attr_key': 'attr_value'}]}}, 'schema': {'cls': <class 'aiida_gromacs.data.editconf.EditconfParameters.AttributesWriteModel'>, 'config': {'extra_fields_behavior': 'allow', 'serialize_by_alias': True, 'title': 'EditconfParametersAttributesWriteModel', 'validate_by_alias': True, 'validate_by_name': True}, 'custom_init': False, 'metadata': {'pydantic_js_functions': [<bound method BaseModel.__get_pydantic_json_schema__ of <class 'aiida_gromacs.data.editconf.EditconfParameters.AttributesWriteModel'>>]}, 'post_init': 'model_post_init', 'ref': 'aiida_gromacs.data.editconf.EditconfParameters.AttributesWriteModel:109607548165504', 'root_model': False, 'schema': {'computed_fields': [], 'fields': {'source': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'Source of the data'}}, 'schema': {'default': None, 'schema': {'schema': {'keys_schema': {'type': 'any'}, 'type': 'dict', 'values_schema': {'type': 'any'}}, 'type': 'nullable'}, 'type': 'default'}, 'type': 'model-field'}}, 'model_name': 'AttributesWriteModel', 'type': 'model-fields'}, 'type': 'model'}, 'type': 'model-field'}, 'description': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'The node description', 'examples': ['This is my node description.']}}, 'schema': {'default': '', 'schema': {'type': 'str'}, 'type': 'default'}, 'type': 'model-field'}, 'extras': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'The node extras', 'examples': [{'extra_key': 'extra_value'}]}}, 'schema': {'default_factory': <class 'dict'>, 'default_factory_takes_data': False, 'schema': {'keys_schema': {'type': 'str'}, 'type': 'dict', 'values_schema': {'type': 'any'}}, 'type': 'default'}, 'type': 'model-field'}, 'label': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'The node label', 'examples': ['my_node']}}, 'schema': {'default': '', 'schema': {'type': 'str'}, 'type': 'default'}, 'type': 'model-field'}, 'node_type': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'The type of the node.'}}, 'schema': {'expected': ['data.gromacs.editconf.EditconfParameters.'], 'type': 'literal'}, 'type': 'model-field'}, 'repository_metadata': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'Virtual hierarchy of the file repository', 'examples': [{'o': {'file.txt': {'k': '<file_hash>'}}}]}}, 'schema': {'default_factory': <class 'dict'>, 'default_factory_takes_data': False, 'schema': {'keys_schema': {'type': 'str'}, 'type': 'dict', 'values_schema': {'type': 'any'}}, 'type': 'default'}, 'type': 'model-field'}}, 'model_name': 'WriteModel', 'type': 'model-fields'}, 'type': 'model'}¶
The core schema of the model.
- __pydantic_custom_init__ = False¶
Whether the model has a custom __init__ method.
- __pydantic_decorators__ = DecoratorInfos(validators={}, field_validators={}, root_validators={}, field_serializers={}, model_serializers={}, model_validators={}, computed_fields={})¶
Metadata containing the decorators defined on the model. This replaces Model.__validators__ and Model.__root_validators__ from Pydantic V1.
- __pydantic_extra__¶
A dictionary containing extra values, if [extra][pydantic.config.ConfigDict.extra] is set to ‘allow’.
- __pydantic_extra_info__ = None¶
A wrapper around the __pydantic_extra__ annotation, if explicitly annotated on a model.
This is a private attribute, not meant to be used outside Pydantic.
- __pydantic_fields__ = {'attributes': FieldInfo(annotation=EditconfParameters.AttributesWriteModel, required=True, description='The node attributes', examples=[{'attr_key': 'attr_value'}], json_schema_extra={}, metadata=[{'priority': 0}, {'read_only': False}, {'write_only': False}, {'may_be_large': True}]), 'description': FieldInfo(annotation=str, required=False, default='', description='The node description', examples=['This is my node description.'], json_schema_extra={}, metadata=[{'priority': 0}, {'read_only': False}, {'write_only': False}, {'may_be_large': False}]), 'extras': FieldInfo(annotation=dict[str, Any], required=False, default_factory=dict, description='The node extras', examples=[{'extra_key': 'extra_value'}], json_schema_extra={}, metadata=[{'priority': 0}, {'read_only': False}, {'write_only': False}, {'may_be_large': True}, {'orm_to_model': <function Node.MutableNodeFields.<lambda>>}]), 'label': FieldInfo(annotation=str, required=False, default='', description='The node label', examples=['my_node'], json_schema_extra={}, metadata=[{'priority': 0}, {'read_only': False}, {'write_only': False}, {'may_be_large': False}]), 'node_type': FieldInfo(annotation=Literal['data.gromacs.editconf.EditconfParameters.'], required=True, description='The type of the node.', json_schema_extra={}, metadata=[{'priority': 0}, {'read_only': False}, {'write_only': False}, {'may_be_large': False}]), 'repository_metadata': FieldInfo(annotation=dict[str, Any], required=False, default_factory=dict, description='Virtual hierarchy of the file repository', examples=[{'o': {'file.txt': {'k': '<file_hash>'}}}], json_schema_extra={}, metadata=[{'priority': 0}, {'read_only': False}, {'write_only': False}, {'may_be_large': True}, {'orm_to_model': <function Node.WritableFields.<lambda>>}])}¶
A dictionary of field names and their corresponding [FieldInfo][pydantic.fields.FieldInfo] objects. This replaces Model.__fields__ from Pydantic V1.
- __pydantic_fields_set__¶
The names of fields explicitly set during instantiation.
- __pydantic_generic_metadata__ = {'args': (), 'origin': None, 'parameters': ()}¶
A dictionary containing metadata about generic Pydantic models.
The origin and args items map to the [__origin__][genericalias.__origin__] and [__args__][genericalias.__args__] attributes of [generic aliases][types-genericalias], and the parameter item maps to the __parameter__ attribute of generic classes.
- __pydantic_post_init__ = 'model_post_init'¶
The name of the post-init method for the model, if defined.
- __pydantic_private__¶
Values of private attributes set on the model instance.
- __pydantic_serializer__ = SchemaSerializer(serializer=PolymorphismTrampoline( PolymorphismTrampoline { class: Py( 0x000063affef90280, ), serializer: PolymorphismTrampoline( PolymorphismTrampoline { class: Py( 0x000063affef90280, ), serializer: Model( ModelSerializer { class: Py( 0x000063affef90280, ), serializer: Fields( GeneralFieldsSerializer { fields: { "label": SerField { key: "label", alias: None, serializer: Some( WithDefault( WithDefaultSerializer { default: Default( Py( 0x00007310e7482e40, ), ), serializer: Str( StrSerializer, ), }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "description": SerField { key: "description", alias: None, serializer: Some( WithDefault( WithDefaultSerializer { default: Default( Py( 0x00007310e7482e40, ), ), serializer: Str( StrSerializer, ), }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "extras": SerField { key: "extras", alias: None, serializer: Some( WithDefault( WithDefaultSerializer { default: DefaultFactory( Py( 0x00007310e74524a0, ), false, ), serializer: Dict( DictSerializer { key_serializer: Str( StrSerializer, ), value_serializer: Any( AnySerializer, ), filter: SchemaFilter { include: None, exclude: None, }, name: "dict[str, any]", }, ), }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "node_type": SerField { key: "node_type", alias: None, serializer: Some( Literal( LiteralSerializer { expected_int: {}, expected_str: { "data.gromacs.editconf.EditconfParameters.", }, expected_py: None, name: "literal['data.gromacs.editconf.EditconfParameters.']", }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "attributes": SerField { key: "attributes", alias: None, serializer: Some( PolymorphismTrampoline( PolymorphismTrampoline { class: Py( 0x000063affef91d80, ), serializer: PolymorphismTrampoline( PolymorphismTrampoline { class: Py( 0x000063affef91d80, ), serializer: Model( ModelSerializer { class: Py( 0x000063affef91d80, ), serializer: Fields( GeneralFieldsSerializer { fields: { "source": SerField { key: "source", alias: None, serializer: Some( WithDefault( WithDefaultSerializer { default: Default( Py( 0x00007310e7455800, ), ), serializer: Nullable( NullableSerializer { serializer: Dict( DictSerializer { key_serializer: Any( AnySerializer, ), value_serializer: Any( AnySerializer, ), filter: SchemaFilter { include: None, exclude: None, }, name: "dict[any, any]", }, ), }, ), }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, }, computed_fields: Some( ComputedFields( [], ), ), mode: ModelExtra, extra_serializer: None, filter: SchemaFilter { include: None, exclude: None, }, required_fields: 1, }, ), has_extra: true, root_model: false, name: "AttributesWriteModel", }, ), enabled_from_config: false, }, ), enabled_from_config: false, }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "repository_metadata": SerField { key: "repository_metadata", alias: None, serializer: Some( WithDefault( WithDefaultSerializer { default: DefaultFactory( Py( 0x00007310e74524a0, ), false, ), serializer: Dict( DictSerializer { key_serializer: Str( StrSerializer, ), value_serializer: Any( AnySerializer, ), filter: SchemaFilter { include: None, exclude: None, }, name: "dict[str, any]", }, ), }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, }, computed_fields: Some( ComputedFields( [], ), ), mode: SimpleDict, extra_serializer: None, filter: SchemaFilter { include: None, exclude: None, }, required_fields: 6, }, ), has_extra: false, root_model: false, name: "WriteModel", }, ), enabled_from_config: false, }, ), enabled_from_config: false, }, ), definitions=[])¶
The pydantic-core SchemaSerializer used to dump instances of the model.
- __pydantic_setattr_handlers__ = {}¶
__setattr__ handlers. Memoizing the handlers leads to a dramatic performance improvement in __setattr__
- __pydantic_validator__ = SchemaValidator(title="EditconfParametersWriteModel", validator=Model( ModelValidator { revalidate: Never, validator: ModelFields( ModelFieldsValidator { fields: [ Field { name: "label", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "label", ), rest: [], }, by_alias: [], }, validator: WithDefault( WithDefaultValidator { default: Default( Py( 0x00007310e7482e40, ), ), on_error: Raise, validator: Str( StrValidator { strict: false, coerce_numbers_to_str: false, }, ), validate_default: false, copy_default: false, name: "default[str]", undefined: Py( 0x00007310e53bdb90, ), }, ), frozen: false, }, Field { name: "description", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "description", ), rest: [], }, by_alias: [], }, validator: WithDefault( WithDefaultValidator { default: Default( Py( 0x00007310e7482e40, ), ), on_error: Raise, validator: Str( StrValidator { strict: false, coerce_numbers_to_str: false, }, ), validate_default: false, copy_default: false, name: "default[str]", undefined: Py( 0x00007310e53bdb90, ), }, ), frozen: false, }, Field { name: "extras", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "extras", ), rest: [], }, by_alias: [], }, validator: WithDefault( WithDefaultValidator { default: DefaultFactory( Py( 0x00007310e74524a0, ), false, ), on_error: Raise, validator: Dict( DictValidator { strict: false, key_validator: Str( StrValidator { strict: false, coerce_numbers_to_str: false, }, ), value_validator: Any( AnyValidator, ), min_length: None, max_length: None, fail_fast: false, name: "dict[str,any]", }, ), validate_default: false, copy_default: false, name: "default[dict[str,any]]", undefined: Py( 0x00007310e53bdb90, ), }, ), frozen: false, }, Field { name: "node_type", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "node_type", ), rest: [], }, by_alias: [], }, validator: Literal( LiteralValidator { lookup: LiteralLookup { expected_bool: None, expected_int: None, expected_str: Some( { "data.gromacs.editconf.EditconfParameters.": 0, }, ), expected_py_dict: None, expected_py_values: None, expected_py_primitives: Some( Py( 0x00007310d2944740, ), ), values: [ Py( 0x00007310d9122a90, ), ], }, expected_repr: "'data.gromacs.editconf.EditconfParameters.'", name: "literal['data.gromacs.editconf.EditconfParameters.']", }, ), frozen: false, }, Field { name: "attributes", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "attributes", ), rest: [], }, by_alias: [], }, validator: Model( ModelValidator { revalidate: Never, validator: ModelFields( ModelFieldsValidator { fields: [ Field { name: "source", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "source", ), rest: [], }, by_alias: [], }, validator: WithDefault( WithDefaultValidator { default: Default( Py( 0x00007310e7455800, ), ), on_error: Raise, validator: Nullable( NullableValidator { validator: Dict( DictValidator { strict: false, key_validator: Any( AnyValidator, ), value_validator: Any( AnyValidator, ), min_length: None, max_length: None, fail_fast: false, name: "dict[any,any]", }, ), name: "nullable[dict[any,any]]", }, ), validate_default: false, copy_default: false, name: "default[nullable[dict[any,any]]]", undefined: Py( 0x00007310e53bdb90, ), }, ), frozen: false, }, ], model_name: "AttributesWriteModel", extra_behavior: Allow, extras_validator: None, extras_keys_validator: None, strict: false, from_attributes: false, loc_by_alias: true, lookup: LookupTree { inner: { PathItemString( "source", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 0, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, }, }, validate_by_alias: Some( true, ), validate_by_name: Some( true, ), }, ), class: Py( 0x000063affef91d80, ), generic_origin: None, post_init: Some( Py( 0x00007310e2571630, ), ), frozen: false, custom_init: false, root_model: false, undefined: Py( 0x00007310e53bdb90, ), name: "AttributesWriteModel", }, ), frozen: false, }, Field { name: "repository_metadata", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "repository_metadata", ), rest: [], }, by_alias: [], }, validator: WithDefault( WithDefaultValidator { default: DefaultFactory( Py( 0x00007310e74524a0, ), false, ), on_error: Raise, validator: Dict( DictValidator { strict: false, key_validator: Str( StrValidator { strict: false, coerce_numbers_to_str: false, }, ), value_validator: Any( AnyValidator, ), min_length: None, max_length: None, fail_fast: false, name: "dict[str,any]", }, ), validate_default: false, copy_default: false, name: "default[dict[str,any]]", undefined: Py( 0x00007310e53bdb90, ), }, ), frozen: false, }, ], model_name: "WriteModel", extra_behavior: Forbid, extras_validator: None, extras_keys_validator: None, strict: false, from_attributes: false, loc_by_alias: true, lookup: LookupTree { inner: { PathItemString( "description", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 1, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "attributes", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 4, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "label", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 0, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "node_type", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 3, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "extras", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 2, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "repository_metadata", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 5, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, }, }, validate_by_alias: Some( true, ), validate_by_name: Some( true, ), }, ), class: Py( 0x000063affef90280, ), generic_origin: None, post_init: Some( Py( 0x00007310e2571630, ), ), frozen: false, custom_init: false, root_model: false, undefined: Py( 0x00007310e53bdb90, ), name: "WriteModel", }, ), definitions=[], cache_strings=True)¶
The pydantic-core SchemaValidator used to validate instances of the model.
- _abc_impl = <_abc._abc_data object>¶
- attributes: AttributesWriteModel¶
- model_config = {'defer_build': True, 'extra': 'forbid', 'json_encoders': {<class 'datetime.datetime'>: <function OrmModel.<lambda>>}, 'serialize_by_alias': True, 'title': 'EditconfParametersWriteModel', 'validate_by_alias': True, 'validate_by_name': True}¶
Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].
- _COMPAT_MODEL¶
alias of
Model
- _ConstructorModel¶
alias of
ConstructorModel
- _MODEL_MAP = {'read': <class 'aiida_gromacs.data.editconf.EditconfParameters.ReadModel'>, 'write': <class 'aiida_gromacs.data.editconf.EditconfParameters.WriteModel'>}¶
- __abstractmethods__ = frozenset({})¶
- __annotations__ = {}¶
- __firstlineno__ = 44¶
- __init__(dict=None, **kwargs)[source]¶
Constructor for the data class
Usage:
EditconfParameters(dict{'ignore-case': True})- Parameters:
parameters_dict (type) – dictionary with commandline parameters
parameters_dict – dict
- __module__ = 'aiida_gromacs.data.editconf'¶
- __parameters__ = ()¶
- __static_attributes__ = ()¶
- __str__()[source]¶
String representation of node.
Append values of dictionary to usual representation. E.g.:
uuid: b416cbee-24e8-47a8-8c11-6d668770158b (pk: 590) {'ignore-case': True}
- _abc_impl = <_abc._abc_data object>¶
- _logger = <Logger aiida_gromacs.data.editconf.EditconfParameters (WARNING)>¶
- cmdline_params(input_files)[source]¶
Synthesize command line parameters.
e.g. [ ‘–ignore-case’, ‘filename1’, ‘filename2’]
- Parameters:
grofile (type) – Name of input gro file
grofile – str
- fields = {'attributes': "QbAttributesField('attributes', dtype=<class 'aiida_gromacs.data.editconf.EditconfParameters.AttributesModel'>, doc='The node attributes')", 'computer': "QbNumericField('computer', dtype=int | None, doc='The PK of the computer')", 'ctime': "QbNumericField('ctime', dtype=<class 'datetime.datetime'>, doc='The creation time of the node')", 'description': "QbStrField('description', dtype=<class 'str'>, doc='The node description')", 'extras': "QbDictField('extras', dtype=dict[str, typing.Any], doc='The node extras')", 'label': "QbStrField('label', dtype=<class 'str'>, doc='The node label')", 'mtime': "QbNumericField('mtime', dtype=<class 'datetime.datetime'>, doc='The modification time of the node')", 'node_type': "QbStrField('node_type', dtype=typing.Literal['data.gromacs.editconf.EditconfParameters.'], doc='The type of the node.')", 'pk': "QbNumericField('pk', dtype=<class 'int'>, doc='The primary key of the entity')", 'process_type': "QbStrField('process_type', dtype=str | None, doc='The process type of the node')", 'repository_metadata': "QbDictField('repository_metadata', dtype=dict[str, typing.Any], doc='Virtual hierarchy of the file repository')", 'source': "QbDictField('attributes.source', dtype=dict | None, doc='Source of the data')", 'user': "QbNumericField('user', dtype=<class 'int'>, doc='The PK of the user who owns the node')", 'uuid': "QbStrField('uuid', dtype=<class 'uuid.UUID'>, doc='The UUID of the node')"}¶
- schema = <Schema({'o': <class 'str'>, 'mead': <class 'str'>, 'w': <class 'str'>, 'ndef': <class 'str'>, 'bt': <class 'str'>, 'box': <class 'str'>, 'angle': <class 'str'>, 'd': <class 'str'>, 'c': <class 'str'>, 'center': <class 'str'>, 'aligncenter': <class 'str'>, 'align': <class 'str'>, 'translate': <class 'str'>, 'rotate': <class 'str'>, 'princ': <class 'str'>, 'scale': <class 'str'>, 'density': <class 'str'>, 'pbc': <class 'str'>, 'resnr': <class 'str'>, 'grasp': <class 'str'>, 'rvdw': <class 'str'>, 'sig56': <class 'str'>, 'vdwread': <class 'str'>, 'atom': <class 'str'>, 'legend': <class 'str'>, 'label': <class 'str'>, 'conect': <class 'str'>}, extra=PREVENT_EXTRA, required=False) object>¶
- validate(parameters_dict)[source]¶
Validate command line options.
Uses the voluptuous package for validation. Find out about allowed keys using:
print(EditconfParameters).schema.schema
- Parameters:
parameters_dict (type) – dictionary with commandline parameters
parameters_dict – dict
- Returns:
validated dictionary
aiida_gromacs.data.genion module¶
Data types provided by plugin
Register data types via the “aiida.data” entry point in setup.json.
- class aiida_gromacs.data.genion.GenionParameters(dict=None, **kwargs)[source]¶
Bases:
DictCommand line options for diff.
This class represents a python dictionary used to pass command line options to the executable.
- class AttributesModel(**data: Any)¶
Bases:
AttributesModel- __abstractmethods__ = frozenset({})¶
- __annotations__ = {}¶
- __class_vars__ = {}¶
The names of the class variables defined on the model.
- __dict__¶
- __module__ = 'aiida_gromacs.data.genion'¶
- __private_attributes__ = {'_AIIDA_MINIMAL_MODEL': ModelPrivateAttr()}¶
Metadata about the private attributes of the model.
- __pydantic_complete__ = True¶
Whether model building is completed, or if there are still undefined fields.
- __pydantic_computed_fields__ = {}¶
A dictionary of computed field names and their corresponding [ComputedFieldInfo][pydantic.fields.ComputedFieldInfo] objects.
- __pydantic_core_schema__ = {'cls': <class 'aiida_gromacs.data.genion.GenionParameters.AttributesModel'>, 'config': {'extra_fields_behavior': 'allow', 'serialize_by_alias': True, 'title': 'GenionParametersAttributesModel', 'validate_by_alias': True, 'validate_by_name': True}, 'custom_init': False, 'metadata': {'pydantic_js_functions': [<bound method BaseModel.__get_pydantic_json_schema__ of <class 'aiida_gromacs.data.genion.GenionParameters.AttributesModel'>>]}, 'post_init': 'model_post_init', 'ref': 'aiida_gromacs.data.genion.GenionParameters.AttributesModel:109607548419968', 'root_model': False, 'schema': {'computed_fields': [], 'fields': {'source': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'Source of the data'}}, 'schema': {'default': None, 'schema': {'schema': {'keys_schema': {'type': 'any'}, 'type': 'dict', 'values_schema': {'type': 'any'}}, 'type': 'nullable'}, 'type': 'default'}, 'type': 'model-field'}}, 'model_name': 'AttributesModel', 'type': 'model-fields'}, 'type': 'model'}¶
The core schema of the model.
- __pydantic_custom_init__ = False¶
Whether the model has a custom __init__ method.
- __pydantic_decorators__ = DecoratorInfos(validators={}, field_validators={}, root_validators={}, field_serializers={}, model_serializers={}, model_validators={}, computed_fields={})¶
Metadata containing the decorators defined on the model. This replaces Model.__validators__ and Model.__root_validators__ from Pydantic V1.
- __pydantic_extra__¶
A dictionary containing extra values, if [extra][pydantic.config.ConfigDict.extra] is set to ‘allow’.
- __pydantic_extra_info__ = None¶
A wrapper around the __pydantic_extra__ annotation, if explicitly annotated on a model.
This is a private attribute, not meant to be used outside Pydantic.
- __pydantic_fields__ = {'source': FieldInfo(annotation=Union[dict, NoneType], required=False, default=None, description='Source of the data', json_schema_extra={}, metadata=[{'priority': 0}, {'read_only': False}, {'write_only': False}, {'may_be_large': False}])}¶
A dictionary of field names and their corresponding [FieldInfo][pydantic.fields.FieldInfo] objects. This replaces Model.__fields__ from Pydantic V1.
- __pydantic_fields_set__¶
The names of fields explicitly set during instantiation.
- __pydantic_generic_metadata__ = {'args': (), 'origin': None, 'parameters': ()}¶
A dictionary containing metadata about generic Pydantic models.
The origin and args items map to the [__origin__][genericalias.__origin__] and [__args__][genericalias.__args__] attributes of [generic aliases][types-genericalias], and the parameter item maps to the __parameter__ attribute of generic classes.
- __pydantic_post_init__ = 'model_post_init'¶
The name of the post-init method for the model, if defined.
- __pydantic_private__¶
Values of private attributes set on the model instance.
- __pydantic_serializer__ = SchemaSerializer(serializer=PolymorphismTrampoline( PolymorphismTrampoline { class: Py( 0x000063affefcff80, ), serializer: PolymorphismTrampoline( PolymorphismTrampoline { class: Py( 0x000063affefcff80, ), serializer: Model( ModelSerializer { class: Py( 0x000063affefcff80, ), serializer: Fields( GeneralFieldsSerializer { fields: { "source": SerField { key: "source", alias: None, serializer: Some( WithDefault( WithDefaultSerializer { default: Default( Py( 0x00007310e7455800, ), ), serializer: Nullable( NullableSerializer { serializer: Dict( DictSerializer { key_serializer: Any( AnySerializer, ), value_serializer: Any( AnySerializer, ), filter: SchemaFilter { include: None, exclude: None, }, name: "dict[any, any]", }, ), }, ), }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, }, computed_fields: Some( ComputedFields( [], ), ), mode: ModelExtra, extra_serializer: None, filter: SchemaFilter { include: None, exclude: None, }, required_fields: 1, }, ), has_extra: true, root_model: false, name: "AttributesModel", }, ), enabled_from_config: false, }, ), enabled_from_config: false, }, ), definitions=[])¶
The pydantic-core SchemaSerializer used to dump instances of the model.
- __pydantic_setattr_handlers__ = {}¶
__setattr__ handlers. Memoizing the handlers leads to a dramatic performance improvement in __setattr__
- __pydantic_validator__ = SchemaValidator(title="GenionParametersAttributesModel", validator=Model( ModelValidator { revalidate: Never, validator: ModelFields( ModelFieldsValidator { fields: [ Field { name: "source", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "source", ), rest: [], }, by_alias: [], }, validator: WithDefault( WithDefaultValidator { default: Default( Py( 0x00007310e7455800, ), ), on_error: Raise, validator: Nullable( NullableValidator { validator: Dict( DictValidator { strict: false, key_validator: Any( AnyValidator, ), value_validator: Any( AnyValidator, ), min_length: None, max_length: None, fail_fast: false, name: "dict[any,any]", }, ), name: "nullable[dict[any,any]]", }, ), validate_default: false, copy_default: false, name: "default[nullable[dict[any,any]]]", undefined: Py( 0x00007310e53bdb90, ), }, ), frozen: false, }, ], model_name: "AttributesModel", extra_behavior: Allow, extras_validator: None, extras_keys_validator: None, strict: false, from_attributes: false, loc_by_alias: true, lookup: LookupTree { inner: { PathItemString( "source", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 0, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, }, }, validate_by_alias: Some( true, ), validate_by_name: Some( true, ), }, ), class: Py( 0x000063affefcff80, ), generic_origin: None, post_init: Some( Py( 0x00007310e2571630, ), ), frozen: false, custom_init: false, root_model: false, undefined: Py( 0x00007310e53bdb90, ), name: "AttributesModel", }, ), definitions=[], cache_strings=True)¶
The pydantic-core SchemaValidator used to validate instances of the model.
- _abc_impl = <_abc._abc_data object>¶
- model_config = {'arbitrary_types_allowed': True, 'defer_build': True, 'extra': 'allow', 'json_encoders': {<class 'datetime.datetime'>: <function OrmModel.<lambda>>}, 'serialize_by_alias': True, 'title': 'GenionParametersAttributesModel', 'validate_by_alias': True, 'validate_by_name': True}¶
Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].
- class ReadModel(**data: Any)¶
Bases:
ReadModel- __abstractmethods__ = frozenset({})¶
- __annotations__ = {'attributes': <class 'aiida_gromacs.data.genion.GenionParameters.AttributesModel'>, 'node_type': typing.Literal['data.gromacs.genion.GenionParameters.']}¶
- __class_vars__ = {}¶
The names of the class variables defined on the model.
- __dict__¶
- __module__ = 'aiida_gromacs.data.genion'¶
- __private_attributes__ = {'_AIIDA_MINIMAL_MODEL': ModelPrivateAttr()}¶
Metadata about the private attributes of the model.
- __pydantic_complete__ = True¶
Whether model building is completed, or if there are still undefined fields.
- __pydantic_computed_fields__ = {}¶
A dictionary of computed field names and their corresponding [ComputedFieldInfo][pydantic.fields.ComputedFieldInfo] objects.
- __pydantic_core_schema__ = {'cls': <class 'aiida_gromacs.data.genion.GenionParameters.ReadModel'>, 'config': {'extra_fields_behavior': 'forbid', 'serialize_by_alias': True, 'title': 'GenionParametersReadModel', 'validate_by_alias': True, 'validate_by_name': True}, 'custom_init': False, 'metadata': {'pydantic_js_functions': [<bound method BaseModel.__get_pydantic_json_schema__ of <class 'aiida_gromacs.data.genion.GenionParameters.ReadModel'>>]}, 'post_init': 'model_post_init', 'ref': 'aiida_gromacs.data.genion.GenionParameters.ReadModel:109607548445536', 'root_model': False, 'schema': {'computed_fields': [], 'fields': {'attributes': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'The node attributes', 'examples': [{'attr_key': 'attr_value'}]}}, 'schema': {'cls': <class 'aiida_gromacs.data.genion.GenionParameters.AttributesModel'>, 'config': {'extra_fields_behavior': 'allow', 'serialize_by_alias': True, 'title': 'GenionParametersAttributesModel', 'validate_by_alias': True, 'validate_by_name': True}, 'custom_init': False, 'metadata': {'pydantic_js_functions': [<bound method BaseModel.__get_pydantic_json_schema__ of <class 'aiida_gromacs.data.genion.GenionParameters.AttributesModel'>>]}, 'post_init': 'model_post_init', 'ref': 'aiida_gromacs.data.genion.GenionParameters.AttributesModel:109607548419968', 'root_model': False, 'schema': {'computed_fields': [], 'fields': {'source': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'Source of the data'}}, 'schema': {'default': None, 'schema': {'schema': {'keys_schema': {'type': 'any'}, 'type': 'dict', 'values_schema': {'type': 'any'}}, 'type': 'nullable'}, 'type': 'default'}, 'type': 'model-field'}}, 'model_name': 'AttributesModel', 'type': 'model-fields'}, 'type': 'model'}, 'type': 'model-field'}, 'computer': {'metadata': {'pydantic_js_extra': {'readOnly': True}, 'pydantic_js_updates': {'description': 'The PK of the computer', 'examples': [42]}}, 'schema': {'default': None, 'schema': {'schema': {'type': 'int'}, 'type': 'nullable'}, 'type': 'default'}, 'type': 'model-field'}, 'ctime': {'metadata': {'pydantic_js_extra': {'readOnly': True}, 'pydantic_js_updates': {'description': 'The creation time of the node', 'examples': ['2024-01-01T12:00:00+00:00']}}, 'schema': {'microseconds_precision': 'truncate', 'serialization': {'function': <function OrmModel.<lambda>>, 'type': 'function-plain', 'when_used': 'json'}, 'type': 'datetime'}, 'type': 'model-field'}, 'description': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'The node description', 'examples': ['This is my node description.']}}, 'schema': {'default': '', 'schema': {'type': 'str'}, 'type': 'default'}, 'type': 'model-field'}, 'extras': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'The node extras', 'examples': [{'extra_key': 'extra_value'}]}}, 'schema': {'default_factory': <class 'dict'>, 'default_factory_takes_data': False, 'schema': {'keys_schema': {'type': 'str'}, 'type': 'dict', 'values_schema': {'type': 'any'}}, 'type': 'default'}, 'type': 'model-field'}, 'label': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'The node label', 'examples': ['my_node']}}, 'schema': {'default': '', 'schema': {'type': 'str'}, 'type': 'default'}, 'type': 'model-field'}, 'mtime': {'metadata': {'pydantic_js_extra': {'readOnly': True}, 'pydantic_js_updates': {'description': 'The modification time of the node', 'examples': ['2024-01-02T12:00:00+00:00']}}, 'schema': {'microseconds_precision': 'truncate', 'serialization': {'function': <function OrmModel.<lambda>>, 'type': 'function-plain', 'when_used': 'json'}, 'type': 'datetime'}, 'type': 'model-field'}, 'node_type': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'The type of the node.'}}, 'schema': {'expected': ['data.gromacs.genion.GenionParameters.'], 'type': 'literal'}, 'type': 'model-field'}, 'pk': {'metadata': {'pydantic_js_extra': {'readOnly': True}, 'pydantic_js_updates': {'description': 'The primary key of the entity', 'examples': [42]}}, 'schema': {'type': 'int'}, 'type': 'model-field'}, 'process_type': {'metadata': {'pydantic_js_extra': {'readOnly': True}, 'pydantic_js_updates': {'description': 'The process type of the node', 'examples': ['aiida.calculations:arithmetic.add.']}}, 'schema': {'default': None, 'schema': {'schema': {'type': 'str'}, 'type': 'nullable'}, 'type': 'default'}, 'type': 'model-field'}, 'repository_metadata': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'Virtual hierarchy of the file repository', 'examples': [{'o': {'file.txt': {'k': '<file_hash>'}}}]}}, 'schema': {'default_factory': <class 'dict'>, 'default_factory_takes_data': False, 'schema': {'keys_schema': {'type': 'str'}, 'type': 'dict', 'values_schema': {'type': 'any'}}, 'type': 'default'}, 'type': 'model-field'}, 'user': {'metadata': {'pydantic_js_extra': {'readOnly': True}, 'pydantic_js_updates': {'description': 'The PK of the user who owns the node', 'examples': [7]}}, 'schema': {'type': 'int'}, 'type': 'model-field'}, 'uuid': {'metadata': {'pydantic_js_extra': {'readOnly': True}, 'pydantic_js_updates': {'description': 'The UUID of the node', 'examples': ['123e4567-e89b-12d3-a456-426614174000']}}, 'schema': {'type': 'uuid'}, 'type': 'model-field'}}, 'model_name': 'ReadModel', 'type': 'model-fields'}, 'type': 'model'}¶
The core schema of the model.
- __pydantic_custom_init__ = False¶
Whether the model has a custom __init__ method.
- __pydantic_decorators__ = DecoratorInfos(validators={}, field_validators={}, root_validators={}, field_serializers={}, model_serializers={}, model_validators={}, computed_fields={})¶
Metadata containing the decorators defined on the model. This replaces Model.__validators__ and Model.__root_validators__ from Pydantic V1.
- __pydantic_extra__¶
A dictionary containing extra values, if [extra][pydantic.config.ConfigDict.extra] is set to ‘allow’.
- __pydantic_extra_info__ = None¶
A wrapper around the __pydantic_extra__ annotation, if explicitly annotated on a model.
This is a private attribute, not meant to be used outside Pydantic.
- __pydantic_fields__ = {'attributes': FieldInfo(annotation=GenionParameters.AttributesModel, required=True, description='The node attributes', examples=[{'attr_key': 'attr_value'}], json_schema_extra={}, metadata=[{'priority': 0}, {'read_only': False}, {'write_only': False}, {'may_be_large': True}]), 'computer': FieldInfo(annotation=Union[int, NoneType], required=False, default=None, description='The PK of the computer', examples=[42], json_schema_extra={'readOnly': True}, metadata=[{'priority': 0}, {'read_only': True}, {'write_only': False}, {'may_be_large': False}, {'orm_class': <class 'aiida.orm.computers.Computer'>}, {'orm_to_model': <function Node.ReadModel.<lambda>>}]), 'ctime': FieldInfo(annotation=datetime, required=True, description='The creation time of the node', examples=['2024-01-01T12:00:00+00:00'], json_schema_extra={'readOnly': True}, metadata=[{'priority': 0}, {'read_only': True}, {'write_only': False}, {'may_be_large': False}]), 'description': FieldInfo(annotation=str, required=False, default='', description='The node description', examples=['This is my node description.'], json_schema_extra={}, metadata=[{'priority': 0}, {'read_only': False}, {'write_only': False}, {'may_be_large': False}]), 'extras': FieldInfo(annotation=dict[str, Any], required=False, default_factory=dict, description='The node extras', examples=[{'extra_key': 'extra_value'}], json_schema_extra={}, metadata=[{'priority': 0}, {'read_only': False}, {'write_only': False}, {'may_be_large': True}, {'orm_to_model': <function Node.MutableNodeFields.<lambda>>}]), 'label': FieldInfo(annotation=str, required=False, default='', description='The node label', examples=['my_node'], json_schema_extra={}, metadata=[{'priority': 0}, {'read_only': False}, {'write_only': False}, {'may_be_large': False}]), 'mtime': FieldInfo(annotation=datetime, required=True, description='The modification time of the node', examples=['2024-01-02T12:00:00+00:00'], json_schema_extra={'readOnly': True}, metadata=[{'priority': 0}, {'read_only': True}, {'write_only': False}, {'may_be_large': False}]), 'node_type': FieldInfo(annotation=Literal['data.gromacs.genion.GenionParameters.'], required=True, description='The type of the node.', json_schema_extra={}, metadata=[{'priority': 0}, {'read_only': False}, {'write_only': False}, {'may_be_large': False}]), 'pk': FieldInfo(annotation=int, required=True, description='The primary key of the entity', examples=[42], json_schema_extra={'readOnly': True}, metadata=[{'priority': 0}, {'read_only': True}, {'write_only': False}, {'may_be_large': False}]), 'process_type': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, description='The process type of the node', examples=['aiida.calculations:arithmetic.add.'], json_schema_extra={'readOnly': True}, metadata=[{'priority': 0}, {'read_only': True}, {'write_only': False}, {'may_be_large': False}]), 'repository_metadata': FieldInfo(annotation=dict[str, Any], required=False, default_factory=dict, description='Virtual hierarchy of the file repository', examples=[{'o': {'file.txt': {'k': '<file_hash>'}}}], json_schema_extra={}, metadata=[{'priority': 0}, {'read_only': False}, {'write_only': False}, {'may_be_large': True}, {'orm_to_model': <function Node.WritableFields.<lambda>>}]), 'user': FieldInfo(annotation=int, required=True, description='The PK of the user who owns the node', examples=[7], json_schema_extra={'readOnly': True}, metadata=[{'priority': 0}, {'read_only': True}, {'write_only': False}, {'may_be_large': False}, {'orm_class': <class 'aiida.orm.users.User'>}, {'orm_to_model': <function Node.ReadModel.<lambda>>}]), 'uuid': FieldInfo(annotation=UUID, required=True, description='The UUID of the node', examples=['123e4567-e89b-12d3-a456-426614174000'], json_schema_extra={'readOnly': True}, metadata=[{'priority': 0}, {'read_only': True}, {'write_only': False}, {'may_be_large': False}])}¶
A dictionary of field names and their corresponding [FieldInfo][pydantic.fields.FieldInfo] objects. This replaces Model.__fields__ from Pydantic V1.
- __pydantic_fields_set__¶
The names of fields explicitly set during instantiation.
- __pydantic_generic_metadata__ = {'args': (), 'origin': None, 'parameters': ()}¶
A dictionary containing metadata about generic Pydantic models.
The origin and args items map to the [__origin__][genericalias.__origin__] and [__args__][genericalias.__args__] attributes of [generic aliases][types-genericalias], and the parameter item maps to the __parameter__ attribute of generic classes.
- __pydantic_post_init__ = 'model_post_init'¶
The name of the post-init method for the model, if defined.
- __pydantic_private__¶
Values of private attributes set on the model instance.
- __pydantic_serializer__ = SchemaSerializer(serializer=PolymorphismTrampoline( PolymorphismTrampoline { class: Py( 0x000063affefd6360, ), serializer: PolymorphismTrampoline( PolymorphismTrampoline { class: Py( 0x000063affefd6360, ), serializer: Model( ModelSerializer { class: Py( 0x000063affefd6360, ), serializer: Fields( GeneralFieldsSerializer { fields: { "computer": SerField { key: "computer", alias: None, serializer: Some( WithDefault( WithDefaultSerializer { default: Default( Py( 0x00007310e7455800, ), ), serializer: Nullable( NullableSerializer { serializer: Int( IntSerializer, ), }, ), }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "label": SerField { key: "label", alias: None, serializer: Some( WithDefault( WithDefaultSerializer { default: Default( Py( 0x00007310e7482e40, ), ), serializer: Str( StrSerializer, ), }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "uuid": SerField { key: "uuid", alias: None, serializer: Some( Uuid( UuidSerializer, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "mtime": SerField { key: "mtime", alias: None, serializer: Some( Function( FunctionPlainSerializer { func: Py( 0x00007310e2355c60, ), name: "plain_function[<lambda>]", function_name: "<lambda>", return_serializer: Any( AnySerializer, ), fallback_serializer: Some( Datetime( DatetimeSerializer { temporal_mode: Iso8601, }, ), ), when_used: Json, is_field_serializer: false, info_arg: false, }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "description": SerField { key: "description", alias: None, serializer: Some( WithDefault( WithDefaultSerializer { default: Default( Py( 0x00007310e7482e40, ), ), serializer: Str( StrSerializer, ), }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "node_type": SerField { key: "node_type", alias: None, serializer: Some( Literal( LiteralSerializer { expected_int: {}, expected_str: { "data.gromacs.genion.GenionParameters.", }, expected_py: None, name: "literal['data.gromacs.genion.GenionParameters.']", }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "repository_metadata": SerField { key: "repository_metadata", alias: None, serializer: Some( WithDefault( WithDefaultSerializer { default: DefaultFactory( Py( 0x00007310e74524a0, ), false, ), serializer: Dict( DictSerializer { key_serializer: Str( StrSerializer, ), value_serializer: Any( AnySerializer, ), filter: SchemaFilter { include: None, exclude: None, }, name: "dict[str, any]", }, ), }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "pk": SerField { key: "pk", alias: None, serializer: Some( Int( IntSerializer, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "extras": SerField { key: "extras", alias: None, serializer: Some( WithDefault( WithDefaultSerializer { default: DefaultFactory( Py( 0x00007310e74524a0, ), false, ), serializer: Dict( DictSerializer { key_serializer: Str( StrSerializer, ), value_serializer: Any( AnySerializer, ), filter: SchemaFilter { include: None, exclude: None, }, name: "dict[str, any]", }, ), }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "user": SerField { key: "user", alias: None, serializer: Some( Int( IntSerializer, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "ctime": SerField { key: "ctime", alias: None, serializer: Some( Function( FunctionPlainSerializer { func: Py( 0x00007310e2355c60, ), name: "plain_function[<lambda>]", function_name: "<lambda>", return_serializer: Any( AnySerializer, ), fallback_serializer: Some( Datetime( DatetimeSerializer { temporal_mode: Iso8601, }, ), ), when_used: Json, is_field_serializer: false, info_arg: false, }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "process_type": SerField { key: "process_type", alias: None, serializer: Some( WithDefault( WithDefaultSerializer { default: Default( Py( 0x00007310e7455800, ), ), serializer: Nullable( NullableSerializer { serializer: Str( StrSerializer, ), }, ), }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "attributes": SerField { key: "attributes", alias: None, serializer: Some( PolymorphismTrampoline( PolymorphismTrampoline { class: Py( 0x000063affefcff80, ), serializer: Prebuilt( PrebuiltSerializer { schema_serializer: Py( 0x00007310d2c63eb0, ), }, ), enabled_from_config: false, }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, }, computed_fields: Some( ComputedFields( [], ), ), mode: SimpleDict, extra_serializer: None, filter: SchemaFilter { include: None, exclude: None, }, required_fields: 13, }, ), has_extra: false, root_model: false, name: "ReadModel", }, ), enabled_from_config: false, }, ), enabled_from_config: false, }, ), definitions=[])¶
The pydantic-core SchemaSerializer used to dump instances of the model.
- __pydantic_setattr_handlers__ = {}¶
__setattr__ handlers. Memoizing the handlers leads to a dramatic performance improvement in __setattr__
- __pydantic_validator__ = SchemaValidator(title="GenionParametersReadModel", validator=Model( ModelValidator { revalidate: Never, validator: ModelFields( ModelFieldsValidator { fields: [ Field { name: "pk", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "pk", ), rest: [], }, by_alias: [], }, validator: Int( IntValidator { strict: false, }, ), frozen: false, }, Field { name: "label", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "label", ), rest: [], }, by_alias: [], }, validator: WithDefault( WithDefaultValidator { default: Default( Py( 0x00007310e7482e40, ), ), on_error: Raise, validator: Str( StrValidator { strict: false, coerce_numbers_to_str: false, }, ), validate_default: false, copy_default: false, name: "default[str]", undefined: Py( 0x00007310e53bdb90, ), }, ), frozen: false, }, Field { name: "description", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "description", ), rest: [], }, by_alias: [], }, validator: WithDefault( WithDefaultValidator { default: Default( Py( 0x00007310e7482e40, ), ), on_error: Raise, validator: Str( StrValidator { strict: false, coerce_numbers_to_str: false, }, ), validate_default: false, copy_default: false, name: "default[str]", undefined: Py( 0x00007310e53bdb90, ), }, ), frozen: false, }, Field { name: "extras", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "extras", ), rest: [], }, by_alias: [], }, validator: WithDefault( WithDefaultValidator { default: DefaultFactory( Py( 0x00007310e74524a0, ), false, ), on_error: Raise, validator: Dict( DictValidator { strict: false, key_validator: Str( StrValidator { strict: false, coerce_numbers_to_str: false, }, ), value_validator: Any( AnyValidator, ), min_length: None, max_length: None, fail_fast: false, name: "dict[str,any]", }, ), validate_default: false, copy_default: false, name: "default[dict[str,any]]", undefined: Py( 0x00007310e53bdb90, ), }, ), frozen: false, }, Field { name: "node_type", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "node_type", ), rest: [], }, by_alias: [], }, validator: Literal( LiteralValidator { lookup: LiteralLookup { expected_bool: None, expected_int: None, expected_str: Some( { "data.gromacs.genion.GenionParameters.": 0, }, ), expected_py_dict: None, expected_py_values: None, expected_py_primitives: Some( Py( 0x00007310d2901040, ), ), values: [ Py( 0x00007310d30c32d0, ), ], }, expected_repr: "'data.gromacs.genion.GenionParameters.'", name: "literal['data.gromacs.genion.GenionParameters.']", }, ), frozen: false, }, Field { name: "attributes", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "attributes", ), rest: [], }, by_alias: [], }, validator: Prebuilt( PrebuiltValidator { schema_validator: Py( 0x00007310d2c63e20, ), }, ), frozen: false, }, Field { name: "repository_metadata", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "repository_metadata", ), rest: [], }, by_alias: [], }, validator: WithDefault( WithDefaultValidator { default: DefaultFactory( Py( 0x00007310e74524a0, ), false, ), on_error: Raise, validator: Dict( DictValidator { strict: false, key_validator: Str( StrValidator { strict: false, coerce_numbers_to_str: false, }, ), value_validator: Any( AnyValidator, ), min_length: None, max_length: None, fail_fast: false, name: "dict[str,any]", }, ), validate_default: false, copy_default: false, name: "default[dict[str,any]]", undefined: Py( 0x00007310e53bdb90, ), }, ), frozen: false, }, Field { name: "uuid", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "uuid", ), rest: [], }, by_alias: [], }, validator: Uuid( UuidValidator { strict: false, version: None, }, ), frozen: false, }, Field { name: "process_type", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "process_type", ), rest: [], }, by_alias: [], }, validator: WithDefault( WithDefaultValidator { default: Default( Py( 0x00007310e7455800, ), ), on_error: Raise, validator: Nullable( NullableValidator { validator: Str( StrValidator { strict: false, coerce_numbers_to_str: false, }, ), name: "nullable[str]", }, ), validate_default: false, copy_default: false, name: "default[nullable[str]]", undefined: Py( 0x00007310e53bdb90, ), }, ), frozen: false, }, Field { name: "ctime", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "ctime", ), rest: [], }, by_alias: [], }, validator: Datetime( DateTimeValidator { strict: false, constraints: None, microseconds_precision: Truncate, val_temporal_unit: Infer, }, ), frozen: false, }, Field { name: "mtime", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "mtime", ), rest: [], }, by_alias: [], }, validator: Datetime( DateTimeValidator { strict: false, constraints: None, microseconds_precision: Truncate, val_temporal_unit: Infer, }, ), frozen: false, }, Field { name: "computer", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "computer", ), rest: [], }, by_alias: [], }, validator: WithDefault( WithDefaultValidator { default: Default( Py( 0x00007310e7455800, ), ), on_error: Raise, validator: Nullable( NullableValidator { validator: Int( IntValidator { strict: false, }, ), name: "nullable[int]", }, ), validate_default: false, copy_default: false, name: "default[nullable[int]]", undefined: Py( 0x00007310e53bdb90, ), }, ), frozen: false, }, Field { name: "user", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "user", ), rest: [], }, by_alias: [], }, validator: Int( IntValidator { strict: false, }, ), frozen: false, }, ], model_name: "ReadModel", extra_behavior: Forbid, extras_validator: None, extras_keys_validator: None, strict: false, from_attributes: false, loc_by_alias: true, lookup: LookupTree { inner: { PathItemString( "process_type", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 8, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "extras", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 3, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "ctime", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 9, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "label", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 1, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "node_type", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 4, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "mtime", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 10, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "attributes", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 5, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "repository_metadata", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 6, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "computer", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 11, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "uuid", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 7, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "user", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 12, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "pk", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 0, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "description", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 2, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, }, }, validate_by_alias: Some( true, ), validate_by_name: Some( true, ), }, ), class: Py( 0x000063affefd6360, ), generic_origin: None, post_init: Some( Py( 0x00007310e2571630, ), ), frozen: false, custom_init: false, root_model: false, undefined: Py( 0x00007310e53bdb90, ), name: "ReadModel", }, ), definitions=[], cache_strings=True)¶
The pydantic-core SchemaValidator used to validate instances of the model.
- _abc_impl = <_abc._abc_data object>¶
- attributes: AttributesModel¶
- model_config = {'defer_build': True, 'extra': 'forbid', 'json_encoders': {<class 'datetime.datetime'>: <function OrmModel.<lambda>>}, 'serialize_by_alias': True, 'title': 'GenionParametersReadModel', 'validate_by_alias': True, 'validate_by_name': True}¶
Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].
- class WriteModel(**data: Any)¶
Bases:
WriteModel- __abstractmethods__ = frozenset({})¶
- __annotations__ = {'attributes': <class 'aiida_gromacs.data.genion.GenionParameters.AttributesWriteModel'>, 'description': <class 'str'>, 'extras': dict[str, typing.Any], 'label': <class 'str'>, 'node_type': typing.Literal['data.gromacs.genion.GenionParameters.'], 'repository_metadata': dict[str, typing.Any]}¶
- __class_vars__ = {}¶
The names of the class variables defined on the model.
- __dict__¶
- __module__ = 'aiida_gromacs.data.genion'¶
- __private_attributes__ = {'_AIIDA_MINIMAL_MODEL': ModelPrivateAttr()}¶
Metadata about the private attributes of the model.
- __pydantic_complete__ = True¶
Whether model building is completed, or if there are still undefined fields.
- __pydantic_computed_fields__ = {}¶
A dictionary of computed field names and their corresponding [ComputedFieldInfo][pydantic.fields.ComputedFieldInfo] objects.
- __pydantic_core_schema__ = {'cls': <class 'aiida_gromacs.data.genion.GenionParameters.WriteModel'>, 'config': {'extra_fields_behavior': 'forbid', 'serialize_by_alias': True, 'title': 'GenionParametersWriteModel', 'validate_by_alias': True, 'validate_by_name': True}, 'custom_init': False, 'metadata': {'pydantic_js_functions': [<bound method BaseModel.__get_pydantic_json_schema__ of <class 'aiida_gromacs.data.genion.GenionParameters.WriteModel'>>]}, 'post_init': 'model_post_init', 'ref': 'aiida_gromacs.data.genion.GenionParameters.WriteModel:109607548464000', 'root_model': False, 'schema': {'computed_fields': [], 'fields': {'attributes': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'The node attributes', 'examples': [{'attr_key': 'attr_value'}]}}, 'schema': {'cls': <class 'aiida_gromacs.data.genion.GenionParameters.AttributesWriteModel'>, 'config': {'extra_fields_behavior': 'allow', 'serialize_by_alias': True, 'title': 'GenionParametersAttributesWriteModel', 'validate_by_alias': True, 'validate_by_name': True}, 'custom_init': False, 'metadata': {'pydantic_js_functions': [<bound method BaseModel.__get_pydantic_json_schema__ of <class 'aiida_gromacs.data.genion.GenionParameters.AttributesWriteModel'>>]}, 'post_init': 'model_post_init', 'ref': 'aiida_gromacs.data.genion.GenionParameters.AttributesWriteModel:109607548454768', 'root_model': False, 'schema': {'computed_fields': [], 'fields': {'source': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'Source of the data'}}, 'schema': {'default': None, 'schema': {'schema': {'keys_schema': {'type': 'any'}, 'type': 'dict', 'values_schema': {'type': 'any'}}, 'type': 'nullable'}, 'type': 'default'}, 'type': 'model-field'}}, 'model_name': 'AttributesWriteModel', 'type': 'model-fields'}, 'type': 'model'}, 'type': 'model-field'}, 'description': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'The node description', 'examples': ['This is my node description.']}}, 'schema': {'default': '', 'schema': {'type': 'str'}, 'type': 'default'}, 'type': 'model-field'}, 'extras': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'The node extras', 'examples': [{'extra_key': 'extra_value'}]}}, 'schema': {'default_factory': <class 'dict'>, 'default_factory_takes_data': False, 'schema': {'keys_schema': {'type': 'str'}, 'type': 'dict', 'values_schema': {'type': 'any'}}, 'type': 'default'}, 'type': 'model-field'}, 'label': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'The node label', 'examples': ['my_node']}}, 'schema': {'default': '', 'schema': {'type': 'str'}, 'type': 'default'}, 'type': 'model-field'}, 'node_type': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'The type of the node.'}}, 'schema': {'expected': ['data.gromacs.genion.GenionParameters.'], 'type': 'literal'}, 'type': 'model-field'}, 'repository_metadata': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'Virtual hierarchy of the file repository', 'examples': [{'o': {'file.txt': {'k': '<file_hash>'}}}]}}, 'schema': {'default_factory': <class 'dict'>, 'default_factory_takes_data': False, 'schema': {'keys_schema': {'type': 'str'}, 'type': 'dict', 'values_schema': {'type': 'any'}}, 'type': 'default'}, 'type': 'model-field'}}, 'model_name': 'WriteModel', 'type': 'model-fields'}, 'type': 'model'}¶
The core schema of the model.
- __pydantic_custom_init__ = False¶
Whether the model has a custom __init__ method.
- __pydantic_decorators__ = DecoratorInfos(validators={}, field_validators={}, root_validators={}, field_serializers={}, model_serializers={}, model_validators={}, computed_fields={})¶
Metadata containing the decorators defined on the model. This replaces Model.__validators__ and Model.__root_validators__ from Pydantic V1.
- __pydantic_extra__¶
A dictionary containing extra values, if [extra][pydantic.config.ConfigDict.extra] is set to ‘allow’.
- __pydantic_extra_info__ = None¶
A wrapper around the __pydantic_extra__ annotation, if explicitly annotated on a model.
This is a private attribute, not meant to be used outside Pydantic.
- __pydantic_fields__ = {'attributes': FieldInfo(annotation=GenionParameters.AttributesWriteModel, required=True, description='The node attributes', examples=[{'attr_key': 'attr_value'}], json_schema_extra={}, metadata=[{'priority': 0}, {'read_only': False}, {'write_only': False}, {'may_be_large': True}]), 'description': FieldInfo(annotation=str, required=False, default='', description='The node description', examples=['This is my node description.'], json_schema_extra={}, metadata=[{'priority': 0}, {'read_only': False}, {'write_only': False}, {'may_be_large': False}]), 'extras': FieldInfo(annotation=dict[str, Any], required=False, default_factory=dict, description='The node extras', examples=[{'extra_key': 'extra_value'}], json_schema_extra={}, metadata=[{'priority': 0}, {'read_only': False}, {'write_only': False}, {'may_be_large': True}, {'orm_to_model': <function Node.MutableNodeFields.<lambda>>}]), 'label': FieldInfo(annotation=str, required=False, default='', description='The node label', examples=['my_node'], json_schema_extra={}, metadata=[{'priority': 0}, {'read_only': False}, {'write_only': False}, {'may_be_large': False}]), 'node_type': FieldInfo(annotation=Literal['data.gromacs.genion.GenionParameters.'], required=True, description='The type of the node.', json_schema_extra={}, metadata=[{'priority': 0}, {'read_only': False}, {'write_only': False}, {'may_be_large': False}]), 'repository_metadata': FieldInfo(annotation=dict[str, Any], required=False, default_factory=dict, description='Virtual hierarchy of the file repository', examples=[{'o': {'file.txt': {'k': '<file_hash>'}}}], json_schema_extra={}, metadata=[{'priority': 0}, {'read_only': False}, {'write_only': False}, {'may_be_large': True}, {'orm_to_model': <function Node.WritableFields.<lambda>>}])}¶
A dictionary of field names and their corresponding [FieldInfo][pydantic.fields.FieldInfo] objects. This replaces Model.__fields__ from Pydantic V1.
- __pydantic_fields_set__¶
The names of fields explicitly set during instantiation.
- __pydantic_generic_metadata__ = {'args': (), 'origin': None, 'parameters': ()}¶
A dictionary containing metadata about generic Pydantic models.
The origin and args items map to the [__origin__][genericalias.__origin__] and [__args__][genericalias.__args__] attributes of [generic aliases][types-genericalias], and the parameter item maps to the __parameter__ attribute of generic classes.
- __pydantic_post_init__ = 'model_post_init'¶
The name of the post-init method for the model, if defined.
- __pydantic_private__¶
Values of private attributes set on the model instance.
- __pydantic_serializer__ = SchemaSerializer(serializer=PolymorphismTrampoline( PolymorphismTrampoline { class: Py( 0x000063affefdab80, ), serializer: PolymorphismTrampoline( PolymorphismTrampoline { class: Py( 0x000063affefdab80, ), serializer: Model( ModelSerializer { class: Py( 0x000063affefdab80, ), serializer: Fields( GeneralFieldsSerializer { fields: { "description": SerField { key: "description", alias: None, serializer: Some( WithDefault( WithDefaultSerializer { default: Default( Py( 0x00007310e7482e40, ), ), serializer: Str( StrSerializer, ), }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "extras": SerField { key: "extras", alias: None, serializer: Some( WithDefault( WithDefaultSerializer { default: DefaultFactory( Py( 0x00007310e74524a0, ), false, ), serializer: Dict( DictSerializer { key_serializer: Str( StrSerializer, ), value_serializer: Any( AnySerializer, ), filter: SchemaFilter { include: None, exclude: None, }, name: "dict[str, any]", }, ), }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "node_type": SerField { key: "node_type", alias: None, serializer: Some( Literal( LiteralSerializer { expected_int: {}, expected_str: { "data.gromacs.genion.GenionParameters.", }, expected_py: None, name: "literal['data.gromacs.genion.GenionParameters.']", }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "repository_metadata": SerField { key: "repository_metadata", alias: None, serializer: Some( WithDefault( WithDefaultSerializer { default: DefaultFactory( Py( 0x00007310e74524a0, ), false, ), serializer: Dict( DictSerializer { key_serializer: Str( StrSerializer, ), value_serializer: Any( AnySerializer, ), filter: SchemaFilter { include: None, exclude: None, }, name: "dict[str, any]", }, ), }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "attributes": SerField { key: "attributes", alias: None, serializer: Some( PolymorphismTrampoline( PolymorphismTrampoline { class: Py( 0x000063affefd8770, ), serializer: PolymorphismTrampoline( PolymorphismTrampoline { class: Py( 0x000063affefd8770, ), serializer: Model( ModelSerializer { class: Py( 0x000063affefd8770, ), serializer: Fields( GeneralFieldsSerializer { fields: { "source": SerField { key: "source", alias: None, serializer: Some( WithDefault( WithDefaultSerializer { default: Default( Py( 0x00007310e7455800, ), ), serializer: Nullable( NullableSerializer { serializer: Dict( DictSerializer { key_serializer: Any( AnySerializer, ), value_serializer: Any( AnySerializer, ), filter: SchemaFilter { include: None, exclude: None, }, name: "dict[any, any]", }, ), }, ), }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, }, computed_fields: Some( ComputedFields( [], ), ), mode: ModelExtra, extra_serializer: None, filter: SchemaFilter { include: None, exclude: None, }, required_fields: 1, }, ), has_extra: true, root_model: false, name: "AttributesWriteModel", }, ), enabled_from_config: false, }, ), enabled_from_config: false, }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "label": SerField { key: "label", alias: None, serializer: Some( WithDefault( WithDefaultSerializer { default: Default( Py( 0x00007310e7482e40, ), ), serializer: Str( StrSerializer, ), }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, }, computed_fields: Some( ComputedFields( [], ), ), mode: SimpleDict, extra_serializer: None, filter: SchemaFilter { include: None, exclude: None, }, required_fields: 6, }, ), has_extra: false, root_model: false, name: "WriteModel", }, ), enabled_from_config: false, }, ), enabled_from_config: false, }, ), definitions=[])¶
The pydantic-core SchemaSerializer used to dump instances of the model.
- __pydantic_setattr_handlers__ = {}¶
__setattr__ handlers. Memoizing the handlers leads to a dramatic performance improvement in __setattr__
- __pydantic_validator__ = SchemaValidator(title="GenionParametersWriteModel", validator=Model( ModelValidator { revalidate: Never, validator: ModelFields( ModelFieldsValidator { fields: [ Field { name: "label", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "label", ), rest: [], }, by_alias: [], }, validator: WithDefault( WithDefaultValidator { default: Default( Py( 0x00007310e7482e40, ), ), on_error: Raise, validator: Str( StrValidator { strict: false, coerce_numbers_to_str: false, }, ), validate_default: false, copy_default: false, name: "default[str]", undefined: Py( 0x00007310e53bdb90, ), }, ), frozen: false, }, Field { name: "description", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "description", ), rest: [], }, by_alias: [], }, validator: WithDefault( WithDefaultValidator { default: Default( Py( 0x00007310e7482e40, ), ), on_error: Raise, validator: Str( StrValidator { strict: false, coerce_numbers_to_str: false, }, ), validate_default: false, copy_default: false, name: "default[str]", undefined: Py( 0x00007310e53bdb90, ), }, ), frozen: false, }, Field { name: "extras", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "extras", ), rest: [], }, by_alias: [], }, validator: WithDefault( WithDefaultValidator { default: DefaultFactory( Py( 0x00007310e74524a0, ), false, ), on_error: Raise, validator: Dict( DictValidator { strict: false, key_validator: Str( StrValidator { strict: false, coerce_numbers_to_str: false, }, ), value_validator: Any( AnyValidator, ), min_length: None, max_length: None, fail_fast: false, name: "dict[str,any]", }, ), validate_default: false, copy_default: false, name: "default[dict[str,any]]", undefined: Py( 0x00007310e53bdb90, ), }, ), frozen: false, }, Field { name: "node_type", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "node_type", ), rest: [], }, by_alias: [], }, validator: Literal( LiteralValidator { lookup: LiteralLookup { expected_bool: None, expected_int: None, expected_str: Some( { "data.gromacs.genion.GenionParameters.": 0, }, ), expected_py_dict: None, expected_py_values: None, expected_py_primitives: Some( Py( 0x00007310d2c5eb80, ), ), values: [ Py( 0x00007310d30c32d0, ), ], }, expected_repr: "'data.gromacs.genion.GenionParameters.'", name: "literal['data.gromacs.genion.GenionParameters.']", }, ), frozen: false, }, Field { name: "attributes", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "attributes", ), rest: [], }, by_alias: [], }, validator: Model( ModelValidator { revalidate: Never, validator: ModelFields( ModelFieldsValidator { fields: [ Field { name: "source", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "source", ), rest: [], }, by_alias: [], }, validator: WithDefault( WithDefaultValidator { default: Default( Py( 0x00007310e7455800, ), ), on_error: Raise, validator: Nullable( NullableValidator { validator: Dict( DictValidator { strict: false, key_validator: Any( AnyValidator, ), value_validator: Any( AnyValidator, ), min_length: None, max_length: None, fail_fast: false, name: "dict[any,any]", }, ), name: "nullable[dict[any,any]]", }, ), validate_default: false, copy_default: false, name: "default[nullable[dict[any,any]]]", undefined: Py( 0x00007310e53bdb90, ), }, ), frozen: false, }, ], model_name: "AttributesWriteModel", extra_behavior: Allow, extras_validator: None, extras_keys_validator: None, strict: false, from_attributes: false, loc_by_alias: true, lookup: LookupTree { inner: { PathItemString( "source", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 0, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, }, }, validate_by_alias: Some( true, ), validate_by_name: Some( true, ), }, ), class: Py( 0x000063affefd8770, ), generic_origin: None, post_init: Some( Py( 0x00007310e2571630, ), ), frozen: false, custom_init: false, root_model: false, undefined: Py( 0x00007310e53bdb90, ), name: "AttributesWriteModel", }, ), frozen: false, }, Field { name: "repository_metadata", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "repository_metadata", ), rest: [], }, by_alias: [], }, validator: WithDefault( WithDefaultValidator { default: DefaultFactory( Py( 0x00007310e74524a0, ), false, ), on_error: Raise, validator: Dict( DictValidator { strict: false, key_validator: Str( StrValidator { strict: false, coerce_numbers_to_str: false, }, ), value_validator: Any( AnyValidator, ), min_length: None, max_length: None, fail_fast: false, name: "dict[str,any]", }, ), validate_default: false, copy_default: false, name: "default[dict[str,any]]", undefined: Py( 0x00007310e53bdb90, ), }, ), frozen: false, }, ], model_name: "WriteModel", extra_behavior: Forbid, extras_validator: None, extras_keys_validator: None, strict: false, from_attributes: false, loc_by_alias: true, lookup: LookupTree { inner: { PathItemString( "label", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 0, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "extras", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 2, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "attributes", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 4, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "repository_metadata", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 5, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "node_type", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 3, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "description", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 1, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, }, }, validate_by_alias: Some( true, ), validate_by_name: Some( true, ), }, ), class: Py( 0x000063affefdab80, ), generic_origin: None, post_init: Some( Py( 0x00007310e2571630, ), ), frozen: false, custom_init: false, root_model: false, undefined: Py( 0x00007310e53bdb90, ), name: "WriteModel", }, ), definitions=[], cache_strings=True)¶
The pydantic-core SchemaValidator used to validate instances of the model.
- _abc_impl = <_abc._abc_data object>¶
- attributes: AttributesWriteModel¶
- model_config = {'defer_build': True, 'extra': 'forbid', 'json_encoders': {<class 'datetime.datetime'>: <function OrmModel.<lambda>>}, 'serialize_by_alias': True, 'title': 'GenionParametersWriteModel', 'validate_by_alias': True, 'validate_by_name': True}¶
Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].
- _COMPAT_MODEL¶
alias of
Model
- _ConstructorModel¶
alias of
ConstructorModel
- _MODEL_MAP = {'read': <class 'aiida_gromacs.data.genion.GenionParameters.ReadModel'>, 'write': <class 'aiida_gromacs.data.genion.GenionParameters.WriteModel'>}¶
- __abstractmethods__ = frozenset({})¶
- __annotations__ = {}¶
- __firstlineno__ = 28¶
- __init__(dict=None, **kwargs)[source]¶
Constructor for the data class
Usage:
GenionParameters(dict{'ignore-case': True})- Parameters:
parameters_dict (type) – dictionary with commandline parameters
parameters_dict – dict
- __module__ = 'aiida_gromacs.data.genion'¶
- __parameters__ = ()¶
- __static_attributes__ = ()¶
- __str__()[source]¶
String representation of node.
Append values of dictionary to usual representation. E.g.:
uuid: b416cbee-24e8-47a8-8c11-6d668770158b (pk: 590) {'ignore-case': True}
- _abc_impl = <_abc._abc_data object>¶
- _logger = <Logger aiida_gromacs.data.genion.GenionParameters (WARNING)>¶
- cmdline_params(input_files)[source]¶
Synthesize command line parameters.
e.g. [ ‘–ignore-case’, ‘filename1’, ‘filename2’]
- Parameters:
pdbfile (type) – Name of input pdb file
pdbfile – str
- fields = {'attributes': "QbAttributesField('attributes', dtype=<class 'aiida_gromacs.data.genion.GenionParameters.AttributesModel'>, doc='The node attributes')", 'computer': "QbNumericField('computer', dtype=int | None, doc='The PK of the computer')", 'ctime': "QbNumericField('ctime', dtype=<class 'datetime.datetime'>, doc='The creation time of the node')", 'description': "QbStrField('description', dtype=<class 'str'>, doc='The node description')", 'extras': "QbDictField('extras', dtype=dict[str, typing.Any], doc='The node extras')", 'label': "QbStrField('label', dtype=<class 'str'>, doc='The node label')", 'mtime': "QbNumericField('mtime', dtype=<class 'datetime.datetime'>, doc='The modification time of the node')", 'node_type': "QbStrField('node_type', dtype=typing.Literal['data.gromacs.genion.GenionParameters.'], doc='The type of the node.')", 'pk': "QbNumericField('pk', dtype=<class 'int'>, doc='The primary key of the entity')", 'process_type': "QbStrField('process_type', dtype=str | None, doc='The process type of the node')", 'repository_metadata': "QbDictField('repository_metadata', dtype=dict[str, typing.Any], doc='Virtual hierarchy of the file repository')", 'source': "QbDictField('attributes.source', dtype=dict | None, doc='Source of the data')", 'user': "QbNumericField('user', dtype=<class 'int'>, doc='The PK of the user who owns the node')", 'uuid': "QbStrField('uuid', dtype=<class 'uuid.UUID'>, doc='The UUID of the node')"}¶
- schema = <Schema({'o': <class 'str'>, 'np': <class 'str'>, 'pname': <class 'str'>, 'pq': <class 'str'>, 'nn': <class 'str'>, 'nname': <class 'str'>, 'nq': <class 'str'>, 'rmin': <class 'str'>, 'seed': <class 'str'>, 'conc': <class 'str'>, 'neutral': <class 'str'>}, extra=PREVENT_EXTRA, required=False) object>¶
- validate(parameters_dict)[source]¶
Validate command line options.
Uses the voluptuous package for validation. Find out about allowed keys using:
print(GenionParameters).schema.schema
- Parameters:
parameters_dict (type) – dictionary with commandline parameters
parameters_dict – dict
- Returns:
validated dictionary
aiida_gromacs.data.grompp module¶
Data types provided by plugin
Register data types via the “aiida.data” entry point in setup.json.
- class aiida_gromacs.data.grompp.GromppParameters(dict=None, **kwargs)[source]¶
Bases:
DictCommand line options for diff.
This class represents a python dictionary used to pass command line options to the executable.
- class AttributesModel(**data: Any)¶
Bases:
AttributesModel- __abstractmethods__ = frozenset({})¶
- __annotations__ = {}¶
- __class_vars__ = {}¶
The names of the class variables defined on the model.
- __dict__¶
- __module__ = 'aiida_gromacs.data.grompp'¶
- __private_attributes__ = {'_AIIDA_MINIMAL_MODEL': ModelPrivateAttr()}¶
Metadata about the private attributes of the model.
- __pydantic_complete__ = True¶
Whether model building is completed, or if there are still undefined fields.
- __pydantic_computed_fields__ = {}¶
A dictionary of computed field names and their corresponding [ComputedFieldInfo][pydantic.fields.ComputedFieldInfo] objects.
- __pydantic_core_schema__ = {'cls': <class 'aiida_gromacs.data.grompp.GromppParameters.AttributesModel'>, 'config': {'extra_fields_behavior': 'allow', 'serialize_by_alias': True, 'title': 'GromppParametersAttributesModel', 'validate_by_alias': True, 'validate_by_name': True}, 'custom_init': False, 'metadata': {'pydantic_js_functions': [<bound method BaseModel.__get_pydantic_json_schema__ of <class 'aiida_gromacs.data.grompp.GromppParameters.AttributesModel'>>]}, 'post_init': 'model_post_init', 'ref': 'aiida_gromacs.data.grompp.GromppParameters.AttributesModel:109607548451488', 'root_model': False, 'schema': {'computed_fields': [], 'fields': {'source': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'Source of the data'}}, 'schema': {'default': None, 'schema': {'schema': {'keys_schema': {'type': 'any'}, 'type': 'dict', 'values_schema': {'type': 'any'}}, 'type': 'nullable'}, 'type': 'default'}, 'type': 'model-field'}}, 'model_name': 'AttributesModel', 'type': 'model-fields'}, 'type': 'model'}¶
The core schema of the model.
- __pydantic_custom_init__ = False¶
Whether the model has a custom __init__ method.
- __pydantic_decorators__ = DecoratorInfos(validators={}, field_validators={}, root_validators={}, field_serializers={}, model_serializers={}, model_validators={}, computed_fields={})¶
Metadata containing the decorators defined on the model. This replaces Model.__validators__ and Model.__root_validators__ from Pydantic V1.
- __pydantic_extra__¶
A dictionary containing extra values, if [extra][pydantic.config.ConfigDict.extra] is set to ‘allow’.
- __pydantic_extra_info__ = None¶
A wrapper around the __pydantic_extra__ annotation, if explicitly annotated on a model.
This is a private attribute, not meant to be used outside Pydantic.
- __pydantic_fields__ = {'source': FieldInfo(annotation=Union[dict, NoneType], required=False, default=None, description='Source of the data', json_schema_extra={}, metadata=[{'priority': 0}, {'read_only': False}, {'write_only': False}, {'may_be_large': False}])}¶
A dictionary of field names and their corresponding [FieldInfo][pydantic.fields.FieldInfo] objects. This replaces Model.__fields__ from Pydantic V1.
- __pydantic_fields_set__¶
The names of fields explicitly set during instantiation.
- __pydantic_generic_metadata__ = {'args': (), 'origin': None, 'parameters': ()}¶
A dictionary containing metadata about generic Pydantic models.
The origin and args items map to the [__origin__][genericalias.__origin__] and [__args__][genericalias.__args__] attributes of [generic aliases][types-genericalias], and the parameter item maps to the __parameter__ attribute of generic classes.
- __pydantic_post_init__ = 'model_post_init'¶
The name of the post-init method for the model, if defined.
- __pydantic_private__¶
Values of private attributes set on the model instance.
- __pydantic_serializer__ = SchemaSerializer(serializer=PolymorphismTrampoline( PolymorphismTrampoline { class: Py( 0x000063affefd7aa0, ), serializer: PolymorphismTrampoline( PolymorphismTrampoline { class: Py( 0x000063affefd7aa0, ), serializer: Model( ModelSerializer { class: Py( 0x000063affefd7aa0, ), serializer: Fields( GeneralFieldsSerializer { fields: { "source": SerField { key: "source", alias: None, serializer: Some( WithDefault( WithDefaultSerializer { default: Default( Py( 0x00007310e7455800, ), ), serializer: Nullable( NullableSerializer { serializer: Dict( DictSerializer { key_serializer: Any( AnySerializer, ), value_serializer: Any( AnySerializer, ), filter: SchemaFilter { include: None, exclude: None, }, name: "dict[any, any]", }, ), }, ), }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, }, computed_fields: Some( ComputedFields( [], ), ), mode: ModelExtra, extra_serializer: None, filter: SchemaFilter { include: None, exclude: None, }, required_fields: 1, }, ), has_extra: true, root_model: false, name: "AttributesModel", }, ), enabled_from_config: false, }, ), enabled_from_config: false, }, ), definitions=[])¶
The pydantic-core SchemaSerializer used to dump instances of the model.
- __pydantic_setattr_handlers__ = {}¶
__setattr__ handlers. Memoizing the handlers leads to a dramatic performance improvement in __setattr__
- __pydantic_validator__ = SchemaValidator(title="GromppParametersAttributesModel", validator=Model( ModelValidator { revalidate: Never, validator: ModelFields( ModelFieldsValidator { fields: [ Field { name: "source", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "source", ), rest: [], }, by_alias: [], }, validator: WithDefault( WithDefaultValidator { default: Default( Py( 0x00007310e7455800, ), ), on_error: Raise, validator: Nullable( NullableValidator { validator: Dict( DictValidator { strict: false, key_validator: Any( AnyValidator, ), value_validator: Any( AnyValidator, ), min_length: None, max_length: None, fail_fast: false, name: "dict[any,any]", }, ), name: "nullable[dict[any,any]]", }, ), validate_default: false, copy_default: false, name: "default[nullable[dict[any,any]]]", undefined: Py( 0x00007310e53bdb90, ), }, ), frozen: false, }, ], model_name: "AttributesModel", extra_behavior: Allow, extras_validator: None, extras_keys_validator: None, strict: false, from_attributes: false, loc_by_alias: true, lookup: LookupTree { inner: { PathItemString( "source", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 0, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, }, }, validate_by_alias: Some( true, ), validate_by_name: Some( true, ), }, ), class: Py( 0x000063affefd7aa0, ), generic_origin: None, post_init: Some( Py( 0x00007310e2571630, ), ), frozen: false, custom_init: false, root_model: false, undefined: Py( 0x00007310e53bdb90, ), name: "AttributesModel", }, ), definitions=[], cache_strings=True)¶
The pydantic-core SchemaValidator used to validate instances of the model.
- _abc_impl = <_abc._abc_data object>¶
- model_config = {'arbitrary_types_allowed': True, 'defer_build': True, 'extra': 'allow', 'json_encoders': {<class 'datetime.datetime'>: <function OrmModel.<lambda>>}, 'serialize_by_alias': True, 'title': 'GromppParametersAttributesModel', 'validate_by_alias': True, 'validate_by_name': True}¶
Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].
- class ReadModel(**data: Any)¶
Bases:
ReadModel- __abstractmethods__ = frozenset({})¶
- __annotations__ = {'attributes': <class 'aiida_gromacs.data.grompp.GromppParameters.AttributesModel'>, 'node_type': typing.Literal['data.gromacs.grompp.GromppParameters.']}¶
- __class_vars__ = {}¶
The names of the class variables defined on the model.
- __dict__¶
- __module__ = 'aiida_gromacs.data.grompp'¶
- __private_attributes__ = {'_AIIDA_MINIMAL_MODEL': ModelPrivateAttr()}¶
Metadata about the private attributes of the model.
- __pydantic_complete__ = True¶
Whether model building is completed, or if there are still undefined fields.
- __pydantic_computed_fields__ = {}¶
A dictionary of computed field names and their corresponding [ComputedFieldInfo][pydantic.fields.ComputedFieldInfo] objects.
- __pydantic_core_schema__ = {'cls': <class 'aiida_gromacs.data.grompp.GromppParameters.ReadModel'>, 'config': {'extra_fields_behavior': 'forbid', 'serialize_by_alias': True, 'title': 'GromppParametersReadModel', 'validate_by_alias': True, 'validate_by_name': True}, 'custom_init': False, 'metadata': {'pydantic_js_functions': [<bound method BaseModel.__get_pydantic_json_schema__ of <class 'aiida_gromacs.data.grompp.GromppParameters.ReadModel'>>]}, 'post_init': 'model_post_init', 'ref': 'aiida_gromacs.data.grompp.GromppParameters.ReadModel:109607548480704', 'root_model': False, 'schema': {'computed_fields': [], 'fields': {'attributes': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'The node attributes', 'examples': [{'attr_key': 'attr_value'}]}}, 'schema': {'cls': <class 'aiida_gromacs.data.grompp.GromppParameters.AttributesModel'>, 'config': {'extra_fields_behavior': 'allow', 'serialize_by_alias': True, 'title': 'GromppParametersAttributesModel', 'validate_by_alias': True, 'validate_by_name': True}, 'custom_init': False, 'metadata': {'pydantic_js_functions': [<bound method BaseModel.__get_pydantic_json_schema__ of <class 'aiida_gromacs.data.grompp.GromppParameters.AttributesModel'>>]}, 'post_init': 'model_post_init', 'ref': 'aiida_gromacs.data.grompp.GromppParameters.AttributesModel:109607548451488', 'root_model': False, 'schema': {'computed_fields': [], 'fields': {'source': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'Source of the data'}}, 'schema': {'default': None, 'schema': {'schema': {'keys_schema': {'type': 'any'}, 'type': 'dict', 'values_schema': {'type': 'any'}}, 'type': 'nullable'}, 'type': 'default'}, 'type': 'model-field'}}, 'model_name': 'AttributesModel', 'type': 'model-fields'}, 'type': 'model'}, 'type': 'model-field'}, 'computer': {'metadata': {'pydantic_js_extra': {'readOnly': True}, 'pydantic_js_updates': {'description': 'The PK of the computer', 'examples': [42]}}, 'schema': {'default': None, 'schema': {'schema': {'type': 'int'}, 'type': 'nullable'}, 'type': 'default'}, 'type': 'model-field'}, 'ctime': {'metadata': {'pydantic_js_extra': {'readOnly': True}, 'pydantic_js_updates': {'description': 'The creation time of the node', 'examples': ['2024-01-01T12:00:00+00:00']}}, 'schema': {'microseconds_precision': 'truncate', 'serialization': {'function': <function OrmModel.<lambda>>, 'type': 'function-plain', 'when_used': 'json'}, 'type': 'datetime'}, 'type': 'model-field'}, 'description': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'The node description', 'examples': ['This is my node description.']}}, 'schema': {'default': '', 'schema': {'type': 'str'}, 'type': 'default'}, 'type': 'model-field'}, 'extras': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'The node extras', 'examples': [{'extra_key': 'extra_value'}]}}, 'schema': {'default_factory': <class 'dict'>, 'default_factory_takes_data': False, 'schema': {'keys_schema': {'type': 'str'}, 'type': 'dict', 'values_schema': {'type': 'any'}}, 'type': 'default'}, 'type': 'model-field'}, 'label': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'The node label', 'examples': ['my_node']}}, 'schema': {'default': '', 'schema': {'type': 'str'}, 'type': 'default'}, 'type': 'model-field'}, 'mtime': {'metadata': {'pydantic_js_extra': {'readOnly': True}, 'pydantic_js_updates': {'description': 'The modification time of the node', 'examples': ['2024-01-02T12:00:00+00:00']}}, 'schema': {'microseconds_precision': 'truncate', 'serialization': {'function': <function OrmModel.<lambda>>, 'type': 'function-plain', 'when_used': 'json'}, 'type': 'datetime'}, 'type': 'model-field'}, 'node_type': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'The type of the node.'}}, 'schema': {'expected': ['data.gromacs.grompp.GromppParameters.'], 'type': 'literal'}, 'type': 'model-field'}, 'pk': {'metadata': {'pydantic_js_extra': {'readOnly': True}, 'pydantic_js_updates': {'description': 'The primary key of the entity', 'examples': [42]}}, 'schema': {'type': 'int'}, 'type': 'model-field'}, 'process_type': {'metadata': {'pydantic_js_extra': {'readOnly': True}, 'pydantic_js_updates': {'description': 'The process type of the node', 'examples': ['aiida.calculations:arithmetic.add.']}}, 'schema': {'default': None, 'schema': {'schema': {'type': 'str'}, 'type': 'nullable'}, 'type': 'default'}, 'type': 'model-field'}, 'repository_metadata': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'Virtual hierarchy of the file repository', 'examples': [{'o': {'file.txt': {'k': '<file_hash>'}}}]}}, 'schema': {'default_factory': <class 'dict'>, 'default_factory_takes_data': False, 'schema': {'keys_schema': {'type': 'str'}, 'type': 'dict', 'values_schema': {'type': 'any'}}, 'type': 'default'}, 'type': 'model-field'}, 'user': {'metadata': {'pydantic_js_extra': {'readOnly': True}, 'pydantic_js_updates': {'description': 'The PK of the user who owns the node', 'examples': [7]}}, 'schema': {'type': 'int'}, 'type': 'model-field'}, 'uuid': {'metadata': {'pydantic_js_extra': {'readOnly': True}, 'pydantic_js_updates': {'description': 'The UUID of the node', 'examples': ['123e4567-e89b-12d3-a456-426614174000']}}, 'schema': {'type': 'uuid'}, 'type': 'model-field'}}, 'model_name': 'ReadModel', 'type': 'model-fields'}, 'type': 'model'}¶
The core schema of the model.
- __pydantic_custom_init__ = False¶
Whether the model has a custom __init__ method.
- __pydantic_decorators__ = DecoratorInfos(validators={}, field_validators={}, root_validators={}, field_serializers={}, model_serializers={}, model_validators={}, computed_fields={})¶
Metadata containing the decorators defined on the model. This replaces Model.__validators__ and Model.__root_validators__ from Pydantic V1.
- __pydantic_extra__¶
A dictionary containing extra values, if [extra][pydantic.config.ConfigDict.extra] is set to ‘allow’.
- __pydantic_extra_info__ = None¶
A wrapper around the __pydantic_extra__ annotation, if explicitly annotated on a model.
This is a private attribute, not meant to be used outside Pydantic.
- __pydantic_fields__ = {'attributes': FieldInfo(annotation=GromppParameters.AttributesModel, required=True, description='The node attributes', examples=[{'attr_key': 'attr_value'}], json_schema_extra={}, metadata=[{'priority': 0}, {'read_only': False}, {'write_only': False}, {'may_be_large': True}]), 'computer': FieldInfo(annotation=Union[int, NoneType], required=False, default=None, description='The PK of the computer', examples=[42], json_schema_extra={'readOnly': True}, metadata=[{'priority': 0}, {'read_only': True}, {'write_only': False}, {'may_be_large': False}, {'orm_class': <class 'aiida.orm.computers.Computer'>}, {'orm_to_model': <function Node.ReadModel.<lambda>>}]), 'ctime': FieldInfo(annotation=datetime, required=True, description='The creation time of the node', examples=['2024-01-01T12:00:00+00:00'], json_schema_extra={'readOnly': True}, metadata=[{'priority': 0}, {'read_only': True}, {'write_only': False}, {'may_be_large': False}]), 'description': FieldInfo(annotation=str, required=False, default='', description='The node description', examples=['This is my node description.'], json_schema_extra={}, metadata=[{'priority': 0}, {'read_only': False}, {'write_only': False}, {'may_be_large': False}]), 'extras': FieldInfo(annotation=dict[str, Any], required=False, default_factory=dict, description='The node extras', examples=[{'extra_key': 'extra_value'}], json_schema_extra={}, metadata=[{'priority': 0}, {'read_only': False}, {'write_only': False}, {'may_be_large': True}, {'orm_to_model': <function Node.MutableNodeFields.<lambda>>}]), 'label': FieldInfo(annotation=str, required=False, default='', description='The node label', examples=['my_node'], json_schema_extra={}, metadata=[{'priority': 0}, {'read_only': False}, {'write_only': False}, {'may_be_large': False}]), 'mtime': FieldInfo(annotation=datetime, required=True, description='The modification time of the node', examples=['2024-01-02T12:00:00+00:00'], json_schema_extra={'readOnly': True}, metadata=[{'priority': 0}, {'read_only': True}, {'write_only': False}, {'may_be_large': False}]), 'node_type': FieldInfo(annotation=Literal['data.gromacs.grompp.GromppParameters.'], required=True, description='The type of the node.', json_schema_extra={}, metadata=[{'priority': 0}, {'read_only': False}, {'write_only': False}, {'may_be_large': False}]), 'pk': FieldInfo(annotation=int, required=True, description='The primary key of the entity', examples=[42], json_schema_extra={'readOnly': True}, metadata=[{'priority': 0}, {'read_only': True}, {'write_only': False}, {'may_be_large': False}]), 'process_type': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, description='The process type of the node', examples=['aiida.calculations:arithmetic.add.'], json_schema_extra={'readOnly': True}, metadata=[{'priority': 0}, {'read_only': True}, {'write_only': False}, {'may_be_large': False}]), 'repository_metadata': FieldInfo(annotation=dict[str, Any], required=False, default_factory=dict, description='Virtual hierarchy of the file repository', examples=[{'o': {'file.txt': {'k': '<file_hash>'}}}], json_schema_extra={}, metadata=[{'priority': 0}, {'read_only': False}, {'write_only': False}, {'may_be_large': True}, {'orm_to_model': <function Node.WritableFields.<lambda>>}]), 'user': FieldInfo(annotation=int, required=True, description='The PK of the user who owns the node', examples=[7], json_schema_extra={'readOnly': True}, metadata=[{'priority': 0}, {'read_only': True}, {'write_only': False}, {'may_be_large': False}, {'orm_class': <class 'aiida.orm.users.User'>}, {'orm_to_model': <function Node.ReadModel.<lambda>>}]), 'uuid': FieldInfo(annotation=UUID, required=True, description='The UUID of the node', examples=['123e4567-e89b-12d3-a456-426614174000'], json_schema_extra={'readOnly': True}, metadata=[{'priority': 0}, {'read_only': True}, {'write_only': False}, {'may_be_large': False}])}¶
A dictionary of field names and their corresponding [FieldInfo][pydantic.fields.FieldInfo] objects. This replaces Model.__fields__ from Pydantic V1.
- __pydantic_fields_set__¶
The names of fields explicitly set during instantiation.
- __pydantic_generic_metadata__ = {'args': (), 'origin': None, 'parameters': ()}¶
A dictionary containing metadata about generic Pydantic models.
The origin and args items map to the [__origin__][genericalias.__origin__] and [__args__][genericalias.__args__] attributes of [generic aliases][types-genericalias], and the parameter item maps to the __parameter__ attribute of generic classes.
- __pydantic_post_init__ = 'model_post_init'¶
The name of the post-init method for the model, if defined.
- __pydantic_private__¶
Values of private attributes set on the model instance.
- __pydantic_serializer__ = SchemaSerializer(serializer=PolymorphismTrampoline( PolymorphismTrampoline { class: Py( 0x000063affefdecc0, ), serializer: PolymorphismTrampoline( PolymorphismTrampoline { class: Py( 0x000063affefdecc0, ), serializer: Model( ModelSerializer { class: Py( 0x000063affefdecc0, ), serializer: Fields( GeneralFieldsSerializer { fields: { "computer": SerField { key: "computer", alias: None, serializer: Some( WithDefault( WithDefaultSerializer { default: Default( Py( 0x00007310e7455800, ), ), serializer: Nullable( NullableSerializer { serializer: Int( IntSerializer, ), }, ), }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "mtime": SerField { key: "mtime", alias: None, serializer: Some( Function( FunctionPlainSerializer { func: Py( 0x00007310e2355c60, ), name: "plain_function[<lambda>]", function_name: "<lambda>", return_serializer: Any( AnySerializer, ), fallback_serializer: Some( Datetime( DatetimeSerializer { temporal_mode: Iso8601, }, ), ), when_used: Json, is_field_serializer: false, info_arg: false, }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "attributes": SerField { key: "attributes", alias: None, serializer: Some( PolymorphismTrampoline( PolymorphismTrampoline { class: Py( 0x000063affefd7aa0, ), serializer: Prebuilt( PrebuiltSerializer { schema_serializer: Py( 0x00007310d2a28280, ), }, ), enabled_from_config: false, }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "user": SerField { key: "user", alias: None, serializer: Some( Int( IntSerializer, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "ctime": SerField { key: "ctime", alias: None, serializer: Some( Function( FunctionPlainSerializer { func: Py( 0x00007310e2355c60, ), name: "plain_function[<lambda>]", function_name: "<lambda>", return_serializer: Any( AnySerializer, ), fallback_serializer: Some( Datetime( DatetimeSerializer { temporal_mode: Iso8601, }, ), ), when_used: Json, is_field_serializer: false, info_arg: false, }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "description": SerField { key: "description", alias: None, serializer: Some( WithDefault( WithDefaultSerializer { default: Default( Py( 0x00007310e7482e40, ), ), serializer: Str( StrSerializer, ), }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "pk": SerField { key: "pk", alias: None, serializer: Some( Int( IntSerializer, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "label": SerField { key: "label", alias: None, serializer: Some( WithDefault( WithDefaultSerializer { default: Default( Py( 0x00007310e7482e40, ), ), serializer: Str( StrSerializer, ), }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "extras": SerField { key: "extras", alias: None, serializer: Some( WithDefault( WithDefaultSerializer { default: DefaultFactory( Py( 0x00007310e74524a0, ), false, ), serializer: Dict( DictSerializer { key_serializer: Str( StrSerializer, ), value_serializer: Any( AnySerializer, ), filter: SchemaFilter { include: None, exclude: None, }, name: "dict[str, any]", }, ), }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "node_type": SerField { key: "node_type", alias: None, serializer: Some( Literal( LiteralSerializer { expected_int: {}, expected_str: { "data.gromacs.grompp.GromppParameters.", }, expected_py: None, name: "literal['data.gromacs.grompp.GromppParameters.']", }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "repository_metadata": SerField { key: "repository_metadata", alias: None, serializer: Some( WithDefault( WithDefaultSerializer { default: DefaultFactory( Py( 0x00007310e74524a0, ), false, ), serializer: Dict( DictSerializer { key_serializer: Str( StrSerializer, ), value_serializer: Any( AnySerializer, ), filter: SchemaFilter { include: None, exclude: None, }, name: "dict[str, any]", }, ), }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "uuid": SerField { key: "uuid", alias: None, serializer: Some( Uuid( UuidSerializer, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "process_type": SerField { key: "process_type", alias: None, serializer: Some( WithDefault( WithDefaultSerializer { default: Default( Py( 0x00007310e7455800, ), ), serializer: Nullable( NullableSerializer { serializer: Str( StrSerializer, ), }, ), }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, }, computed_fields: Some( ComputedFields( [], ), ), mode: SimpleDict, extra_serializer: None, filter: SchemaFilter { include: None, exclude: None, }, required_fields: 13, }, ), has_extra: false, root_model: false, name: "ReadModel", }, ), enabled_from_config: false, }, ), enabled_from_config: false, }, ), definitions=[])¶
The pydantic-core SchemaSerializer used to dump instances of the model.
- __pydantic_setattr_handlers__ = {}¶
__setattr__ handlers. Memoizing the handlers leads to a dramatic performance improvement in __setattr__
- __pydantic_validator__ = SchemaValidator(title="GromppParametersReadModel", validator=Model( ModelValidator { revalidate: Never, validator: ModelFields( ModelFieldsValidator { fields: [ Field { name: "pk", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "pk", ), rest: [], }, by_alias: [], }, validator: Int( IntValidator { strict: false, }, ), frozen: false, }, Field { name: "label", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "label", ), rest: [], }, by_alias: [], }, validator: WithDefault( WithDefaultValidator { default: Default( Py( 0x00007310e7482e40, ), ), on_error: Raise, validator: Str( StrValidator { strict: false, coerce_numbers_to_str: false, }, ), validate_default: false, copy_default: false, name: "default[str]", undefined: Py( 0x00007310e53bdb90, ), }, ), frozen: false, }, Field { name: "description", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "description", ), rest: [], }, by_alias: [], }, validator: WithDefault( WithDefaultValidator { default: Default( Py( 0x00007310e7482e40, ), ), on_error: Raise, validator: Str( StrValidator { strict: false, coerce_numbers_to_str: false, }, ), validate_default: false, copy_default: false, name: "default[str]", undefined: Py( 0x00007310e53bdb90, ), }, ), frozen: false, }, Field { name: "extras", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "extras", ), rest: [], }, by_alias: [], }, validator: WithDefault( WithDefaultValidator { default: DefaultFactory( Py( 0x00007310e74524a0, ), false, ), on_error: Raise, validator: Dict( DictValidator { strict: false, key_validator: Str( StrValidator { strict: false, coerce_numbers_to_str: false, }, ), value_validator: Any( AnyValidator, ), min_length: None, max_length: None, fail_fast: false, name: "dict[str,any]", }, ), validate_default: false, copy_default: false, name: "default[dict[str,any]]", undefined: Py( 0x00007310e53bdb90, ), }, ), frozen: false, }, Field { name: "node_type", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "node_type", ), rest: [], }, by_alias: [], }, validator: Literal( LiteralValidator { lookup: LiteralLookup { expected_bool: None, expected_int: None, expected_str: Some( { "data.gromacs.grompp.GromppParameters.": 0, }, ), expected_py_dict: None, expected_py_values: None, expected_py_primitives: Some( Py( 0x00007310d2a314c0, ), ), values: [ Py( 0x00007310d314fc30, ), ], }, expected_repr: "'data.gromacs.grompp.GromppParameters.'", name: "literal['data.gromacs.grompp.GromppParameters.']", }, ), frozen: false, }, Field { name: "attributes", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "attributes", ), rest: [], }, by_alias: [], }, validator: Prebuilt( PrebuiltValidator { schema_validator: Py( 0x00007310d2a2ab00, ), }, ), frozen: false, }, Field { name: "repository_metadata", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "repository_metadata", ), rest: [], }, by_alias: [], }, validator: WithDefault( WithDefaultValidator { default: DefaultFactory( Py( 0x00007310e74524a0, ), false, ), on_error: Raise, validator: Dict( DictValidator { strict: false, key_validator: Str( StrValidator { strict: false, coerce_numbers_to_str: false, }, ), value_validator: Any( AnyValidator, ), min_length: None, max_length: None, fail_fast: false, name: "dict[str,any]", }, ), validate_default: false, copy_default: false, name: "default[dict[str,any]]", undefined: Py( 0x00007310e53bdb90, ), }, ), frozen: false, }, Field { name: "uuid", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "uuid", ), rest: [], }, by_alias: [], }, validator: Uuid( UuidValidator { strict: false, version: None, }, ), frozen: false, }, Field { name: "process_type", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "process_type", ), rest: [], }, by_alias: [], }, validator: WithDefault( WithDefaultValidator { default: Default( Py( 0x00007310e7455800, ), ), on_error: Raise, validator: Nullable( NullableValidator { validator: Str( StrValidator { strict: false, coerce_numbers_to_str: false, }, ), name: "nullable[str]", }, ), validate_default: false, copy_default: false, name: "default[nullable[str]]", undefined: Py( 0x00007310e53bdb90, ), }, ), frozen: false, }, Field { name: "ctime", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "ctime", ), rest: [], }, by_alias: [], }, validator: Datetime( DateTimeValidator { strict: false, constraints: None, microseconds_precision: Truncate, val_temporal_unit: Infer, }, ), frozen: false, }, Field { name: "mtime", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "mtime", ), rest: [], }, by_alias: [], }, validator: Datetime( DateTimeValidator { strict: false, constraints: None, microseconds_precision: Truncate, val_temporal_unit: Infer, }, ), frozen: false, }, Field { name: "computer", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "computer", ), rest: [], }, by_alias: [], }, validator: WithDefault( WithDefaultValidator { default: Default( Py( 0x00007310e7455800, ), ), on_error: Raise, validator: Nullable( NullableValidator { validator: Int( IntValidator { strict: false, }, ), name: "nullable[int]", }, ), validate_default: false, copy_default: false, name: "default[nullable[int]]", undefined: Py( 0x00007310e53bdb90, ), }, ), frozen: false, }, Field { name: "user", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "user", ), rest: [], }, by_alias: [], }, validator: Int( IntValidator { strict: false, }, ), frozen: false, }, ], model_name: "ReadModel", extra_behavior: Forbid, extras_validator: None, extras_keys_validator: None, strict: false, from_attributes: false, loc_by_alias: true, lookup: LookupTree { inner: { PathItemString( "ctime", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 9, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "user", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 12, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "process_type", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 8, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "attributes", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 5, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "uuid", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 7, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "node_type", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 4, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "repository_metadata", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 6, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "description", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 2, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "mtime", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 10, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "computer", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 11, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "extras", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 3, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "pk", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 0, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "label", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 1, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, }, }, validate_by_alias: Some( true, ), validate_by_name: Some( true, ), }, ), class: Py( 0x000063affefdecc0, ), generic_origin: None, post_init: Some( Py( 0x00007310e2571630, ), ), frozen: false, custom_init: false, root_model: false, undefined: Py( 0x00007310e53bdb90, ), name: "ReadModel", }, ), definitions=[], cache_strings=True)¶
The pydantic-core SchemaValidator used to validate instances of the model.
- _abc_impl = <_abc._abc_data object>¶
- attributes: AttributesModel¶
- model_config = {'defer_build': True, 'extra': 'forbid', 'json_encoders': {<class 'datetime.datetime'>: <function OrmModel.<lambda>>}, 'serialize_by_alias': True, 'title': 'GromppParametersReadModel', 'validate_by_alias': True, 'validate_by_name': True}¶
Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].
- class WriteModel(**data: Any)¶
Bases:
WriteModel- __abstractmethods__ = frozenset({})¶
- __annotations__ = {'attributes': <class 'aiida_gromacs.data.grompp.GromppParameters.AttributesWriteModel'>, 'description': <class 'str'>, 'extras': dict[str, typing.Any], 'label': <class 'str'>, 'node_type': typing.Literal['data.gromacs.grompp.GromppParameters.'], 'repository_metadata': dict[str, typing.Any]}¶
- __class_vars__ = {}¶
The names of the class variables defined on the model.
- __dict__¶
- __module__ = 'aiida_gromacs.data.grompp'¶
- __private_attributes__ = {'_AIIDA_MINIMAL_MODEL': ModelPrivateAttr()}¶
Metadata about the private attributes of the model.
- __pydantic_complete__ = True¶
Whether model building is completed, or if there are still undefined fields.
- __pydantic_computed_fields__ = {}¶
A dictionary of computed field names and their corresponding [ComputedFieldInfo][pydantic.fields.ComputedFieldInfo] objects.
- __pydantic_core_schema__ = {'cls': <class 'aiida_gromacs.data.grompp.GromppParameters.WriteModel'>, 'config': {'extra_fields_behavior': 'forbid', 'serialize_by_alias': True, 'title': 'GromppParametersWriteModel', 'validate_by_alias': True, 'validate_by_name': True}, 'custom_init': False, 'metadata': {'pydantic_js_functions': [<bound method BaseModel.__get_pydantic_json_schema__ of <class 'aiida_gromacs.data.grompp.GromppParameters.WriteModel'>>]}, 'post_init': 'model_post_init', 'ref': 'aiida_gromacs.data.grompp.GromppParameters.WriteModel:109607548569200', 'root_model': False, 'schema': {'computed_fields': [], 'fields': {'attributes': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'The node attributes', 'examples': [{'attr_key': 'attr_value'}]}}, 'schema': {'cls': <class 'aiida_gromacs.data.grompp.GromppParameters.AttributesWriteModel'>, 'config': {'extra_fields_behavior': 'allow', 'serialize_by_alias': True, 'title': 'GromppParametersAttributesWriteModel', 'validate_by_alias': True, 'validate_by_name': True}, 'custom_init': False, 'metadata': {'pydantic_js_functions': [<bound method BaseModel.__get_pydantic_json_schema__ of <class 'aiida_gromacs.data.grompp.GromppParameters.AttributesWriteModel'>>]}, 'post_init': 'model_post_init', 'ref': 'aiida_gromacs.data.grompp.GromppParameters.AttributesWriteModel:109607548575872', 'root_model': False, 'schema': {'computed_fields': [], 'fields': {'source': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'Source of the data'}}, 'schema': {'default': None, 'schema': {'schema': {'keys_schema': {'type': 'any'}, 'type': 'dict', 'values_schema': {'type': 'any'}}, 'type': 'nullable'}, 'type': 'default'}, 'type': 'model-field'}}, 'model_name': 'AttributesWriteModel', 'type': 'model-fields'}, 'type': 'model'}, 'type': 'model-field'}, 'description': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'The node description', 'examples': ['This is my node description.']}}, 'schema': {'default': '', 'schema': {'type': 'str'}, 'type': 'default'}, 'type': 'model-field'}, 'extras': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'The node extras', 'examples': [{'extra_key': 'extra_value'}]}}, 'schema': {'default_factory': <class 'dict'>, 'default_factory_takes_data': False, 'schema': {'keys_schema': {'type': 'str'}, 'type': 'dict', 'values_schema': {'type': 'any'}}, 'type': 'default'}, 'type': 'model-field'}, 'label': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'The node label', 'examples': ['my_node']}}, 'schema': {'default': '', 'schema': {'type': 'str'}, 'type': 'default'}, 'type': 'model-field'}, 'node_type': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'The type of the node.'}}, 'schema': {'expected': ['data.gromacs.grompp.GromppParameters.'], 'type': 'literal'}, 'type': 'model-field'}, 'repository_metadata': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'Virtual hierarchy of the file repository', 'examples': [{'o': {'file.txt': {'k': '<file_hash>'}}}]}}, 'schema': {'default_factory': <class 'dict'>, 'default_factory_takes_data': False, 'schema': {'keys_schema': {'type': 'str'}, 'type': 'dict', 'values_schema': {'type': 'any'}}, 'type': 'default'}, 'type': 'model-field'}}, 'model_name': 'WriteModel', 'type': 'model-fields'}, 'type': 'model'}¶
The core schema of the model.
- __pydantic_custom_init__ = False¶
Whether the model has a custom __init__ method.
- __pydantic_decorators__ = DecoratorInfos(validators={}, field_validators={}, root_validators={}, field_serializers={}, model_serializers={}, model_validators={}, computed_fields={})¶
Metadata containing the decorators defined on the model. This replaces Model.__validators__ and Model.__root_validators__ from Pydantic V1.
- __pydantic_extra__¶
A dictionary containing extra values, if [extra][pydantic.config.ConfigDict.extra] is set to ‘allow’.
- __pydantic_extra_info__ = None¶
A wrapper around the __pydantic_extra__ annotation, if explicitly annotated on a model.
This is a private attribute, not meant to be used outside Pydantic.
- __pydantic_fields__ = {'attributes': FieldInfo(annotation=GromppParameters.AttributesWriteModel, required=True, description='The node attributes', examples=[{'attr_key': 'attr_value'}], json_schema_extra={}, metadata=[{'priority': 0}, {'read_only': False}, {'write_only': False}, {'may_be_large': True}]), 'description': FieldInfo(annotation=str, required=False, default='', description='The node description', examples=['This is my node description.'], json_schema_extra={}, metadata=[{'priority': 0}, {'read_only': False}, {'write_only': False}, {'may_be_large': False}]), 'extras': FieldInfo(annotation=dict[str, Any], required=False, default_factory=dict, description='The node extras', examples=[{'extra_key': 'extra_value'}], json_schema_extra={}, metadata=[{'priority': 0}, {'read_only': False}, {'write_only': False}, {'may_be_large': True}, {'orm_to_model': <function Node.MutableNodeFields.<lambda>>}]), 'label': FieldInfo(annotation=str, required=False, default='', description='The node label', examples=['my_node'], json_schema_extra={}, metadata=[{'priority': 0}, {'read_only': False}, {'write_only': False}, {'may_be_large': False}]), 'node_type': FieldInfo(annotation=Literal['data.gromacs.grompp.GromppParameters.'], required=True, description='The type of the node.', json_schema_extra={}, metadata=[{'priority': 0}, {'read_only': False}, {'write_only': False}, {'may_be_large': False}]), 'repository_metadata': FieldInfo(annotation=dict[str, Any], required=False, default_factory=dict, description='Virtual hierarchy of the file repository', examples=[{'o': {'file.txt': {'k': '<file_hash>'}}}], json_schema_extra={}, metadata=[{'priority': 0}, {'read_only': False}, {'write_only': False}, {'may_be_large': True}, {'orm_to_model': <function Node.WritableFields.<lambda>>}])}¶
A dictionary of field names and their corresponding [FieldInfo][pydantic.fields.FieldInfo] objects. This replaces Model.__fields__ from Pydantic V1.
- __pydantic_fields_set__¶
The names of fields explicitly set during instantiation.
- __pydantic_generic_metadata__ = {'args': (), 'origin': None, 'parameters': ()}¶
A dictionary containing metadata about generic Pydantic models.
The origin and args items map to the [__origin__][genericalias.__origin__] and [__args__][genericalias.__args__] attributes of [generic aliases][types-genericalias], and the parameter item maps to the __parameter__ attribute of generic classes.
- __pydantic_post_init__ = 'model_post_init'¶
The name of the post-init method for the model, if defined.
- __pydantic_private__¶
Values of private attributes set on the model instance.
- __pydantic_serializer__ = SchemaSerializer(serializer=PolymorphismTrampoline( PolymorphismTrampoline { class: Py( 0x000063affeff4670, ), serializer: PolymorphismTrampoline( PolymorphismTrampoline { class: Py( 0x000063affeff4670, ), serializer: Model( ModelSerializer { class: Py( 0x000063affeff4670, ), serializer: Fields( GeneralFieldsSerializer { fields: { "node_type": SerField { key: "node_type", alias: None, serializer: Some( Literal( LiteralSerializer { expected_int: {}, expected_str: { "data.gromacs.grompp.GromppParameters.", }, expected_py: None, name: "literal['data.gromacs.grompp.GromppParameters.']", }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "extras": SerField { key: "extras", alias: None, serializer: Some( WithDefault( WithDefaultSerializer { default: DefaultFactory( Py( 0x00007310e74524a0, ), false, ), serializer: Dict( DictSerializer { key_serializer: Str( StrSerializer, ), value_serializer: Any( AnySerializer, ), filter: SchemaFilter { include: None, exclude: None, }, name: "dict[str, any]", }, ), }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "attributes": SerField { key: "attributes", alias: None, serializer: Some( PolymorphismTrampoline( PolymorphismTrampoline { class: Py( 0x000063affeff6080, ), serializer: PolymorphismTrampoline( PolymorphismTrampoline { class: Py( 0x000063affeff6080, ), serializer: Model( ModelSerializer { class: Py( 0x000063affeff6080, ), serializer: Fields( GeneralFieldsSerializer { fields: { "source": SerField { key: "source", alias: None, serializer: Some( WithDefault( WithDefaultSerializer { default: Default( Py( 0x00007310e7455800, ), ), serializer: Nullable( NullableSerializer { serializer: Dict( DictSerializer { key_serializer: Any( AnySerializer, ), value_serializer: Any( AnySerializer, ), filter: SchemaFilter { include: None, exclude: None, }, name: "dict[any, any]", }, ), }, ), }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, }, computed_fields: Some( ComputedFields( [], ), ), mode: ModelExtra, extra_serializer: None, filter: SchemaFilter { include: None, exclude: None, }, required_fields: 1, }, ), has_extra: true, root_model: false, name: "AttributesWriteModel", }, ), enabled_from_config: false, }, ), enabled_from_config: false, }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "repository_metadata": SerField { key: "repository_metadata", alias: None, serializer: Some( WithDefault( WithDefaultSerializer { default: DefaultFactory( Py( 0x00007310e74524a0, ), false, ), serializer: Dict( DictSerializer { key_serializer: Str( StrSerializer, ), value_serializer: Any( AnySerializer, ), filter: SchemaFilter { include: None, exclude: None, }, name: "dict[str, any]", }, ), }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "label": SerField { key: "label", alias: None, serializer: Some( WithDefault( WithDefaultSerializer { default: Default( Py( 0x00007310e7482e40, ), ), serializer: Str( StrSerializer, ), }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "description": SerField { key: "description", alias: None, serializer: Some( WithDefault( WithDefaultSerializer { default: Default( Py( 0x00007310e7482e40, ), ), serializer: Str( StrSerializer, ), }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, }, computed_fields: Some( ComputedFields( [], ), ), mode: SimpleDict, extra_serializer: None, filter: SchemaFilter { include: None, exclude: None, }, required_fields: 6, }, ), has_extra: false, root_model: false, name: "WriteModel", }, ), enabled_from_config: false, }, ), enabled_from_config: false, }, ), definitions=[])¶
The pydantic-core SchemaSerializer used to dump instances of the model.
- __pydantic_setattr_handlers__ = {}¶
__setattr__ handlers. Memoizing the handlers leads to a dramatic performance improvement in __setattr__
- __pydantic_validator__ = SchemaValidator(title="GromppParametersWriteModel", validator=Model( ModelValidator { revalidate: Never, validator: ModelFields( ModelFieldsValidator { fields: [ Field { name: "label", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "label", ), rest: [], }, by_alias: [], }, validator: WithDefault( WithDefaultValidator { default: Default( Py( 0x00007310e7482e40, ), ), on_error: Raise, validator: Str( StrValidator { strict: false, coerce_numbers_to_str: false, }, ), validate_default: false, copy_default: false, name: "default[str]", undefined: Py( 0x00007310e53bdb90, ), }, ), frozen: false, }, Field { name: "description", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "description", ), rest: [], }, by_alias: [], }, validator: WithDefault( WithDefaultValidator { default: Default( Py( 0x00007310e7482e40, ), ), on_error: Raise, validator: Str( StrValidator { strict: false, coerce_numbers_to_str: false, }, ), validate_default: false, copy_default: false, name: "default[str]", undefined: Py( 0x00007310e53bdb90, ), }, ), frozen: false, }, Field { name: "extras", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "extras", ), rest: [], }, by_alias: [], }, validator: WithDefault( WithDefaultValidator { default: DefaultFactory( Py( 0x00007310e74524a0, ), false, ), on_error: Raise, validator: Dict( DictValidator { strict: false, key_validator: Str( StrValidator { strict: false, coerce_numbers_to_str: false, }, ), value_validator: Any( AnyValidator, ), min_length: None, max_length: None, fail_fast: false, name: "dict[str,any]", }, ), validate_default: false, copy_default: false, name: "default[dict[str,any]]", undefined: Py( 0x00007310e53bdb90, ), }, ), frozen: false, }, Field { name: "node_type", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "node_type", ), rest: [], }, by_alias: [], }, validator: Literal( LiteralValidator { lookup: LiteralLookup { expected_bool: None, expected_int: None, expected_str: Some( { "data.gromacs.grompp.GromppParameters.": 0, }, ), expected_py_dict: None, expected_py_values: None, expected_py_primitives: Some( Py( 0x00007310d2a76800, ), ), values: [ Py( 0x00007310d314fc30, ), ], }, expected_repr: "'data.gromacs.grompp.GromppParameters.'", name: "literal['data.gromacs.grompp.GromppParameters.']", }, ), frozen: false, }, Field { name: "attributes", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "attributes", ), rest: [], }, by_alias: [], }, validator: Model( ModelValidator { revalidate: Never, validator: ModelFields( ModelFieldsValidator { fields: [ Field { name: "source", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "source", ), rest: [], }, by_alias: [], }, validator: WithDefault( WithDefaultValidator { default: Default( Py( 0x00007310e7455800, ), ), on_error: Raise, validator: Nullable( NullableValidator { validator: Dict( DictValidator { strict: false, key_validator: Any( AnyValidator, ), value_validator: Any( AnyValidator, ), min_length: None, max_length: None, fail_fast: false, name: "dict[any,any]", }, ), name: "nullable[dict[any,any]]", }, ), validate_default: false, copy_default: false, name: "default[nullable[dict[any,any]]]", undefined: Py( 0x00007310e53bdb90, ), }, ), frozen: false, }, ], model_name: "AttributesWriteModel", extra_behavior: Allow, extras_validator: None, extras_keys_validator: None, strict: false, from_attributes: false, loc_by_alias: true, lookup: LookupTree { inner: { PathItemString( "source", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 0, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, }, }, validate_by_alias: Some( true, ), validate_by_name: Some( true, ), }, ), class: Py( 0x000063affeff6080, ), generic_origin: None, post_init: Some( Py( 0x00007310e2571630, ), ), frozen: false, custom_init: false, root_model: false, undefined: Py( 0x00007310e53bdb90, ), name: "AttributesWriteModel", }, ), frozen: false, }, Field { name: "repository_metadata", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "repository_metadata", ), rest: [], }, by_alias: [], }, validator: WithDefault( WithDefaultValidator { default: DefaultFactory( Py( 0x00007310e74524a0, ), false, ), on_error: Raise, validator: Dict( DictValidator { strict: false, key_validator: Str( StrValidator { strict: false, coerce_numbers_to_str: false, }, ), value_validator: Any( AnyValidator, ), min_length: None, max_length: None, fail_fast: false, name: "dict[str,any]", }, ), validate_default: false, copy_default: false, name: "default[dict[str,any]]", undefined: Py( 0x00007310e53bdb90, ), }, ), frozen: false, }, ], model_name: "WriteModel", extra_behavior: Forbid, extras_validator: None, extras_keys_validator: None, strict: false, from_attributes: false, loc_by_alias: true, lookup: LookupTree { inner: { PathItemString( "label", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 0, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "extras", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 2, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "description", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 1, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "attributes", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 4, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "repository_metadata", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 5, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "node_type", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 3, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, }, }, validate_by_alias: Some( true, ), validate_by_name: Some( true, ), }, ), class: Py( 0x000063affeff4670, ), generic_origin: None, post_init: Some( Py( 0x00007310e2571630, ), ), frozen: false, custom_init: false, root_model: false, undefined: Py( 0x00007310e53bdb90, ), name: "WriteModel", }, ), definitions=[], cache_strings=True)¶
The pydantic-core SchemaValidator used to validate instances of the model.
- _abc_impl = <_abc._abc_data object>¶
- attributes: AttributesWriteModel¶
- model_config = {'defer_build': True, 'extra': 'forbid', 'json_encoders': {<class 'datetime.datetime'>: <function OrmModel.<lambda>>}, 'serialize_by_alias': True, 'title': 'GromppParametersWriteModel', 'validate_by_alias': True, 'validate_by_name': True}¶
Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].
- _COMPAT_MODEL¶
alias of
Model
- _ConstructorModel¶
alias of
ConstructorModel
- _MODEL_MAP = {'read': <class 'aiida_gromacs.data.grompp.GromppParameters.ReadModel'>, 'write': <class 'aiida_gromacs.data.grompp.GromppParameters.WriteModel'>}¶
- __abstractmethods__ = frozenset({})¶
- __annotations__ = {}¶
- __firstlineno__ = 28¶
- __init__(dict=None, **kwargs)[source]¶
Constructor for the data class
Usage:
GromppParameters(dict{'ignore-case': True})- Parameters:
parameters_dict (type) – dictionary with commandline parameters
parameters_dict – dict
- __module__ = 'aiida_gromacs.data.grompp'¶
- __parameters__ = ()¶
- __static_attributes__ = ()¶
- __str__()[source]¶
String representation of node.
Append values of dictionary to usual representation. E.g.:
uuid: b416cbee-24e8-47a8-8c11-6d668770158b (pk: 590) {'ignore-case': True}
- _abc_impl = <_abc._abc_data object>¶
- _logger = <Logger aiida_gromacs.data.grompp.GromppParameters (WARNING)>¶
- cmdline_params(input_files)[source]¶
Synthesize command line parameters.
e.g. [ ‘–ignore-case’, ‘filename1’, ‘filename2’]
- Parameters:
pdbfile (type) – Name of input pdb file
pdbfile – str
- fields = {'attributes': "QbAttributesField('attributes', dtype=<class 'aiida_gromacs.data.grompp.GromppParameters.AttributesModel'>, doc='The node attributes')", 'computer': "QbNumericField('computer', dtype=int | None, doc='The PK of the computer')", 'ctime': "QbNumericField('ctime', dtype=<class 'datetime.datetime'>, doc='The creation time of the node')", 'description': "QbStrField('description', dtype=<class 'str'>, doc='The node description')", 'extras': "QbDictField('extras', dtype=dict[str, typing.Any], doc='The node extras')", 'label': "QbStrField('label', dtype=<class 'str'>, doc='The node label')", 'mtime': "QbNumericField('mtime', dtype=<class 'datetime.datetime'>, doc='The modification time of the node')", 'node_type': "QbStrField('node_type', dtype=typing.Literal['data.gromacs.grompp.GromppParameters.'], doc='The type of the node.')", 'pk': "QbNumericField('pk', dtype=<class 'int'>, doc='The primary key of the entity')", 'process_type': "QbStrField('process_type', dtype=str | None, doc='The process type of the node')", 'repository_metadata': "QbDictField('repository_metadata', dtype=dict[str, typing.Any], doc='Virtual hierarchy of the file repository')", 'source': "QbDictField('attributes.source', dtype=dict | None, doc='Source of the data')", 'user': "QbNumericField('user', dtype=<class 'int'>, doc='The PK of the user who owns the node')", 'uuid': "QbStrField('uuid', dtype=<class 'uuid.UUID'>, doc='The UUID of the node')"}¶
- schema = <Schema({'o': <class 'str'>, 'po': <class 'str'>, 'pp': <class 'str'>, 'imd': <class 'str'>, 'r': <class 'str'>, 'v': <class 'str'>, 'time': <class 'str'>, 'rmvsbds': <class 'str'>, 'maxwarn': <class 'str'>, 'zero': <class 'str'>, 'renum': <class 'str'>}, extra=PREVENT_EXTRA, required=False) object>¶
- validate(parameters_dict)[source]¶
Validate command line options.
Uses the voluptuous package for validation. Find out about allowed keys using:
print(GromppParameters).schema.schema
- Parameters:
parameters_dict (type) – dictionary with commandline parameters
parameters_dict – dict
- Returns:
validated dictionary
aiida_gromacs.data.make_ndx module¶
Data types provided by plugin
Register data types via the “aiida.data” entry point in setup.json.
- class aiida_gromacs.data.make_ndx.Make_ndxParameters(dict=None, **kwargs)[source]¶
Bases:
DictCommand line options for diff.
This class represents a python dictionary used to pass command line options to the executable.
- class AttributesModel(**data: Any)¶
Bases:
AttributesModel- __abstractmethods__ = frozenset({})¶
- __annotations__ = {}¶
- __class_vars__ = {}¶
The names of the class variables defined on the model.
- __dict__¶
- __module__ = 'aiida_gromacs.data.make_ndx'¶
- __private_attributes__ = {'_AIIDA_MINIMAL_MODEL': ModelPrivateAttr()}¶
Metadata about the private attributes of the model.
- __pydantic_complete__ = True¶
Whether model building is completed, or if there are still undefined fields.
- __pydantic_computed_fields__ = {}¶
A dictionary of computed field names and their corresponding [ComputedFieldInfo][pydantic.fields.ComputedFieldInfo] objects.
- __pydantic_core_schema__ = {'cls': <class 'aiida_gromacs.data.make_ndx.Make_ndxParameters.AttributesModel'>, 'config': {'extra_fields_behavior': 'allow', 'serialize_by_alias': True, 'title': 'Make_ndxParametersAttributesModel', 'validate_by_alias': True, 'validate_by_name': True}, 'custom_init': False, 'metadata': {'pydantic_js_functions': [<bound method BaseModel.__get_pydantic_json_schema__ of <class 'aiida_gromacs.data.make_ndx.Make_ndxParameters.AttributesModel'>>]}, 'post_init': 'model_post_init', 'ref': 'aiida_gromacs.data.make_ndx.Make_ndxParameters.AttributesModel:109607535650784', 'root_model': False, 'schema': {'computed_fields': [], 'fields': {'source': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'Source of the data'}}, 'schema': {'default': None, 'schema': {'schema': {'keys_schema': {'type': 'any'}, 'type': 'dict', 'values_schema': {'type': 'any'}}, 'type': 'nullable'}, 'type': 'default'}, 'type': 'model-field'}}, 'model_name': 'AttributesModel', 'type': 'model-fields'}, 'type': 'model'}¶
The core schema of the model.
- __pydantic_custom_init__ = False¶
Whether the model has a custom __init__ method.
- __pydantic_decorators__ = DecoratorInfos(validators={}, field_validators={}, root_validators={}, field_serializers={}, model_serializers={}, model_validators={}, computed_fields={})¶
Metadata containing the decorators defined on the model. This replaces Model.__validators__ and Model.__root_validators__ from Pydantic V1.
- __pydantic_extra__¶
A dictionary containing extra values, if [extra][pydantic.config.ConfigDict.extra] is set to ‘allow’.
- __pydantic_extra_info__ = None¶
A wrapper around the __pydantic_extra__ annotation, if explicitly annotated on a model.
This is a private attribute, not meant to be used outside Pydantic.
- __pydantic_fields__ = {'source': FieldInfo(annotation=Union[dict, NoneType], required=False, default=None, description='Source of the data', json_schema_extra={}, metadata=[{'priority': 0}, {'read_only': False}, {'write_only': False}, {'may_be_large': False}])}¶
A dictionary of field names and their corresponding [FieldInfo][pydantic.fields.FieldInfo] objects. This replaces Model.__fields__ from Pydantic V1.
- __pydantic_fields_set__¶
The names of fields explicitly set during instantiation.
- __pydantic_generic_metadata__ = {'args': (), 'origin': None, 'parameters': ()}¶
A dictionary containing metadata about generic Pydantic models.
The origin and args items map to the [__origin__][genericalias.__origin__] and [__args__][genericalias.__args__] attributes of [generic aliases][types-genericalias], and the parameter item maps to the __parameter__ attribute of generic classes.
- __pydantic_post_init__ = 'model_post_init'¶
The name of the post-init method for the model, if defined.
- __pydantic_private__¶
Values of private attributes set on the model instance.
- __pydantic_serializer__ = SchemaSerializer(serializer=PolymorphismTrampoline( PolymorphismTrampoline { class: Py( 0x000063affe3a27e0, ), serializer: PolymorphismTrampoline( PolymorphismTrampoline { class: Py( 0x000063affe3a27e0, ), serializer: Model( ModelSerializer { class: Py( 0x000063affe3a27e0, ), serializer: Fields( GeneralFieldsSerializer { fields: { "source": SerField { key: "source", alias: None, serializer: Some( WithDefault( WithDefaultSerializer { default: Default( Py( 0x00007310e7455800, ), ), serializer: Nullable( NullableSerializer { serializer: Dict( DictSerializer { key_serializer: Any( AnySerializer, ), value_serializer: Any( AnySerializer, ), filter: SchemaFilter { include: None, exclude: None, }, name: "dict[any, any]", }, ), }, ), }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, }, computed_fields: Some( ComputedFields( [], ), ), mode: ModelExtra, extra_serializer: None, filter: SchemaFilter { include: None, exclude: None, }, required_fields: 1, }, ), has_extra: true, root_model: false, name: "AttributesModel", }, ), enabled_from_config: false, }, ), enabled_from_config: false, }, ), definitions=[])¶
The pydantic-core SchemaSerializer used to dump instances of the model.
- __pydantic_setattr_handlers__ = {}¶
__setattr__ handlers. Memoizing the handlers leads to a dramatic performance improvement in __setattr__
- __pydantic_validator__ = SchemaValidator(title="Make_ndxParametersAttributesModel", validator=Model( ModelValidator { revalidate: Never, validator: ModelFields( ModelFieldsValidator { fields: [ Field { name: "source", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "source", ), rest: [], }, by_alias: [], }, validator: WithDefault( WithDefaultValidator { default: Default( Py( 0x00007310e7455800, ), ), on_error: Raise, validator: Nullable( NullableValidator { validator: Dict( DictValidator { strict: false, key_validator: Any( AnyValidator, ), value_validator: Any( AnyValidator, ), min_length: None, max_length: None, fail_fast: false, name: "dict[any,any]", }, ), name: "nullable[dict[any,any]]", }, ), validate_default: false, copy_default: false, name: "default[nullable[dict[any,any]]]", undefined: Py( 0x00007310e53bdb90, ), }, ), frozen: false, }, ], model_name: "AttributesModel", extra_behavior: Allow, extras_validator: None, extras_keys_validator: None, strict: false, from_attributes: false, loc_by_alias: true, lookup: LookupTree { inner: { PathItemString( "source", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 0, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, }, }, validate_by_alias: Some( true, ), validate_by_name: Some( true, ), }, ), class: Py( 0x000063affe3a27e0, ), generic_origin: None, post_init: Some( Py( 0x00007310e2571630, ), ), frozen: false, custom_init: false, root_model: false, undefined: Py( 0x00007310e53bdb90, ), name: "AttributesModel", }, ), definitions=[], cache_strings=True)¶
The pydantic-core SchemaValidator used to validate instances of the model.
- _abc_impl = <_abc._abc_data object>¶
- model_config = {'arbitrary_types_allowed': True, 'defer_build': True, 'extra': 'allow', 'json_encoders': {<class 'datetime.datetime'>: <function OrmModel.<lambda>>}, 'serialize_by_alias': True, 'title': 'Make_ndxParametersAttributesModel', 'validate_by_alias': True, 'validate_by_name': True}¶
Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].
- class ReadModel(**data: Any)¶
Bases:
ReadModel- __abstractmethods__ = frozenset({})¶
- __annotations__ = {'attributes': <class 'aiida_gromacs.data.make_ndx.Make_ndxParameters.AttributesModel'>, 'node_type': typing.Literal['data.gromacs.make_ndx.Make_ndxParameters.']}¶
- __class_vars__ = {}¶
The names of the class variables defined on the model.
- __dict__¶
- __module__ = 'aiida_gromacs.data.make_ndx'¶
- __private_attributes__ = {'_AIIDA_MINIMAL_MODEL': ModelPrivateAttr()}¶
Metadata about the private attributes of the model.
- __pydantic_complete__ = True¶
Whether model building is completed, or if there are still undefined fields.
- __pydantic_computed_fields__ = {}¶
A dictionary of computed field names and their corresponding [ComputedFieldInfo][pydantic.fields.ComputedFieldInfo] objects.
- __pydantic_core_schema__ = {'cls': <class 'aiida_gromacs.data.make_ndx.Make_ndxParameters.ReadModel'>, 'config': {'extra_fields_behavior': 'forbid', 'serialize_by_alias': True, 'title': 'Make_ndxParametersReadModel', 'validate_by_alias': True, 'validate_by_name': True}, 'custom_init': False, 'metadata': {'pydantic_js_functions': [<bound method BaseModel.__get_pydantic_json_schema__ of <class 'aiida_gromacs.data.make_ndx.Make_ndxParameters.ReadModel'>>]}, 'post_init': 'model_post_init', 'ref': 'aiida_gromacs.data.make_ndx.Make_ndxParameters.ReadModel:109607548450448', 'root_model': False, 'schema': {'computed_fields': [], 'fields': {'attributes': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'The node attributes', 'examples': [{'attr_key': 'attr_value'}]}}, 'schema': {'cls': <class 'aiida_gromacs.data.make_ndx.Make_ndxParameters.AttributesModel'>, 'config': {'extra_fields_behavior': 'allow', 'serialize_by_alias': True, 'title': 'Make_ndxParametersAttributesModel', 'validate_by_alias': True, 'validate_by_name': True}, 'custom_init': False, 'metadata': {'pydantic_js_functions': [<bound method BaseModel.__get_pydantic_json_schema__ of <class 'aiida_gromacs.data.make_ndx.Make_ndxParameters.AttributesModel'>>]}, 'post_init': 'model_post_init', 'ref': 'aiida_gromacs.data.make_ndx.Make_ndxParameters.AttributesModel:109607535650784', 'root_model': False, 'schema': {'computed_fields': [], 'fields': {'source': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'Source of the data'}}, 'schema': {'default': None, 'schema': {'schema': {'keys_schema': {'type': 'any'}, 'type': 'dict', 'values_schema': {'type': 'any'}}, 'type': 'nullable'}, 'type': 'default'}, 'type': 'model-field'}}, 'model_name': 'AttributesModel', 'type': 'model-fields'}, 'type': 'model'}, 'type': 'model-field'}, 'computer': {'metadata': {'pydantic_js_extra': {'readOnly': True}, 'pydantic_js_updates': {'description': 'The PK of the computer', 'examples': [42]}}, 'schema': {'default': None, 'schema': {'schema': {'type': 'int'}, 'type': 'nullable'}, 'type': 'default'}, 'type': 'model-field'}, 'ctime': {'metadata': {'pydantic_js_extra': {'readOnly': True}, 'pydantic_js_updates': {'description': 'The creation time of the node', 'examples': ['2024-01-01T12:00:00+00:00']}}, 'schema': {'microseconds_precision': 'truncate', 'serialization': {'function': <function OrmModel.<lambda>>, 'type': 'function-plain', 'when_used': 'json'}, 'type': 'datetime'}, 'type': 'model-field'}, 'description': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'The node description', 'examples': ['This is my node description.']}}, 'schema': {'default': '', 'schema': {'type': 'str'}, 'type': 'default'}, 'type': 'model-field'}, 'extras': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'The node extras', 'examples': [{'extra_key': 'extra_value'}]}}, 'schema': {'default_factory': <class 'dict'>, 'default_factory_takes_data': False, 'schema': {'keys_schema': {'type': 'str'}, 'type': 'dict', 'values_schema': {'type': 'any'}}, 'type': 'default'}, 'type': 'model-field'}, 'label': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'The node label', 'examples': ['my_node']}}, 'schema': {'default': '', 'schema': {'type': 'str'}, 'type': 'default'}, 'type': 'model-field'}, 'mtime': {'metadata': {'pydantic_js_extra': {'readOnly': True}, 'pydantic_js_updates': {'description': 'The modification time of the node', 'examples': ['2024-01-02T12:00:00+00:00']}}, 'schema': {'microseconds_precision': 'truncate', 'serialization': {'function': <function OrmModel.<lambda>>, 'type': 'function-plain', 'when_used': 'json'}, 'type': 'datetime'}, 'type': 'model-field'}, 'node_type': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'The type of the node.'}}, 'schema': {'expected': ['data.gromacs.make_ndx.Make_ndxParameters.'], 'type': 'literal'}, 'type': 'model-field'}, 'pk': {'metadata': {'pydantic_js_extra': {'readOnly': True}, 'pydantic_js_updates': {'description': 'The primary key of the entity', 'examples': [42]}}, 'schema': {'type': 'int'}, 'type': 'model-field'}, 'process_type': {'metadata': {'pydantic_js_extra': {'readOnly': True}, 'pydantic_js_updates': {'description': 'The process type of the node', 'examples': ['aiida.calculations:arithmetic.add.']}}, 'schema': {'default': None, 'schema': {'schema': {'type': 'str'}, 'type': 'nullable'}, 'type': 'default'}, 'type': 'model-field'}, 'repository_metadata': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'Virtual hierarchy of the file repository', 'examples': [{'o': {'file.txt': {'k': '<file_hash>'}}}]}}, 'schema': {'default_factory': <class 'dict'>, 'default_factory_takes_data': False, 'schema': {'keys_schema': {'type': 'str'}, 'type': 'dict', 'values_schema': {'type': 'any'}}, 'type': 'default'}, 'type': 'model-field'}, 'user': {'metadata': {'pydantic_js_extra': {'readOnly': True}, 'pydantic_js_updates': {'description': 'The PK of the user who owns the node', 'examples': [7]}}, 'schema': {'type': 'int'}, 'type': 'model-field'}, 'uuid': {'metadata': {'pydantic_js_extra': {'readOnly': True}, 'pydantic_js_updates': {'description': 'The UUID of the node', 'examples': ['123e4567-e89b-12d3-a456-426614174000']}}, 'schema': {'type': 'uuid'}, 'type': 'model-field'}}, 'model_name': 'ReadModel', 'type': 'model-fields'}, 'type': 'model'}¶
The core schema of the model.
- __pydantic_custom_init__ = False¶
Whether the model has a custom __init__ method.
- __pydantic_decorators__ = DecoratorInfos(validators={}, field_validators={}, root_validators={}, field_serializers={}, model_serializers={}, model_validators={}, computed_fields={})¶
Metadata containing the decorators defined on the model. This replaces Model.__validators__ and Model.__root_validators__ from Pydantic V1.
- __pydantic_extra__¶
A dictionary containing extra values, if [extra][pydantic.config.ConfigDict.extra] is set to ‘allow’.
- __pydantic_extra_info__ = None¶
A wrapper around the __pydantic_extra__ annotation, if explicitly annotated on a model.
This is a private attribute, not meant to be used outside Pydantic.
- __pydantic_fields__ = {'attributes': FieldInfo(annotation=Make_ndxParameters.AttributesModel, required=True, description='The node attributes', examples=[{'attr_key': 'attr_value'}], json_schema_extra={}, metadata=[{'priority': 0}, {'read_only': False}, {'write_only': False}, {'may_be_large': True}]), 'computer': FieldInfo(annotation=Union[int, NoneType], required=False, default=None, description='The PK of the computer', examples=[42], json_schema_extra={'readOnly': True}, metadata=[{'priority': 0}, {'read_only': True}, {'write_only': False}, {'may_be_large': False}, {'orm_class': <class 'aiida.orm.computers.Computer'>}, {'orm_to_model': <function Node.ReadModel.<lambda>>}]), 'ctime': FieldInfo(annotation=datetime, required=True, description='The creation time of the node', examples=['2024-01-01T12:00:00+00:00'], json_schema_extra={'readOnly': True}, metadata=[{'priority': 0}, {'read_only': True}, {'write_only': False}, {'may_be_large': False}]), 'description': FieldInfo(annotation=str, required=False, default='', description='The node description', examples=['This is my node description.'], json_schema_extra={}, metadata=[{'priority': 0}, {'read_only': False}, {'write_only': False}, {'may_be_large': False}]), 'extras': FieldInfo(annotation=dict[str, Any], required=False, default_factory=dict, description='The node extras', examples=[{'extra_key': 'extra_value'}], json_schema_extra={}, metadata=[{'priority': 0}, {'read_only': False}, {'write_only': False}, {'may_be_large': True}, {'orm_to_model': <function Node.MutableNodeFields.<lambda>>}]), 'label': FieldInfo(annotation=str, required=False, default='', description='The node label', examples=['my_node'], json_schema_extra={}, metadata=[{'priority': 0}, {'read_only': False}, {'write_only': False}, {'may_be_large': False}]), 'mtime': FieldInfo(annotation=datetime, required=True, description='The modification time of the node', examples=['2024-01-02T12:00:00+00:00'], json_schema_extra={'readOnly': True}, metadata=[{'priority': 0}, {'read_only': True}, {'write_only': False}, {'may_be_large': False}]), 'node_type': FieldInfo(annotation=Literal['data.gromacs.make_ndx.Make_ndxParameters.'], required=True, description='The type of the node.', json_schema_extra={}, metadata=[{'priority': 0}, {'read_only': False}, {'write_only': False}, {'may_be_large': False}]), 'pk': FieldInfo(annotation=int, required=True, description='The primary key of the entity', examples=[42], json_schema_extra={'readOnly': True}, metadata=[{'priority': 0}, {'read_only': True}, {'write_only': False}, {'may_be_large': False}]), 'process_type': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, description='The process type of the node', examples=['aiida.calculations:arithmetic.add.'], json_schema_extra={'readOnly': True}, metadata=[{'priority': 0}, {'read_only': True}, {'write_only': False}, {'may_be_large': False}]), 'repository_metadata': FieldInfo(annotation=dict[str, Any], required=False, default_factory=dict, description='Virtual hierarchy of the file repository', examples=[{'o': {'file.txt': {'k': '<file_hash>'}}}], json_schema_extra={}, metadata=[{'priority': 0}, {'read_only': False}, {'write_only': False}, {'may_be_large': True}, {'orm_to_model': <function Node.WritableFields.<lambda>>}]), 'user': FieldInfo(annotation=int, required=True, description='The PK of the user who owns the node', examples=[7], json_schema_extra={'readOnly': True}, metadata=[{'priority': 0}, {'read_only': True}, {'write_only': False}, {'may_be_large': False}, {'orm_class': <class 'aiida.orm.users.User'>}, {'orm_to_model': <function Node.ReadModel.<lambda>>}]), 'uuid': FieldInfo(annotation=UUID, required=True, description='The UUID of the node', examples=['123e4567-e89b-12d3-a456-426614174000'], json_schema_extra={'readOnly': True}, metadata=[{'priority': 0}, {'read_only': True}, {'write_only': False}, {'may_be_large': False}])}¶
A dictionary of field names and their corresponding [FieldInfo][pydantic.fields.FieldInfo] objects. This replaces Model.__fields__ from Pydantic V1.
- __pydantic_fields_set__¶
The names of fields explicitly set during instantiation.
- __pydantic_generic_metadata__ = {'args': (), 'origin': None, 'parameters': ()}¶
A dictionary containing metadata about generic Pydantic models.
The origin and args items map to the [__origin__][genericalias.__origin__] and [__args__][genericalias.__args__] attributes of [generic aliases][types-genericalias], and the parameter item maps to the __parameter__ attribute of generic classes.
- __pydantic_post_init__ = 'model_post_init'¶
The name of the post-init method for the model, if defined.
- __pydantic_private__¶
Values of private attributes set on the model instance.
- __pydantic_serializer__ = SchemaSerializer(serializer=PolymorphismTrampoline( PolymorphismTrampoline { class: Py( 0x000063affefd7690, ), serializer: PolymorphismTrampoline( PolymorphismTrampoline { class: Py( 0x000063affefd7690, ), serializer: Model( ModelSerializer { class: Py( 0x000063affefd7690, ), serializer: Fields( GeneralFieldsSerializer { fields: { "repository_metadata": SerField { key: "repository_metadata", alias: None, serializer: Some( WithDefault( WithDefaultSerializer { default: DefaultFactory( Py( 0x00007310e74524a0, ), false, ), serializer: Dict( DictSerializer { key_serializer: Str( StrSerializer, ), value_serializer: Any( AnySerializer, ), filter: SchemaFilter { include: None, exclude: None, }, name: "dict[str, any]", }, ), }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "pk": SerField { key: "pk", alias: None, serializer: Some( Int( IntSerializer, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "process_type": SerField { key: "process_type", alias: None, serializer: Some( WithDefault( WithDefaultSerializer { default: Default( Py( 0x00007310e7455800, ), ), serializer: Nullable( NullableSerializer { serializer: Str( StrSerializer, ), }, ), }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "ctime": SerField { key: "ctime", alias: None, serializer: Some( Function( FunctionPlainSerializer { func: Py( 0x00007310e2355c60, ), name: "plain_function[<lambda>]", function_name: "<lambda>", return_serializer: Any( AnySerializer, ), fallback_serializer: Some( Datetime( DatetimeSerializer { temporal_mode: Iso8601, }, ), ), when_used: Json, is_field_serializer: false, info_arg: false, }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "user": SerField { key: "user", alias: None, serializer: Some( Int( IntSerializer, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "attributes": SerField { key: "attributes", alias: None, serializer: Some( PolymorphismTrampoline( PolymorphismTrampoline { class: Py( 0x000063affe3a27e0, ), serializer: Prebuilt( PrebuiltSerializer { schema_serializer: Py( 0x00007310d282cb80, ), }, ), enabled_from_config: false, }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "node_type": SerField { key: "node_type", alias: None, serializer: Some( Literal( LiteralSerializer { expected_int: {}, expected_str: { "data.gromacs.make_ndx.Make_ndxParameters.", }, expected_py: None, name: "literal['data.gromacs.make_ndx.Make_ndxParameters.']", }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "uuid": SerField { key: "uuid", alias: None, serializer: Some( Uuid( UuidSerializer, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "computer": SerField { key: "computer", alias: None, serializer: Some( WithDefault( WithDefaultSerializer { default: Default( Py( 0x00007310e7455800, ), ), serializer: Nullable( NullableSerializer { serializer: Int( IntSerializer, ), }, ), }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "description": SerField { key: "description", alias: None, serializer: Some( WithDefault( WithDefaultSerializer { default: Default( Py( 0x00007310e7482e40, ), ), serializer: Str( StrSerializer, ), }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "mtime": SerField { key: "mtime", alias: None, serializer: Some( Function( FunctionPlainSerializer { func: Py( 0x00007310e2355c60, ), name: "plain_function[<lambda>]", function_name: "<lambda>", return_serializer: Any( AnySerializer, ), fallback_serializer: Some( Datetime( DatetimeSerializer { temporal_mode: Iso8601, }, ), ), when_used: Json, is_field_serializer: false, info_arg: false, }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "extras": SerField { key: "extras", alias: None, serializer: Some( WithDefault( WithDefaultSerializer { default: DefaultFactory( Py( 0x00007310e74524a0, ), false, ), serializer: Dict( DictSerializer { key_serializer: Str( StrSerializer, ), value_serializer: Any( AnySerializer, ), filter: SchemaFilter { include: None, exclude: None, }, name: "dict[str, any]", }, ), }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "label": SerField { key: "label", alias: None, serializer: Some( WithDefault( WithDefaultSerializer { default: Default( Py( 0x00007310e7482e40, ), ), serializer: Str( StrSerializer, ), }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, }, computed_fields: Some( ComputedFields( [], ), ), mode: SimpleDict, extra_serializer: None, filter: SchemaFilter { include: None, exclude: None, }, required_fields: 13, }, ), has_extra: false, root_model: false, name: "ReadModel", }, ), enabled_from_config: false, }, ), enabled_from_config: false, }, ), definitions=[])¶
The pydantic-core SchemaSerializer used to dump instances of the model.
- __pydantic_setattr_handlers__ = {}¶
__setattr__ handlers. Memoizing the handlers leads to a dramatic performance improvement in __setattr__
- __pydantic_validator__ = SchemaValidator(title="Make_ndxParametersReadModel", validator=Model( ModelValidator { revalidate: Never, validator: ModelFields( ModelFieldsValidator { fields: [ Field { name: "pk", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "pk", ), rest: [], }, by_alias: [], }, validator: Int( IntValidator { strict: false, }, ), frozen: false, }, Field { name: "label", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "label", ), rest: [], }, by_alias: [], }, validator: WithDefault( WithDefaultValidator { default: Default( Py( 0x00007310e7482e40, ), ), on_error: Raise, validator: Str( StrValidator { strict: false, coerce_numbers_to_str: false, }, ), validate_default: false, copy_default: false, name: "default[str]", undefined: Py( 0x00007310e53bdb90, ), }, ), frozen: false, }, Field { name: "description", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "description", ), rest: [], }, by_alias: [], }, validator: WithDefault( WithDefaultValidator { default: Default( Py( 0x00007310e7482e40, ), ), on_error: Raise, validator: Str( StrValidator { strict: false, coerce_numbers_to_str: false, }, ), validate_default: false, copy_default: false, name: "default[str]", undefined: Py( 0x00007310e53bdb90, ), }, ), frozen: false, }, Field { name: "extras", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "extras", ), rest: [], }, by_alias: [], }, validator: WithDefault( WithDefaultValidator { default: DefaultFactory( Py( 0x00007310e74524a0, ), false, ), on_error: Raise, validator: Dict( DictValidator { strict: false, key_validator: Str( StrValidator { strict: false, coerce_numbers_to_str: false, }, ), value_validator: Any( AnyValidator, ), min_length: None, max_length: None, fail_fast: false, name: "dict[str,any]", }, ), validate_default: false, copy_default: false, name: "default[dict[str,any]]", undefined: Py( 0x00007310e53bdb90, ), }, ), frozen: false, }, Field { name: "node_type", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "node_type", ), rest: [], }, by_alias: [], }, validator: Literal( LiteralValidator { lookup: LiteralLookup { expected_bool: None, expected_int: None, expected_str: Some( { "data.gromacs.make_ndx.Make_ndxParameters.": 0, }, ), expected_py_dict: None, expected_py_values: None, expected_py_primitives: Some( Py( 0x00007310d283d3c0, ), ), values: [ Py( 0x00007310d8116970, ), ], }, expected_repr: "'data.gromacs.make_ndx.Make_ndxParameters.'", name: "literal['data.gromacs.make_ndx.Make_ndxParameters.']", }, ), frozen: false, }, Field { name: "attributes", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "attributes", ), rest: [], }, by_alias: [], }, validator: Prebuilt( PrebuiltValidator { schema_validator: Py( 0x00007310d282fbe0, ), }, ), frozen: false, }, Field { name: "repository_metadata", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "repository_metadata", ), rest: [], }, by_alias: [], }, validator: WithDefault( WithDefaultValidator { default: DefaultFactory( Py( 0x00007310e74524a0, ), false, ), on_error: Raise, validator: Dict( DictValidator { strict: false, key_validator: Str( StrValidator { strict: false, coerce_numbers_to_str: false, }, ), value_validator: Any( AnyValidator, ), min_length: None, max_length: None, fail_fast: false, name: "dict[str,any]", }, ), validate_default: false, copy_default: false, name: "default[dict[str,any]]", undefined: Py( 0x00007310e53bdb90, ), }, ), frozen: false, }, Field { name: "uuid", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "uuid", ), rest: [], }, by_alias: [], }, validator: Uuid( UuidValidator { strict: false, version: None, }, ), frozen: false, }, Field { name: "process_type", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "process_type", ), rest: [], }, by_alias: [], }, validator: WithDefault( WithDefaultValidator { default: Default( Py( 0x00007310e7455800, ), ), on_error: Raise, validator: Nullable( NullableValidator { validator: Str( StrValidator { strict: false, coerce_numbers_to_str: false, }, ), name: "nullable[str]", }, ), validate_default: false, copy_default: false, name: "default[nullable[str]]", undefined: Py( 0x00007310e53bdb90, ), }, ), frozen: false, }, Field { name: "ctime", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "ctime", ), rest: [], }, by_alias: [], }, validator: Datetime( DateTimeValidator { strict: false, constraints: None, microseconds_precision: Truncate, val_temporal_unit: Infer, }, ), frozen: false, }, Field { name: "mtime", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "mtime", ), rest: [], }, by_alias: [], }, validator: Datetime( DateTimeValidator { strict: false, constraints: None, microseconds_precision: Truncate, val_temporal_unit: Infer, }, ), frozen: false, }, Field { name: "computer", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "computer", ), rest: [], }, by_alias: [], }, validator: WithDefault( WithDefaultValidator { default: Default( Py( 0x00007310e7455800, ), ), on_error: Raise, validator: Nullable( NullableValidator { validator: Int( IntValidator { strict: false, }, ), name: "nullable[int]", }, ), validate_default: false, copy_default: false, name: "default[nullable[int]]", undefined: Py( 0x00007310e53bdb90, ), }, ), frozen: false, }, Field { name: "user", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "user", ), rest: [], }, by_alias: [], }, validator: Int( IntValidator { strict: false, }, ), frozen: false, }, ], model_name: "ReadModel", extra_behavior: Forbid, extras_validator: None, extras_keys_validator: None, strict: false, from_attributes: false, loc_by_alias: true, lookup: LookupTree { inner: { PathItemString( "extras", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 3, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "process_type", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 8, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "ctime", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 9, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "computer", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 11, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "description", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 2, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "mtime", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 10, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "node_type", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 4, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "repository_metadata", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 6, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "attributes", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 5, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "user", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 12, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "uuid", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 7, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "pk", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 0, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "label", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 1, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, }, }, validate_by_alias: Some( true, ), validate_by_name: Some( true, ), }, ), class: Py( 0x000063affefd7690, ), generic_origin: None, post_init: Some( Py( 0x00007310e2571630, ), ), frozen: false, custom_init: false, root_model: false, undefined: Py( 0x00007310e53bdb90, ), name: "ReadModel", }, ), definitions=[], cache_strings=True)¶
The pydantic-core SchemaValidator used to validate instances of the model.
- _abc_impl = <_abc._abc_data object>¶
- attributes: AttributesModel¶
- model_config = {'defer_build': True, 'extra': 'forbid', 'json_encoders': {<class 'datetime.datetime'>: <function OrmModel.<lambda>>}, 'serialize_by_alias': True, 'title': 'Make_ndxParametersReadModel', 'validate_by_alias': True, 'validate_by_name': True}¶
Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].
- class WriteModel(**data: Any)¶
Bases:
WriteModel- __abstractmethods__ = frozenset({})¶
- __annotations__ = {'attributes': <class 'aiida_gromacs.data.make_ndx.Make_ndxParameters.AttributesWriteModel'>, 'description': <class 'str'>, 'extras': dict[str, typing.Any], 'label': <class 'str'>, 'node_type': typing.Literal['data.gromacs.make_ndx.Make_ndxParameters.'], 'repository_metadata': dict[str, typing.Any]}¶
- __class_vars__ = {}¶
The names of the class variables defined on the model.
- __dict__¶
- __module__ = 'aiida_gromacs.data.make_ndx'¶
- __private_attributes__ = {'_AIIDA_MINIMAL_MODEL': ModelPrivateAttr()}¶
Metadata about the private attributes of the model.
- __pydantic_complete__ = True¶
Whether model building is completed, or if there are still undefined fields.
- __pydantic_computed_fields__ = {}¶
A dictionary of computed field names and their corresponding [ComputedFieldInfo][pydantic.fields.ComputedFieldInfo] objects.
- __pydantic_core_schema__ = {'cls': <class 'aiida_gromacs.data.make_ndx.Make_ndxParameters.WriteModel'>, 'config': {'extra_fields_behavior': 'forbid', 'serialize_by_alias': True, 'title': 'Make_ndxParametersWriteModel', 'validate_by_alias': True, 'validate_by_name': True}, 'custom_init': False, 'metadata': {'pydantic_js_functions': [<bound method BaseModel.__get_pydantic_json_schema__ of <class 'aiida_gromacs.data.make_ndx.Make_ndxParameters.WriteModel'>>]}, 'post_init': 'model_post_init', 'ref': 'aiida_gromacs.data.make_ndx.Make_ndxParameters.WriteModel:109607548899840', 'root_model': False, 'schema': {'computed_fields': [], 'fields': {'attributes': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'The node attributes', 'examples': [{'attr_key': 'attr_value'}]}}, 'schema': {'cls': <class 'aiida_gromacs.data.make_ndx.Make_ndxParameters.AttributesWriteModel'>, 'config': {'extra_fields_behavior': 'allow', 'serialize_by_alias': True, 'title': 'Make_ndxParametersAttributesWriteModel', 'validate_by_alias': True, 'validate_by_name': True}, 'custom_init': False, 'metadata': {'pydantic_js_functions': [<bound method BaseModel.__get_pydantic_json_schema__ of <class 'aiida_gromacs.data.make_ndx.Make_ndxParameters.AttributesWriteModel'>>]}, 'post_init': 'model_post_init', 'ref': 'aiida_gromacs.data.make_ndx.Make_ndxParameters.AttributesWriteModel:109607548906512', 'root_model': False, 'schema': {'computed_fields': [], 'fields': {'source': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'Source of the data'}}, 'schema': {'default': None, 'schema': {'schema': {'keys_schema': {'type': 'any'}, 'type': 'dict', 'values_schema': {'type': 'any'}}, 'type': 'nullable'}, 'type': 'default'}, 'type': 'model-field'}}, 'model_name': 'AttributesWriteModel', 'type': 'model-fields'}, 'type': 'model'}, 'type': 'model-field'}, 'description': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'The node description', 'examples': ['This is my node description.']}}, 'schema': {'default': '', 'schema': {'type': 'str'}, 'type': 'default'}, 'type': 'model-field'}, 'extras': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'The node extras', 'examples': [{'extra_key': 'extra_value'}]}}, 'schema': {'default_factory': <class 'dict'>, 'default_factory_takes_data': False, 'schema': {'keys_schema': {'type': 'str'}, 'type': 'dict', 'values_schema': {'type': 'any'}}, 'type': 'default'}, 'type': 'model-field'}, 'label': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'The node label', 'examples': ['my_node']}}, 'schema': {'default': '', 'schema': {'type': 'str'}, 'type': 'default'}, 'type': 'model-field'}, 'node_type': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'The type of the node.'}}, 'schema': {'expected': ['data.gromacs.make_ndx.Make_ndxParameters.'], 'type': 'literal'}, 'type': 'model-field'}, 'repository_metadata': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'Virtual hierarchy of the file repository', 'examples': [{'o': {'file.txt': {'k': '<file_hash>'}}}]}}, 'schema': {'default_factory': <class 'dict'>, 'default_factory_takes_data': False, 'schema': {'keys_schema': {'type': 'str'}, 'type': 'dict', 'values_schema': {'type': 'any'}}, 'type': 'default'}, 'type': 'model-field'}}, 'model_name': 'WriteModel', 'type': 'model-fields'}, 'type': 'model'}¶
The core schema of the model.
- __pydantic_custom_init__ = False¶
Whether the model has a custom __init__ method.
- __pydantic_decorators__ = DecoratorInfos(validators={}, field_validators={}, root_validators={}, field_serializers={}, model_serializers={}, model_validators={}, computed_fields={})¶
Metadata containing the decorators defined on the model. This replaces Model.__validators__ and Model.__root_validators__ from Pydantic V1.
- __pydantic_extra__¶
A dictionary containing extra values, if [extra][pydantic.config.ConfigDict.extra] is set to ‘allow’.
- __pydantic_extra_info__ = None¶
A wrapper around the __pydantic_extra__ annotation, if explicitly annotated on a model.
This is a private attribute, not meant to be used outside Pydantic.
- __pydantic_fields__ = {'attributes': FieldInfo(annotation=Make_ndxParameters.AttributesWriteModel, required=True, description='The node attributes', examples=[{'attr_key': 'attr_value'}], json_schema_extra={}, metadata=[{'priority': 0}, {'read_only': False}, {'write_only': False}, {'may_be_large': True}]), 'description': FieldInfo(annotation=str, required=False, default='', description='The node description', examples=['This is my node description.'], json_schema_extra={}, metadata=[{'priority': 0}, {'read_only': False}, {'write_only': False}, {'may_be_large': False}]), 'extras': FieldInfo(annotation=dict[str, Any], required=False, default_factory=dict, description='The node extras', examples=[{'extra_key': 'extra_value'}], json_schema_extra={}, metadata=[{'priority': 0}, {'read_only': False}, {'write_only': False}, {'may_be_large': True}, {'orm_to_model': <function Node.MutableNodeFields.<lambda>>}]), 'label': FieldInfo(annotation=str, required=False, default='', description='The node label', examples=['my_node'], json_schema_extra={}, metadata=[{'priority': 0}, {'read_only': False}, {'write_only': False}, {'may_be_large': False}]), 'node_type': FieldInfo(annotation=Literal['data.gromacs.make_ndx.Make_ndxParameters.'], required=True, description='The type of the node.', json_schema_extra={}, metadata=[{'priority': 0}, {'read_only': False}, {'write_only': False}, {'may_be_large': False}]), 'repository_metadata': FieldInfo(annotation=dict[str, Any], required=False, default_factory=dict, description='Virtual hierarchy of the file repository', examples=[{'o': {'file.txt': {'k': '<file_hash>'}}}], json_schema_extra={}, metadata=[{'priority': 0}, {'read_only': False}, {'write_only': False}, {'may_be_large': True}, {'orm_to_model': <function Node.WritableFields.<lambda>>}])}¶
A dictionary of field names and their corresponding [FieldInfo][pydantic.fields.FieldInfo] objects. This replaces Model.__fields__ from Pydantic V1.
- __pydantic_fields_set__¶
The names of fields explicitly set during instantiation.
- __pydantic_generic_metadata__ = {'args': (), 'origin': None, 'parameters': ()}¶
A dictionary containing metadata about generic Pydantic models.
The origin and args items map to the [__origin__][genericalias.__origin__] and [__args__][genericalias.__args__] attributes of [generic aliases][types-genericalias], and the parameter item maps to the __parameter__ attribute of generic classes.
- __pydantic_post_init__ = 'model_post_init'¶
The name of the post-init method for the model, if defined.
- __pydantic_private__¶
Values of private attributes set on the model instance.
- __pydantic_serializer__ = SchemaSerializer(serializer=PolymorphismTrampoline( PolymorphismTrampoline { class: Py( 0x000063afff045200, ), serializer: PolymorphismTrampoline( PolymorphismTrampoline { class: Py( 0x000063afff045200, ), serializer: Model( ModelSerializer { class: Py( 0x000063afff045200, ), serializer: Fields( GeneralFieldsSerializer { fields: { "label": SerField { key: "label", alias: None, serializer: Some( WithDefault( WithDefaultSerializer { default: Default( Py( 0x00007310e7482e40, ), ), serializer: Str( StrSerializer, ), }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "repository_metadata": SerField { key: "repository_metadata", alias: None, serializer: Some( WithDefault( WithDefaultSerializer { default: DefaultFactory( Py( 0x00007310e74524a0, ), false, ), serializer: Dict( DictSerializer { key_serializer: Str( StrSerializer, ), value_serializer: Any( AnySerializer, ), filter: SchemaFilter { include: None, exclude: None, }, name: "dict[str, any]", }, ), }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "description": SerField { key: "description", alias: None, serializer: Some( WithDefault( WithDefaultSerializer { default: Default( Py( 0x00007310e7482e40, ), ), serializer: Str( StrSerializer, ), }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "extras": SerField { key: "extras", alias: None, serializer: Some( WithDefault( WithDefaultSerializer { default: DefaultFactory( Py( 0x00007310e74524a0, ), false, ), serializer: Dict( DictSerializer { key_serializer: Str( StrSerializer, ), value_serializer: Any( AnySerializer, ), filter: SchemaFilter { include: None, exclude: None, }, name: "dict[str, any]", }, ), }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "attributes": SerField { key: "attributes", alias: None, serializer: Some( PolymorphismTrampoline( PolymorphismTrampoline { class: Py( 0x000063afff046c10, ), serializer: PolymorphismTrampoline( PolymorphismTrampoline { class: Py( 0x000063afff046c10, ), serializer: Model( ModelSerializer { class: Py( 0x000063afff046c10, ), serializer: Fields( GeneralFieldsSerializer { fields: { "source": SerField { key: "source", alias: None, serializer: Some( WithDefault( WithDefaultSerializer { default: Default( Py( 0x00007310e7455800, ), ), serializer: Nullable( NullableSerializer { serializer: Dict( DictSerializer { key_serializer: Any( AnySerializer, ), value_serializer: Any( AnySerializer, ), filter: SchemaFilter { include: None, exclude: None, }, name: "dict[any, any]", }, ), }, ), }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, }, computed_fields: Some( ComputedFields( [], ), ), mode: ModelExtra, extra_serializer: None, filter: SchemaFilter { include: None, exclude: None, }, required_fields: 1, }, ), has_extra: true, root_model: false, name: "AttributesWriteModel", }, ), enabled_from_config: false, }, ), enabled_from_config: false, }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "node_type": SerField { key: "node_type", alias: None, serializer: Some( Literal( LiteralSerializer { expected_int: {}, expected_str: { "data.gromacs.make_ndx.Make_ndxParameters.", }, expected_py: None, name: "literal['data.gromacs.make_ndx.Make_ndxParameters.']", }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, }, computed_fields: Some( ComputedFields( [], ), ), mode: SimpleDict, extra_serializer: None, filter: SchemaFilter { include: None, exclude: None, }, required_fields: 6, }, ), has_extra: false, root_model: false, name: "WriteModel", }, ), enabled_from_config: false, }, ), enabled_from_config: false, }, ), definitions=[])¶
The pydantic-core SchemaSerializer used to dump instances of the model.
- __pydantic_setattr_handlers__ = {}¶
__setattr__ handlers. Memoizing the handlers leads to a dramatic performance improvement in __setattr__
- __pydantic_validator__ = SchemaValidator(title="Make_ndxParametersWriteModel", validator=Model( ModelValidator { revalidate: Never, validator: ModelFields( ModelFieldsValidator { fields: [ Field { name: "label", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "label", ), rest: [], }, by_alias: [], }, validator: WithDefault( WithDefaultValidator { default: Default( Py( 0x00007310e7482e40, ), ), on_error: Raise, validator: Str( StrValidator { strict: false, coerce_numbers_to_str: false, }, ), validate_default: false, copy_default: false, name: "default[str]", undefined: Py( 0x00007310e53bdb90, ), }, ), frozen: false, }, Field { name: "description", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "description", ), rest: [], }, by_alias: [], }, validator: WithDefault( WithDefaultValidator { default: Default( Py( 0x00007310e7482e40, ), ), on_error: Raise, validator: Str( StrValidator { strict: false, coerce_numbers_to_str: false, }, ), validate_default: false, copy_default: false, name: "default[str]", undefined: Py( 0x00007310e53bdb90, ), }, ), frozen: false, }, Field { name: "extras", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "extras", ), rest: [], }, by_alias: [], }, validator: WithDefault( WithDefaultValidator { default: DefaultFactory( Py( 0x00007310e74524a0, ), false, ), on_error: Raise, validator: Dict( DictValidator { strict: false, key_validator: Str( StrValidator { strict: false, coerce_numbers_to_str: false, }, ), value_validator: Any( AnyValidator, ), min_length: None, max_length: None, fail_fast: false, name: "dict[str,any]", }, ), validate_default: false, copy_default: false, name: "default[dict[str,any]]", undefined: Py( 0x00007310e53bdb90, ), }, ), frozen: false, }, Field { name: "node_type", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "node_type", ), rest: [], }, by_alias: [], }, validator: Literal( LiteralValidator { lookup: LiteralLookup { expected_bool: None, expected_int: None, expected_str: Some( { "data.gromacs.make_ndx.Make_ndxParameters.": 0, }, ), expected_py_dict: None, expected_py_values: None, expected_py_primitives: Some( Py( 0x00007310d285af40, ), ), values: [ Py( 0x00007310d8116970, ), ], }, expected_repr: "'data.gromacs.make_ndx.Make_ndxParameters.'", name: "literal['data.gromacs.make_ndx.Make_ndxParameters.']", }, ), frozen: false, }, Field { name: "attributes", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "attributes", ), rest: [], }, by_alias: [], }, validator: Model( ModelValidator { revalidate: Never, validator: ModelFields( ModelFieldsValidator { fields: [ Field { name: "source", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "source", ), rest: [], }, by_alias: [], }, validator: WithDefault( WithDefaultValidator { default: Default( Py( 0x00007310e7455800, ), ), on_error: Raise, validator: Nullable( NullableValidator { validator: Dict( DictValidator { strict: false, key_validator: Any( AnyValidator, ), value_validator: Any( AnyValidator, ), min_length: None, max_length: None, fail_fast: false, name: "dict[any,any]", }, ), name: "nullable[dict[any,any]]", }, ), validate_default: false, copy_default: false, name: "default[nullable[dict[any,any]]]", undefined: Py( 0x00007310e53bdb90, ), }, ), frozen: false, }, ], model_name: "AttributesWriteModel", extra_behavior: Allow, extras_validator: None, extras_keys_validator: None, strict: false, from_attributes: false, loc_by_alias: true, lookup: LookupTree { inner: { PathItemString( "source", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 0, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, }, }, validate_by_alias: Some( true, ), validate_by_name: Some( true, ), }, ), class: Py( 0x000063afff046c10, ), generic_origin: None, post_init: Some( Py( 0x00007310e2571630, ), ), frozen: false, custom_init: false, root_model: false, undefined: Py( 0x00007310e53bdb90, ), name: "AttributesWriteModel", }, ), frozen: false, }, Field { name: "repository_metadata", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "repository_metadata", ), rest: [], }, by_alias: [], }, validator: WithDefault( WithDefaultValidator { default: DefaultFactory( Py( 0x00007310e74524a0, ), false, ), on_error: Raise, validator: Dict( DictValidator { strict: false, key_validator: Str( StrValidator { strict: false, coerce_numbers_to_str: false, }, ), value_validator: Any( AnyValidator, ), min_length: None, max_length: None, fail_fast: false, name: "dict[str,any]", }, ), validate_default: false, copy_default: false, name: "default[dict[str,any]]", undefined: Py( 0x00007310e53bdb90, ), }, ), frozen: false, }, ], model_name: "WriteModel", extra_behavior: Forbid, extras_validator: None, extras_keys_validator: None, strict: false, from_attributes: false, loc_by_alias: true, lookup: LookupTree { inner: { PathItemString( "node_type", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 3, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "description", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 1, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "label", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 0, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "extras", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 2, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "repository_metadata", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 5, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "attributes", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 4, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, }, }, validate_by_alias: Some( true, ), validate_by_name: Some( true, ), }, ), class: Py( 0x000063afff045200, ), generic_origin: None, post_init: Some( Py( 0x00007310e2571630, ), ), frozen: false, custom_init: false, root_model: false, undefined: Py( 0x00007310e53bdb90, ), name: "WriteModel", }, ), definitions=[], cache_strings=True)¶
The pydantic-core SchemaValidator used to validate instances of the model.
- _abc_impl = <_abc._abc_data object>¶
- attributes: AttributesWriteModel¶
- model_config = {'defer_build': True, 'extra': 'forbid', 'json_encoders': {<class 'datetime.datetime'>: <function OrmModel.<lambda>>}, 'serialize_by_alias': True, 'title': 'Make_ndxParametersWriteModel', 'validate_by_alias': True, 'validate_by_name': True}¶
Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].
- _COMPAT_MODEL¶
alias of
Model
- _ConstructorModel¶
alias of
ConstructorModel
- _MODEL_MAP = {'read': <class 'aiida_gromacs.data.make_ndx.Make_ndxParameters.ReadModel'>, 'write': <class 'aiida_gromacs.data.make_ndx.Make_ndxParameters.WriteModel'>}¶
- __abstractmethods__ = frozenset({})¶
- __annotations__ = {}¶
- __firstlineno__ = 21¶
- __init__(dict=None, **kwargs)[source]¶
Constructor for the data class
Usage:
Make_ndxParameters(dict{'ignore-case': True})- Parameters:
parameters_dict (type) – dictionary with commandline parameters
parameters_dict – dict
- __module__ = 'aiida_gromacs.data.make_ndx'¶
- __parameters__ = ()¶
- __static_attributes__ = ()¶
- __str__()[source]¶
String representation of node.
Append values of dictionary to usual representation. E.g.:
uuid: b416cbee-24e8-47a8-8c11-6d668770158b (pk: 590) {'ignore-case': True}
- _abc_impl = <_abc._abc_data object>¶
- _logger = <Logger aiida_gromacs.data.make_ndx.Make_ndxParameters (WARNING)>¶
- cmdline_params(input_files)[source]¶
Synthesize command line parameters.
e.g. [ ‘–ignore-case’, ‘filename1’, ‘filename2’]
- Parameters:
pdbfile (type) – Name of input pdb file
pdbfile – str
- fields = {'attributes': "QbAttributesField('attributes', dtype=<class 'aiida_gromacs.data.make_ndx.Make_ndxParameters.AttributesModel'>, doc='The node attributes')", 'computer': "QbNumericField('computer', dtype=int | None, doc='The PK of the computer')", 'ctime': "QbNumericField('ctime', dtype=<class 'datetime.datetime'>, doc='The creation time of the node')", 'description': "QbStrField('description', dtype=<class 'str'>, doc='The node description')", 'extras': "QbDictField('extras', dtype=dict[str, typing.Any], doc='The node extras')", 'label': "QbStrField('label', dtype=<class 'str'>, doc='The node label')", 'mtime': "QbNumericField('mtime', dtype=<class 'datetime.datetime'>, doc='The modification time of the node')", 'node_type': "QbStrField('node_type', dtype=typing.Literal['data.gromacs.make_ndx.Make_ndxParameters.'], doc='The type of the node.')", 'pk': "QbNumericField('pk', dtype=<class 'int'>, doc='The primary key of the entity')", 'process_type': "QbStrField('process_type', dtype=str | None, doc='The process type of the node')", 'repository_metadata': "QbDictField('repository_metadata', dtype=dict[str, typing.Any], doc='Virtual hierarchy of the file repository')", 'source': "QbDictField('attributes.source', dtype=dict | None, doc='Source of the data')", 'user': "QbNumericField('user', dtype=<class 'int'>, doc='The PK of the user who owns the node')", 'uuid': "QbStrField('uuid', dtype=<class 'uuid.UUID'>, doc='The UUID of the node')"}¶
- schema = <Schema({'o': <class 'str'>, 'natoms': <class 'str'>, 'notwin': <class 'str'>, 'twin': <class 'str'>}, extra=PREVENT_EXTRA, required=False) object>¶
- validate(parameters_dict)[source]¶
Validate command line options.
Uses the voluptuous package for validation. Find out about allowed keys using:
print(Make_ndxParameters).schema.schema
- Parameters:
parameters_dict (type) – dictionary with commandline parameters
parameters_dict – dict
- Returns:
validated dictionary
aiida_gromacs.data.mdrun module¶
Data types provided by plugin
Register data types via the “aiida.data” entry point in setup.json.
- class aiida_gromacs.data.mdrun.MdrunParameters(dict=None, **kwargs)[source]¶
Bases:
DictCommand line options for diff.
This class represents a python dictionary used to pass command line options to the executable.
- class AttributesModel(**data: Any)¶
Bases:
AttributesModel- __abstractmethods__ = frozenset({})¶
- __annotations__ = {}¶
- __class_vars__ = {}¶
The names of the class variables defined on the model.
- __dict__¶
- __module__ = 'aiida_gromacs.data.mdrun'¶
- __private_attributes__ = {'_AIIDA_MINIMAL_MODEL': ModelPrivateAttr()}¶
Metadata about the private attributes of the model.
- __pydantic_complete__ = True¶
Whether model building is completed, or if there are still undefined fields.
- __pydantic_computed_fields__ = {}¶
A dictionary of computed field names and their corresponding [ComputedFieldInfo][pydantic.fields.ComputedFieldInfo] objects.
- __pydantic_core_schema__ = {'cls': <class 'aiida_gromacs.data.mdrun.MdrunParameters.AttributesModel'>, 'config': {'extra_fields_behavior': 'allow', 'serialize_by_alias': True, 'title': 'MdrunParametersAttributesModel', 'validate_by_alias': True, 'validate_by_name': True}, 'custom_init': False, 'metadata': {'pydantic_js_functions': [<bound method BaseModel.__get_pydantic_json_schema__ of <class 'aiida_gromacs.data.mdrun.MdrunParameters.AttributesModel'>>]}, 'post_init': 'model_post_init', 'ref': 'aiida_gromacs.data.mdrun.MdrunParameters.AttributesModel:109607548923296', 'root_model': False, 'schema': {'computed_fields': [], 'fields': {'source': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'Source of the data'}}, 'schema': {'default': None, 'schema': {'schema': {'keys_schema': {'type': 'any'}, 'type': 'dict', 'values_schema': {'type': 'any'}}, 'type': 'nullable'}, 'type': 'default'}, 'type': 'model-field'}}, 'model_name': 'AttributesModel', 'type': 'model-fields'}, 'type': 'model'}¶
The core schema of the model.
- __pydantic_custom_init__ = False¶
Whether the model has a custom __init__ method.
- __pydantic_decorators__ = DecoratorInfos(validators={}, field_validators={}, root_validators={}, field_serializers={}, model_serializers={}, model_validators={}, computed_fields={})¶
Metadata containing the decorators defined on the model. This replaces Model.__validators__ and Model.__root_validators__ from Pydantic V1.
- __pydantic_extra__¶
A dictionary containing extra values, if [extra][pydantic.config.ConfigDict.extra] is set to ‘allow’.
- __pydantic_extra_info__ = None¶
A wrapper around the __pydantic_extra__ annotation, if explicitly annotated on a model.
This is a private attribute, not meant to be used outside Pydantic.
- __pydantic_fields__ = {'source': FieldInfo(annotation=Union[dict, NoneType], required=False, default=None, description='Source of the data', json_schema_extra={}, metadata=[{'priority': 0}, {'read_only': False}, {'write_only': False}, {'may_be_large': False}])}¶
A dictionary of field names and their corresponding [FieldInfo][pydantic.fields.FieldInfo] objects. This replaces Model.__fields__ from Pydantic V1.
- __pydantic_fields_set__¶
The names of fields explicitly set during instantiation.
- __pydantic_generic_metadata__ = {'args': (), 'origin': None, 'parameters': ()}¶
A dictionary containing metadata about generic Pydantic models.
The origin and args items map to the [__origin__][genericalias.__origin__] and [__args__][genericalias.__args__] attributes of [generic aliases][types-genericalias], and the parameter item maps to the __parameter__ attribute of generic classes.
- __pydantic_post_init__ = 'model_post_init'¶
The name of the post-init method for the model, if defined.
- __pydantic_private__¶
Values of private attributes set on the model instance.
- __pydantic_serializer__ = SchemaSerializer(serializer=PolymorphismTrampoline( PolymorphismTrampoline { class: Py( 0x000063afff04ada0, ), serializer: PolymorphismTrampoline( PolymorphismTrampoline { class: Py( 0x000063afff04ada0, ), serializer: Model( ModelSerializer { class: Py( 0x000063afff04ada0, ), serializer: Fields( GeneralFieldsSerializer { fields: { "source": SerField { key: "source", alias: None, serializer: Some( WithDefault( WithDefaultSerializer { default: Default( Py( 0x00007310e7455800, ), ), serializer: Nullable( NullableSerializer { serializer: Dict( DictSerializer { key_serializer: Any( AnySerializer, ), value_serializer: Any( AnySerializer, ), filter: SchemaFilter { include: None, exclude: None, }, name: "dict[any, any]", }, ), }, ), }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, }, computed_fields: Some( ComputedFields( [], ), ), mode: ModelExtra, extra_serializer: None, filter: SchemaFilter { include: None, exclude: None, }, required_fields: 1, }, ), has_extra: true, root_model: false, name: "AttributesModel", }, ), enabled_from_config: false, }, ), enabled_from_config: false, }, ), definitions=[])¶
The pydantic-core SchemaSerializer used to dump instances of the model.
- __pydantic_setattr_handlers__ = {}¶
__setattr__ handlers. Memoizing the handlers leads to a dramatic performance improvement in __setattr__
- __pydantic_validator__ = SchemaValidator(title="MdrunParametersAttributesModel", validator=Model( ModelValidator { revalidate: Never, validator: ModelFields( ModelFieldsValidator { fields: [ Field { name: "source", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "source", ), rest: [], }, by_alias: [], }, validator: WithDefault( WithDefaultValidator { default: Default( Py( 0x00007310e7455800, ), ), on_error: Raise, validator: Nullable( NullableValidator { validator: Dict( DictValidator { strict: false, key_validator: Any( AnyValidator, ), value_validator: Any( AnyValidator, ), min_length: None, max_length: None, fail_fast: false, name: "dict[any,any]", }, ), name: "nullable[dict[any,any]]", }, ), validate_default: false, copy_default: false, name: "default[nullable[dict[any,any]]]", undefined: Py( 0x00007310e53bdb90, ), }, ), frozen: false, }, ], model_name: "AttributesModel", extra_behavior: Allow, extras_validator: None, extras_keys_validator: None, strict: false, from_attributes: false, loc_by_alias: true, lookup: LookupTree { inner: { PathItemString( "source", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 0, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, }, }, validate_by_alias: Some( true, ), validate_by_name: Some( true, ), }, ), class: Py( 0x000063afff04ada0, ), generic_origin: None, post_init: Some( Py( 0x00007310e2571630, ), ), frozen: false, custom_init: false, root_model: false, undefined: Py( 0x00007310e53bdb90, ), name: "AttributesModel", }, ), definitions=[], cache_strings=True)¶
The pydantic-core SchemaValidator used to validate instances of the model.
- _abc_impl = <_abc._abc_data object>¶
- model_config = {'arbitrary_types_allowed': True, 'defer_build': True, 'extra': 'allow', 'json_encoders': {<class 'datetime.datetime'>: <function OrmModel.<lambda>>}, 'serialize_by_alias': True, 'title': 'MdrunParametersAttributesModel', 'validate_by_alias': True, 'validate_by_name': True}¶
Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].
- class ReadModel(**data: Any)¶
Bases:
ReadModel- __abstractmethods__ = frozenset({})¶
- __annotations__ = {'attributes': <class 'aiida_gromacs.data.mdrun.MdrunParameters.AttributesModel'>, 'node_type': typing.Literal['data.gromacs.mdrun.MdrunParameters.']}¶
- __class_vars__ = {}¶
The names of the class variables defined on the model.
- __dict__¶
- __module__ = 'aiida_gromacs.data.mdrun'¶
- __private_attributes__ = {'_AIIDA_MINIMAL_MODEL': ModelPrivateAttr()}¶
Metadata about the private attributes of the model.
- __pydantic_complete__ = True¶
Whether model building is completed, or if there are still undefined fields.
- __pydantic_computed_fields__ = {}¶
A dictionary of computed field names and their corresponding [ComputedFieldInfo][pydantic.fields.ComputedFieldInfo] objects.
- __pydantic_core_schema__ = {'cls': <class 'aiida_gromacs.data.mdrun.MdrunParameters.ReadModel'>, 'config': {'extra_fields_behavior': 'forbid', 'serialize_by_alias': True, 'title': 'MdrunParametersReadModel', 'validate_by_alias': True, 'validate_by_name': True}, 'custom_init': False, 'metadata': {'pydantic_js_functions': [<bound method BaseModel.__get_pydantic_json_schema__ of <class 'aiida_gromacs.data.mdrun.MdrunParameters.ReadModel'>>]}, 'post_init': 'model_post_init', 'ref': 'aiida_gromacs.data.mdrun.MdrunParameters.ReadModel:109607548509616', 'root_model': False, 'schema': {'computed_fields': [], 'fields': {'attributes': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'The node attributes', 'examples': [{'attr_key': 'attr_value'}]}}, 'schema': {'cls': <class 'aiida_gromacs.data.mdrun.MdrunParameters.AttributesModel'>, 'config': {'extra_fields_behavior': 'allow', 'serialize_by_alias': True, 'title': 'MdrunParametersAttributesModel', 'validate_by_alias': True, 'validate_by_name': True}, 'custom_init': False, 'metadata': {'pydantic_js_functions': [<bound method BaseModel.__get_pydantic_json_schema__ of <class 'aiida_gromacs.data.mdrun.MdrunParameters.AttributesModel'>>]}, 'post_init': 'model_post_init', 'ref': 'aiida_gromacs.data.mdrun.MdrunParameters.AttributesModel:109607548923296', 'root_model': False, 'schema': {'computed_fields': [], 'fields': {'source': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'Source of the data'}}, 'schema': {'default': None, 'schema': {'schema': {'keys_schema': {'type': 'any'}, 'type': 'dict', 'values_schema': {'type': 'any'}}, 'type': 'nullable'}, 'type': 'default'}, 'type': 'model-field'}}, 'model_name': 'AttributesModel', 'type': 'model-fields'}, 'type': 'model'}, 'type': 'model-field'}, 'computer': {'metadata': {'pydantic_js_extra': {'readOnly': True}, 'pydantic_js_updates': {'description': 'The PK of the computer', 'examples': [42]}}, 'schema': {'default': None, 'schema': {'schema': {'type': 'int'}, 'type': 'nullable'}, 'type': 'default'}, 'type': 'model-field'}, 'ctime': {'metadata': {'pydantic_js_extra': {'readOnly': True}, 'pydantic_js_updates': {'description': 'The creation time of the node', 'examples': ['2024-01-01T12:00:00+00:00']}}, 'schema': {'microseconds_precision': 'truncate', 'serialization': {'function': <function OrmModel.<lambda>>, 'type': 'function-plain', 'when_used': 'json'}, 'type': 'datetime'}, 'type': 'model-field'}, 'description': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'The node description', 'examples': ['This is my node description.']}}, 'schema': {'default': '', 'schema': {'type': 'str'}, 'type': 'default'}, 'type': 'model-field'}, 'extras': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'The node extras', 'examples': [{'extra_key': 'extra_value'}]}}, 'schema': {'default_factory': <class 'dict'>, 'default_factory_takes_data': False, 'schema': {'keys_schema': {'type': 'str'}, 'type': 'dict', 'values_schema': {'type': 'any'}}, 'type': 'default'}, 'type': 'model-field'}, 'label': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'The node label', 'examples': ['my_node']}}, 'schema': {'default': '', 'schema': {'type': 'str'}, 'type': 'default'}, 'type': 'model-field'}, 'mtime': {'metadata': {'pydantic_js_extra': {'readOnly': True}, 'pydantic_js_updates': {'description': 'The modification time of the node', 'examples': ['2024-01-02T12:00:00+00:00']}}, 'schema': {'microseconds_precision': 'truncate', 'serialization': {'function': <function OrmModel.<lambda>>, 'type': 'function-plain', 'when_used': 'json'}, 'type': 'datetime'}, 'type': 'model-field'}, 'node_type': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'The type of the node.'}}, 'schema': {'expected': ['data.gromacs.mdrun.MdrunParameters.'], 'type': 'literal'}, 'type': 'model-field'}, 'pk': {'metadata': {'pydantic_js_extra': {'readOnly': True}, 'pydantic_js_updates': {'description': 'The primary key of the entity', 'examples': [42]}}, 'schema': {'type': 'int'}, 'type': 'model-field'}, 'process_type': {'metadata': {'pydantic_js_extra': {'readOnly': True}, 'pydantic_js_updates': {'description': 'The process type of the node', 'examples': ['aiida.calculations:arithmetic.add.']}}, 'schema': {'default': None, 'schema': {'schema': {'type': 'str'}, 'type': 'nullable'}, 'type': 'default'}, 'type': 'model-field'}, 'repository_metadata': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'Virtual hierarchy of the file repository', 'examples': [{'o': {'file.txt': {'k': '<file_hash>'}}}]}}, 'schema': {'default_factory': <class 'dict'>, 'default_factory_takes_data': False, 'schema': {'keys_schema': {'type': 'str'}, 'type': 'dict', 'values_schema': {'type': 'any'}}, 'type': 'default'}, 'type': 'model-field'}, 'user': {'metadata': {'pydantic_js_extra': {'readOnly': True}, 'pydantic_js_updates': {'description': 'The PK of the user who owns the node', 'examples': [7]}}, 'schema': {'type': 'int'}, 'type': 'model-field'}, 'uuid': {'metadata': {'pydantic_js_extra': {'readOnly': True}, 'pydantic_js_updates': {'description': 'The UUID of the node', 'examples': ['123e4567-e89b-12d3-a456-426614174000']}}, 'schema': {'type': 'uuid'}, 'type': 'model-field'}}, 'model_name': 'ReadModel', 'type': 'model-fields'}, 'type': 'model'}¶
The core schema of the model.
- __pydantic_custom_init__ = False¶
Whether the model has a custom __init__ method.
- __pydantic_decorators__ = DecoratorInfos(validators={}, field_validators={}, root_validators={}, field_serializers={}, model_serializers={}, model_validators={}, computed_fields={})¶
Metadata containing the decorators defined on the model. This replaces Model.__validators__ and Model.__root_validators__ from Pydantic V1.
- __pydantic_extra__¶
A dictionary containing extra values, if [extra][pydantic.config.ConfigDict.extra] is set to ‘allow’.
- __pydantic_extra_info__ = None¶
A wrapper around the __pydantic_extra__ annotation, if explicitly annotated on a model.
This is a private attribute, not meant to be used outside Pydantic.
- __pydantic_fields__ = {'attributes': FieldInfo(annotation=MdrunParameters.AttributesModel, required=True, description='The node attributes', examples=[{'attr_key': 'attr_value'}], json_schema_extra={}, metadata=[{'priority': 0}, {'read_only': False}, {'write_only': False}, {'may_be_large': True}]), 'computer': FieldInfo(annotation=Union[int, NoneType], required=False, default=None, description='The PK of the computer', examples=[42], json_schema_extra={'readOnly': True}, metadata=[{'priority': 0}, {'read_only': True}, {'write_only': False}, {'may_be_large': False}, {'orm_class': <class 'aiida.orm.computers.Computer'>}, {'orm_to_model': <function Node.ReadModel.<lambda>>}]), 'ctime': FieldInfo(annotation=datetime, required=True, description='The creation time of the node', examples=['2024-01-01T12:00:00+00:00'], json_schema_extra={'readOnly': True}, metadata=[{'priority': 0}, {'read_only': True}, {'write_only': False}, {'may_be_large': False}]), 'description': FieldInfo(annotation=str, required=False, default='', description='The node description', examples=['This is my node description.'], json_schema_extra={}, metadata=[{'priority': 0}, {'read_only': False}, {'write_only': False}, {'may_be_large': False}]), 'extras': FieldInfo(annotation=dict[str, Any], required=False, default_factory=dict, description='The node extras', examples=[{'extra_key': 'extra_value'}], json_schema_extra={}, metadata=[{'priority': 0}, {'read_only': False}, {'write_only': False}, {'may_be_large': True}, {'orm_to_model': <function Node.MutableNodeFields.<lambda>>}]), 'label': FieldInfo(annotation=str, required=False, default='', description='The node label', examples=['my_node'], json_schema_extra={}, metadata=[{'priority': 0}, {'read_only': False}, {'write_only': False}, {'may_be_large': False}]), 'mtime': FieldInfo(annotation=datetime, required=True, description='The modification time of the node', examples=['2024-01-02T12:00:00+00:00'], json_schema_extra={'readOnly': True}, metadata=[{'priority': 0}, {'read_only': True}, {'write_only': False}, {'may_be_large': False}]), 'node_type': FieldInfo(annotation=Literal['data.gromacs.mdrun.MdrunParameters.'], required=True, description='The type of the node.', json_schema_extra={}, metadata=[{'priority': 0}, {'read_only': False}, {'write_only': False}, {'may_be_large': False}]), 'pk': FieldInfo(annotation=int, required=True, description='The primary key of the entity', examples=[42], json_schema_extra={'readOnly': True}, metadata=[{'priority': 0}, {'read_only': True}, {'write_only': False}, {'may_be_large': False}]), 'process_type': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, description='The process type of the node', examples=['aiida.calculations:arithmetic.add.'], json_schema_extra={'readOnly': True}, metadata=[{'priority': 0}, {'read_only': True}, {'write_only': False}, {'may_be_large': False}]), 'repository_metadata': FieldInfo(annotation=dict[str, Any], required=False, default_factory=dict, description='Virtual hierarchy of the file repository', examples=[{'o': {'file.txt': {'k': '<file_hash>'}}}], json_schema_extra={}, metadata=[{'priority': 0}, {'read_only': False}, {'write_only': False}, {'may_be_large': True}, {'orm_to_model': <function Node.WritableFields.<lambda>>}]), 'user': FieldInfo(annotation=int, required=True, description='The PK of the user who owns the node', examples=[7], json_schema_extra={'readOnly': True}, metadata=[{'priority': 0}, {'read_only': True}, {'write_only': False}, {'may_be_large': False}, {'orm_class': <class 'aiida.orm.users.User'>}, {'orm_to_model': <function Node.ReadModel.<lambda>>}]), 'uuid': FieldInfo(annotation=UUID, required=True, description='The UUID of the node', examples=['123e4567-e89b-12d3-a456-426614174000'], json_schema_extra={'readOnly': True}, metadata=[{'priority': 0}, {'read_only': True}, {'write_only': False}, {'may_be_large': False}])}¶
A dictionary of field names and their corresponding [FieldInfo][pydantic.fields.FieldInfo] objects. This replaces Model.__fields__ from Pydantic V1.
- __pydantic_fields_set__¶
The names of fields explicitly set during instantiation.
- __pydantic_generic_metadata__ = {'args': (), 'origin': None, 'parameters': ()}¶
A dictionary containing metadata about generic Pydantic models.
The origin and args items map to the [__origin__][genericalias.__origin__] and [__args__][genericalias.__args__] attributes of [generic aliases][types-genericalias], and the parameter item maps to the __parameter__ attribute of generic classes.
- __pydantic_post_init__ = 'model_post_init'¶
The name of the post-init method for the model, if defined.
- __pydantic_private__¶
Values of private attributes set on the model instance.
- __pydantic_serializer__ = SchemaSerializer(serializer=PolymorphismTrampoline( PolymorphismTrampoline { class: Py( 0x000063affefe5db0, ), serializer: PolymorphismTrampoline( PolymorphismTrampoline { class: Py( 0x000063affefe5db0, ), serializer: Model( ModelSerializer { class: Py( 0x000063affefe5db0, ), serializer: Fields( GeneralFieldsSerializer { fields: { "ctime": SerField { key: "ctime", alias: None, serializer: Some( Function( FunctionPlainSerializer { func: Py( 0x00007310e2355c60, ), name: "plain_function[<lambda>]", function_name: "<lambda>", return_serializer: Any( AnySerializer, ), fallback_serializer: Some( Datetime( DatetimeSerializer { temporal_mode: Iso8601, }, ), ), when_used: Json, is_field_serializer: false, info_arg: false, }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "description": SerField { key: "description", alias: None, serializer: Some( WithDefault( WithDefaultSerializer { default: Default( Py( 0x00007310e7482e40, ), ), serializer: Str( StrSerializer, ), }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "attributes": SerField { key: "attributes", alias: None, serializer: Some( PolymorphismTrampoline( PolymorphismTrampoline { class: Py( 0x000063afff04ada0, ), serializer: Prebuilt( PrebuiltSerializer { schema_serializer: Py( 0x00007310d2596200, ), }, ), enabled_from_config: false, }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "label": SerField { key: "label", alias: None, serializer: Some( WithDefault( WithDefaultSerializer { default: Default( Py( 0x00007310e7482e40, ), ), serializer: Str( StrSerializer, ), }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "node_type": SerField { key: "node_type", alias: None, serializer: Some( Literal( LiteralSerializer { expected_int: {}, expected_str: { "data.gromacs.mdrun.MdrunParameters.", }, expected_py: None, name: "literal['data.gromacs.mdrun.MdrunParameters.']", }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "uuid": SerField { key: "uuid", alias: None, serializer: Some( Uuid( UuidSerializer, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "repository_metadata": SerField { key: "repository_metadata", alias: None, serializer: Some( WithDefault( WithDefaultSerializer { default: DefaultFactory( Py( 0x00007310e74524a0, ), false, ), serializer: Dict( DictSerializer { key_serializer: Str( StrSerializer, ), value_serializer: Any( AnySerializer, ), filter: SchemaFilter { include: None, exclude: None, }, name: "dict[str, any]", }, ), }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "process_type": SerField { key: "process_type", alias: None, serializer: Some( WithDefault( WithDefaultSerializer { default: Default( Py( 0x00007310e7455800, ), ), serializer: Nullable( NullableSerializer { serializer: Str( StrSerializer, ), }, ), }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "computer": SerField { key: "computer", alias: None, serializer: Some( WithDefault( WithDefaultSerializer { default: Default( Py( 0x00007310e7455800, ), ), serializer: Nullable( NullableSerializer { serializer: Int( IntSerializer, ), }, ), }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "pk": SerField { key: "pk", alias: None, serializer: Some( Int( IntSerializer, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "user": SerField { key: "user", alias: None, serializer: Some( Int( IntSerializer, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "extras": SerField { key: "extras", alias: None, serializer: Some( WithDefault( WithDefaultSerializer { default: DefaultFactory( Py( 0x00007310e74524a0, ), false, ), serializer: Dict( DictSerializer { key_serializer: Str( StrSerializer, ), value_serializer: Any( AnySerializer, ), filter: SchemaFilter { include: None, exclude: None, }, name: "dict[str, any]", }, ), }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "mtime": SerField { key: "mtime", alias: None, serializer: Some( Function( FunctionPlainSerializer { func: Py( 0x00007310e2355c60, ), name: "plain_function[<lambda>]", function_name: "<lambda>", return_serializer: Any( AnySerializer, ), fallback_serializer: Some( Datetime( DatetimeSerializer { temporal_mode: Iso8601, }, ), ), when_used: Json, is_field_serializer: false, info_arg: false, }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, }, computed_fields: Some( ComputedFields( [], ), ), mode: SimpleDict, extra_serializer: None, filter: SchemaFilter { include: None, exclude: None, }, required_fields: 13, }, ), has_extra: false, root_model: false, name: "ReadModel", }, ), enabled_from_config: false, }, ), enabled_from_config: false, }, ), definitions=[])¶
The pydantic-core SchemaSerializer used to dump instances of the model.
- __pydantic_setattr_handlers__ = {}¶
__setattr__ handlers. Memoizing the handlers leads to a dramatic performance improvement in __setattr__
- __pydantic_validator__ = SchemaValidator(title="MdrunParametersReadModel", validator=Model( ModelValidator { revalidate: Never, validator: ModelFields( ModelFieldsValidator { fields: [ Field { name: "pk", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "pk", ), rest: [], }, by_alias: [], }, validator: Int( IntValidator { strict: false, }, ), frozen: false, }, Field { name: "label", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "label", ), rest: [], }, by_alias: [], }, validator: WithDefault( WithDefaultValidator { default: Default( Py( 0x00007310e7482e40, ), ), on_error: Raise, validator: Str( StrValidator { strict: false, coerce_numbers_to_str: false, }, ), validate_default: false, copy_default: false, name: "default[str]", undefined: Py( 0x00007310e53bdb90, ), }, ), frozen: false, }, Field { name: "description", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "description", ), rest: [], }, by_alias: [], }, validator: WithDefault( WithDefaultValidator { default: Default( Py( 0x00007310e7482e40, ), ), on_error: Raise, validator: Str( StrValidator { strict: false, coerce_numbers_to_str: false, }, ), validate_default: false, copy_default: false, name: "default[str]", undefined: Py( 0x00007310e53bdb90, ), }, ), frozen: false, }, Field { name: "extras", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "extras", ), rest: [], }, by_alias: [], }, validator: WithDefault( WithDefaultValidator { default: DefaultFactory( Py( 0x00007310e74524a0, ), false, ), on_error: Raise, validator: Dict( DictValidator { strict: false, key_validator: Str( StrValidator { strict: false, coerce_numbers_to_str: false, }, ), value_validator: Any( AnyValidator, ), min_length: None, max_length: None, fail_fast: false, name: "dict[str,any]", }, ), validate_default: false, copy_default: false, name: "default[dict[str,any]]", undefined: Py( 0x00007310e53bdb90, ), }, ), frozen: false, }, Field { name: "node_type", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "node_type", ), rest: [], }, by_alias: [], }, validator: Literal( LiteralValidator { lookup: LiteralLookup { expected_bool: None, expected_int: None, expected_str: Some( { "data.gromacs.mdrun.MdrunParameters.": 0, }, ), expected_py_dict: None, expected_py_values: None, expected_py_primitives: Some( Py( 0x00007310d2631900, ), ), values: [ Py( 0x00007310d819e920, ), ], }, expected_repr: "'data.gromacs.mdrun.MdrunParameters.'", name: "literal['data.gromacs.mdrun.MdrunParameters.']", }, ), frozen: false, }, Field { name: "attributes", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "attributes", ), rest: [], }, by_alias: [], }, validator: Prebuilt( PrebuiltValidator { schema_validator: Py( 0x00007310d2595cf0, ), }, ), frozen: false, }, Field { name: "repository_metadata", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "repository_metadata", ), rest: [], }, by_alias: [], }, validator: WithDefault( WithDefaultValidator { default: DefaultFactory( Py( 0x00007310e74524a0, ), false, ), on_error: Raise, validator: Dict( DictValidator { strict: false, key_validator: Str( StrValidator { strict: false, coerce_numbers_to_str: false, }, ), value_validator: Any( AnyValidator, ), min_length: None, max_length: None, fail_fast: false, name: "dict[str,any]", }, ), validate_default: false, copy_default: false, name: "default[dict[str,any]]", undefined: Py( 0x00007310e53bdb90, ), }, ), frozen: false, }, Field { name: "uuid", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "uuid", ), rest: [], }, by_alias: [], }, validator: Uuid( UuidValidator { strict: false, version: None, }, ), frozen: false, }, Field { name: "process_type", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "process_type", ), rest: [], }, by_alias: [], }, validator: WithDefault( WithDefaultValidator { default: Default( Py( 0x00007310e7455800, ), ), on_error: Raise, validator: Nullable( NullableValidator { validator: Str( StrValidator { strict: false, coerce_numbers_to_str: false, }, ), name: "nullable[str]", }, ), validate_default: false, copy_default: false, name: "default[nullable[str]]", undefined: Py( 0x00007310e53bdb90, ), }, ), frozen: false, }, Field { name: "ctime", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "ctime", ), rest: [], }, by_alias: [], }, validator: Datetime( DateTimeValidator { strict: false, constraints: None, microseconds_precision: Truncate, val_temporal_unit: Infer, }, ), frozen: false, }, Field { name: "mtime", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "mtime", ), rest: [], }, by_alias: [], }, validator: Datetime( DateTimeValidator { strict: false, constraints: None, microseconds_precision: Truncate, val_temporal_unit: Infer, }, ), frozen: false, }, Field { name: "computer", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "computer", ), rest: [], }, by_alias: [], }, validator: WithDefault( WithDefaultValidator { default: Default( Py( 0x00007310e7455800, ), ), on_error: Raise, validator: Nullable( NullableValidator { validator: Int( IntValidator { strict: false, }, ), name: "nullable[int]", }, ), validate_default: false, copy_default: false, name: "default[nullable[int]]", undefined: Py( 0x00007310e53bdb90, ), }, ), frozen: false, }, Field { name: "user", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "user", ), rest: [], }, by_alias: [], }, validator: Int( IntValidator { strict: false, }, ), frozen: false, }, ], model_name: "ReadModel", extra_behavior: Forbid, extras_validator: None, extras_keys_validator: None, strict: false, from_attributes: false, loc_by_alias: true, lookup: LookupTree { inner: { PathItemString( "repository_metadata", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 6, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "uuid", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 7, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "mtime", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 10, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "extras", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 3, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "computer", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 11, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "node_type", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 4, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "user", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 12, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "pk", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 0, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "attributes", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 5, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "process_type", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 8, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "ctime", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 9, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "label", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 1, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "description", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 2, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, }, }, validate_by_alias: Some( true, ), validate_by_name: Some( true, ), }, ), class: Py( 0x000063affefe5db0, ), generic_origin: None, post_init: Some( Py( 0x00007310e2571630, ), ), frozen: false, custom_init: false, root_model: false, undefined: Py( 0x00007310e53bdb90, ), name: "ReadModel", }, ), definitions=[], cache_strings=True)¶
The pydantic-core SchemaValidator used to validate instances of the model.
- _abc_impl = <_abc._abc_data object>¶
- attributes: AttributesModel¶
- model_config = {'defer_build': True, 'extra': 'forbid', 'json_encoders': {<class 'datetime.datetime'>: <function OrmModel.<lambda>>}, 'serialize_by_alias': True, 'title': 'MdrunParametersReadModel', 'validate_by_alias': True, 'validate_by_name': True}¶
Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].
- class WriteModel(**data: Any)¶
Bases:
WriteModel- __abstractmethods__ = frozenset({})¶
- __annotations__ = {'attributes': <class 'aiida_gromacs.data.mdrun.MdrunParameters.AttributesWriteModel'>, 'description': <class 'str'>, 'extras': dict[str, typing.Any], 'label': <class 'str'>, 'node_type': typing.Literal['data.gromacs.mdrun.MdrunParameters.'], 'repository_metadata': dict[str, typing.Any]}¶
- __class_vars__ = {}¶
The names of the class variables defined on the model.
- __dict__¶
- __module__ = 'aiida_gromacs.data.mdrun'¶
- __private_attributes__ = {'_AIIDA_MINIMAL_MODEL': ModelPrivateAttr()}¶
Metadata about the private attributes of the model.
- __pydantic_complete__ = True¶
Whether model building is completed, or if there are still undefined fields.
- __pydantic_computed_fields__ = {}¶
A dictionary of computed field names and their corresponding [ComputedFieldInfo][pydantic.fields.ComputedFieldInfo] objects.
- __pydantic_core_schema__ = {'cls': <class 'aiida_gromacs.data.mdrun.MdrunParameters.WriteModel'>, 'config': {'extra_fields_behavior': 'forbid', 'serialize_by_alias': True, 'title': 'MdrunParametersWriteModel', 'validate_by_alias': True, 'validate_by_name': True}, 'custom_init': False, 'metadata': {'pydantic_js_functions': [<bound method BaseModel.__get_pydantic_json_schema__ of <class 'aiida_gromacs.data.mdrun.MdrunParameters.WriteModel'>>]}, 'post_init': 'model_post_init', 'ref': 'aiida_gromacs.data.mdrun.MdrunParameters.WriteModel:109607548547792', 'root_model': False, 'schema': {'computed_fields': [], 'fields': {'attributes': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'The node attributes', 'examples': [{'attr_key': 'attr_value'}]}}, 'schema': {'cls': <class 'aiida_gromacs.data.mdrun.MdrunParameters.AttributesWriteModel'>, 'config': {'extra_fields_behavior': 'allow', 'serialize_by_alias': True, 'title': 'MdrunParametersAttributesWriteModel', 'validate_by_alias': True, 'validate_by_name': True}, 'custom_init': False, 'metadata': {'pydantic_js_functions': [<bound method BaseModel.__get_pydantic_json_schema__ of <class 'aiida_gromacs.data.mdrun.MdrunParameters.AttributesWriteModel'>>]}, 'post_init': 'model_post_init', 'ref': 'aiida_gromacs.data.mdrun.MdrunParameters.AttributesWriteModel:109607548525936', 'root_model': False, 'schema': {'computed_fields': [], 'fields': {'source': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'Source of the data'}}, 'schema': {'default': None, 'schema': {'schema': {'keys_schema': {'type': 'any'}, 'type': 'dict', 'values_schema': {'type': 'any'}}, 'type': 'nullable'}, 'type': 'default'}, 'type': 'model-field'}}, 'model_name': 'AttributesWriteModel', 'type': 'model-fields'}, 'type': 'model'}, 'type': 'model-field'}, 'description': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'The node description', 'examples': ['This is my node description.']}}, 'schema': {'default': '', 'schema': {'type': 'str'}, 'type': 'default'}, 'type': 'model-field'}, 'extras': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'The node extras', 'examples': [{'extra_key': 'extra_value'}]}}, 'schema': {'default_factory': <class 'dict'>, 'default_factory_takes_data': False, 'schema': {'keys_schema': {'type': 'str'}, 'type': 'dict', 'values_schema': {'type': 'any'}}, 'type': 'default'}, 'type': 'model-field'}, 'label': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'The node label', 'examples': ['my_node']}}, 'schema': {'default': '', 'schema': {'type': 'str'}, 'type': 'default'}, 'type': 'model-field'}, 'node_type': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'The type of the node.'}}, 'schema': {'expected': ['data.gromacs.mdrun.MdrunParameters.'], 'type': 'literal'}, 'type': 'model-field'}, 'repository_metadata': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'Virtual hierarchy of the file repository', 'examples': [{'o': {'file.txt': {'k': '<file_hash>'}}}]}}, 'schema': {'default_factory': <class 'dict'>, 'default_factory_takes_data': False, 'schema': {'keys_schema': {'type': 'str'}, 'type': 'dict', 'values_schema': {'type': 'any'}}, 'type': 'default'}, 'type': 'model-field'}}, 'model_name': 'WriteModel', 'type': 'model-fields'}, 'type': 'model'}¶
The core schema of the model.
- __pydantic_custom_init__ = False¶
Whether the model has a custom __init__ method.
- __pydantic_decorators__ = DecoratorInfos(validators={}, field_validators={}, root_validators={}, field_serializers={}, model_serializers={}, model_validators={}, computed_fields={})¶
Metadata containing the decorators defined on the model. This replaces Model.__validators__ and Model.__root_validators__ from Pydantic V1.
- __pydantic_extra__¶
A dictionary containing extra values, if [extra][pydantic.config.ConfigDict.extra] is set to ‘allow’.
- __pydantic_extra_info__ = None¶
A wrapper around the __pydantic_extra__ annotation, if explicitly annotated on a model.
This is a private attribute, not meant to be used outside Pydantic.
- __pydantic_fields__ = {'attributes': FieldInfo(annotation=MdrunParameters.AttributesWriteModel, required=True, description='The node attributes', examples=[{'attr_key': 'attr_value'}], json_schema_extra={}, metadata=[{'priority': 0}, {'read_only': False}, {'write_only': False}, {'may_be_large': True}]), 'description': FieldInfo(annotation=str, required=False, default='', description='The node description', examples=['This is my node description.'], json_schema_extra={}, metadata=[{'priority': 0}, {'read_only': False}, {'write_only': False}, {'may_be_large': False}]), 'extras': FieldInfo(annotation=dict[str, Any], required=False, default_factory=dict, description='The node extras', examples=[{'extra_key': 'extra_value'}], json_schema_extra={}, metadata=[{'priority': 0}, {'read_only': False}, {'write_only': False}, {'may_be_large': True}, {'orm_to_model': <function Node.MutableNodeFields.<lambda>>}]), 'label': FieldInfo(annotation=str, required=False, default='', description='The node label', examples=['my_node'], json_schema_extra={}, metadata=[{'priority': 0}, {'read_only': False}, {'write_only': False}, {'may_be_large': False}]), 'node_type': FieldInfo(annotation=Literal['data.gromacs.mdrun.MdrunParameters.'], required=True, description='The type of the node.', json_schema_extra={}, metadata=[{'priority': 0}, {'read_only': False}, {'write_only': False}, {'may_be_large': False}]), 'repository_metadata': FieldInfo(annotation=dict[str, Any], required=False, default_factory=dict, description='Virtual hierarchy of the file repository', examples=[{'o': {'file.txt': {'k': '<file_hash>'}}}], json_schema_extra={}, metadata=[{'priority': 0}, {'read_only': False}, {'write_only': False}, {'may_be_large': True}, {'orm_to_model': <function Node.WritableFields.<lambda>>}])}¶
A dictionary of field names and their corresponding [FieldInfo][pydantic.fields.FieldInfo] objects. This replaces Model.__fields__ from Pydantic V1.
- __pydantic_fields_set__¶
The names of fields explicitly set during instantiation.
- __pydantic_generic_metadata__ = {'args': (), 'origin': None, 'parameters': ()}¶
A dictionary containing metadata about generic Pydantic models.
The origin and args items map to the [__origin__][genericalias.__origin__] and [__args__][genericalias.__args__] attributes of [generic aliases][types-genericalias], and the parameter item maps to the __parameter__ attribute of generic classes.
- __pydantic_post_init__ = 'model_post_init'¶
The name of the post-init method for the model, if defined.
- __pydantic_private__¶
Values of private attributes set on the model instance.
- __pydantic_serializer__ = SchemaSerializer(serializer=PolymorphismTrampoline( PolymorphismTrampoline { class: Py( 0x000063affefef2d0, ), serializer: PolymorphismTrampoline( PolymorphismTrampoline { class: Py( 0x000063affefef2d0, ), serializer: Model( ModelSerializer { class: Py( 0x000063affefef2d0, ), serializer: Fields( GeneralFieldsSerializer { fields: { "extras": SerField { key: "extras", alias: None, serializer: Some( WithDefault( WithDefaultSerializer { default: DefaultFactory( Py( 0x00007310e74524a0, ), false, ), serializer: Dict( DictSerializer { key_serializer: Str( StrSerializer, ), value_serializer: Any( AnySerializer, ), filter: SchemaFilter { include: None, exclude: None, }, name: "dict[str, any]", }, ), }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "description": SerField { key: "description", alias: None, serializer: Some( WithDefault( WithDefaultSerializer { default: Default( Py( 0x00007310e7482e40, ), ), serializer: Str( StrSerializer, ), }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "node_type": SerField { key: "node_type", alias: None, serializer: Some( Literal( LiteralSerializer { expected_int: {}, expected_str: { "data.gromacs.mdrun.MdrunParameters.", }, expected_py: None, name: "literal['data.gromacs.mdrun.MdrunParameters.']", }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "label": SerField { key: "label", alias: None, serializer: Some( WithDefault( WithDefaultSerializer { default: Default( Py( 0x00007310e7482e40, ), ), serializer: Str( StrSerializer, ), }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "attributes": SerField { key: "attributes", alias: None, serializer: Some( PolymorphismTrampoline( PolymorphismTrampoline { class: Py( 0x000063affefe9d70, ), serializer: PolymorphismTrampoline( PolymorphismTrampoline { class: Py( 0x000063affefe9d70, ), serializer: Model( ModelSerializer { class: Py( 0x000063affefe9d70, ), serializer: Fields( GeneralFieldsSerializer { fields: { "source": SerField { key: "source", alias: None, serializer: Some( WithDefault( WithDefaultSerializer { default: Default( Py( 0x00007310e7455800, ), ), serializer: Nullable( NullableSerializer { serializer: Dict( DictSerializer { key_serializer: Any( AnySerializer, ), value_serializer: Any( AnySerializer, ), filter: SchemaFilter { include: None, exclude: None, }, name: "dict[any, any]", }, ), }, ), }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, }, computed_fields: Some( ComputedFields( [], ), ), mode: ModelExtra, extra_serializer: None, filter: SchemaFilter { include: None, exclude: None, }, required_fields: 1, }, ), has_extra: true, root_model: false, name: "AttributesWriteModel", }, ), enabled_from_config: false, }, ), enabled_from_config: false, }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "repository_metadata": SerField { key: "repository_metadata", alias: None, serializer: Some( WithDefault( WithDefaultSerializer { default: DefaultFactory( Py( 0x00007310e74524a0, ), false, ), serializer: Dict( DictSerializer { key_serializer: Str( StrSerializer, ), value_serializer: Any( AnySerializer, ), filter: SchemaFilter { include: None, exclude: None, }, name: "dict[str, any]", }, ), }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, }, computed_fields: Some( ComputedFields( [], ), ), mode: SimpleDict, extra_serializer: None, filter: SchemaFilter { include: None, exclude: None, }, required_fields: 6, }, ), has_extra: false, root_model: false, name: "WriteModel", }, ), enabled_from_config: false, }, ), enabled_from_config: false, }, ), definitions=[])¶
The pydantic-core SchemaSerializer used to dump instances of the model.
- __pydantic_setattr_handlers__ = {}¶
__setattr__ handlers. Memoizing the handlers leads to a dramatic performance improvement in __setattr__
- __pydantic_validator__ = SchemaValidator(title="MdrunParametersWriteModel", validator=Model( ModelValidator { revalidate: Never, validator: ModelFields( ModelFieldsValidator { fields: [ Field { name: "label", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "label", ), rest: [], }, by_alias: [], }, validator: WithDefault( WithDefaultValidator { default: Default( Py( 0x00007310e7482e40, ), ), on_error: Raise, validator: Str( StrValidator { strict: false, coerce_numbers_to_str: false, }, ), validate_default: false, copy_default: false, name: "default[str]", undefined: Py( 0x00007310e53bdb90, ), }, ), frozen: false, }, Field { name: "description", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "description", ), rest: [], }, by_alias: [], }, validator: WithDefault( WithDefaultValidator { default: Default( Py( 0x00007310e7482e40, ), ), on_error: Raise, validator: Str( StrValidator { strict: false, coerce_numbers_to_str: false, }, ), validate_default: false, copy_default: false, name: "default[str]", undefined: Py( 0x00007310e53bdb90, ), }, ), frozen: false, }, Field { name: "extras", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "extras", ), rest: [], }, by_alias: [], }, validator: WithDefault( WithDefaultValidator { default: DefaultFactory( Py( 0x00007310e74524a0, ), false, ), on_error: Raise, validator: Dict( DictValidator { strict: false, key_validator: Str( StrValidator { strict: false, coerce_numbers_to_str: false, }, ), value_validator: Any( AnyValidator, ), min_length: None, max_length: None, fail_fast: false, name: "dict[str,any]", }, ), validate_default: false, copy_default: false, name: "default[dict[str,any]]", undefined: Py( 0x00007310e53bdb90, ), }, ), frozen: false, }, Field { name: "node_type", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "node_type", ), rest: [], }, by_alias: [], }, validator: Literal( LiteralValidator { lookup: LiteralLookup { expected_bool: None, expected_int: None, expected_str: Some( { "data.gromacs.mdrun.MdrunParameters.": 0, }, ), expected_py_dict: None, expected_py_values: None, expected_py_primitives: Some( Py( 0x00007310d2a6e240, ), ), values: [ Py( 0x00007310d819e920, ), ], }, expected_repr: "'data.gromacs.mdrun.MdrunParameters.'", name: "literal['data.gromacs.mdrun.MdrunParameters.']", }, ), frozen: false, }, Field { name: "attributes", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "attributes", ), rest: [], }, by_alias: [], }, validator: Model( ModelValidator { revalidate: Never, validator: ModelFields( ModelFieldsValidator { fields: [ Field { name: "source", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "source", ), rest: [], }, by_alias: [], }, validator: WithDefault( WithDefaultValidator { default: Default( Py( 0x00007310e7455800, ), ), on_error: Raise, validator: Nullable( NullableValidator { validator: Dict( DictValidator { strict: false, key_validator: Any( AnyValidator, ), value_validator: Any( AnyValidator, ), min_length: None, max_length: None, fail_fast: false, name: "dict[any,any]", }, ), name: "nullable[dict[any,any]]", }, ), validate_default: false, copy_default: false, name: "default[nullable[dict[any,any]]]", undefined: Py( 0x00007310e53bdb90, ), }, ), frozen: false, }, ], model_name: "AttributesWriteModel", extra_behavior: Allow, extras_validator: None, extras_keys_validator: None, strict: false, from_attributes: false, loc_by_alias: true, lookup: LookupTree { inner: { PathItemString( "source", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 0, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, }, }, validate_by_alias: Some( true, ), validate_by_name: Some( true, ), }, ), class: Py( 0x000063affefe9d70, ), generic_origin: None, post_init: Some( Py( 0x00007310e2571630, ), ), frozen: false, custom_init: false, root_model: false, undefined: Py( 0x00007310e53bdb90, ), name: "AttributesWriteModel", }, ), frozen: false, }, Field { name: "repository_metadata", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "repository_metadata", ), rest: [], }, by_alias: [], }, validator: WithDefault( WithDefaultValidator { default: DefaultFactory( Py( 0x00007310e74524a0, ), false, ), on_error: Raise, validator: Dict( DictValidator { strict: false, key_validator: Str( StrValidator { strict: false, coerce_numbers_to_str: false, }, ), value_validator: Any( AnyValidator, ), min_length: None, max_length: None, fail_fast: false, name: "dict[str,any]", }, ), validate_default: false, copy_default: false, name: "default[dict[str,any]]", undefined: Py( 0x00007310e53bdb90, ), }, ), frozen: false, }, ], model_name: "WriteModel", extra_behavior: Forbid, extras_validator: None, extras_keys_validator: None, strict: false, from_attributes: false, loc_by_alias: true, lookup: LookupTree { inner: { PathItemString( "description", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 1, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "attributes", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 4, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "repository_metadata", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 5, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "extras", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 2, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "node_type", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 3, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "label", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 0, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, }, }, validate_by_alias: Some( true, ), validate_by_name: Some( true, ), }, ), class: Py( 0x000063affefef2d0, ), generic_origin: None, post_init: Some( Py( 0x00007310e2571630, ), ), frozen: false, custom_init: false, root_model: false, undefined: Py( 0x00007310e53bdb90, ), name: "WriteModel", }, ), definitions=[], cache_strings=True)¶
The pydantic-core SchemaValidator used to validate instances of the model.
- _abc_impl = <_abc._abc_data object>¶
- attributes: AttributesWriteModel¶
- model_config = {'defer_build': True, 'extra': 'forbid', 'json_encoders': {<class 'datetime.datetime'>: <function OrmModel.<lambda>>}, 'serialize_by_alias': True, 'title': 'MdrunParametersWriteModel', 'validate_by_alias': True, 'validate_by_name': True}¶
Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].
- _COMPAT_MODEL¶
alias of
Model
- _ConstructorModel¶
alias of
ConstructorModel
- _MODEL_MAP = {'read': <class 'aiida_gromacs.data.mdrun.MdrunParameters.ReadModel'>, 'write': <class 'aiida_gromacs.data.mdrun.MdrunParameters.WriteModel'>}¶
- __abstractmethods__ = frozenset({})¶
- __annotations__ = {}¶
- __firstlineno__ = 73¶
- __init__(dict=None, **kwargs)[source]¶
Constructor for the data class
Usage:
MdrunParameters(dict{'ignore-case': True})- Parameters:
parameters_dict (type) – dictionary with commandline parameters
parameters_dict – dict
- __module__ = 'aiida_gromacs.data.mdrun'¶
- __parameters__ = ()¶
- __static_attributes__ = ()¶
- __str__()[source]¶
String representation of node.
Append values of dictionary to usual representation. E.g.:
uuid: b416cbee-24e8-47a8-8c11-6d668770158b (pk: 590) {'ignore-case': True}
- _abc_impl = <_abc._abc_data object>¶
- _logger = <Logger aiida_gromacs.data.mdrun.MdrunParameters (WARNING)>¶
- cmdline_params(input_files)[source]¶
Synthesize command line parameters.
e.g. [ ‘–ignore-case’, ‘filename1’, ‘filename2’]
- Parameters:
pdbfile (type) – Name of input pdb file
pdbfile – str
- fields = {'attributes': "QbAttributesField('attributes', dtype=<class 'aiida_gromacs.data.mdrun.MdrunParameters.AttributesModel'>, doc='The node attributes')", 'computer': "QbNumericField('computer', dtype=int | None, doc='The PK of the computer')", 'ctime': "QbNumericField('ctime', dtype=<class 'datetime.datetime'>, doc='The creation time of the node')", 'description': "QbStrField('description', dtype=<class 'str'>, doc='The node description')", 'extras': "QbDictField('extras', dtype=dict[str, typing.Any], doc='The node extras')", 'label': "QbStrField('label', dtype=<class 'str'>, doc='The node label')", 'mtime': "QbNumericField('mtime', dtype=<class 'datetime.datetime'>, doc='The modification time of the node')", 'node_type': "QbStrField('node_type', dtype=typing.Literal['data.gromacs.mdrun.MdrunParameters.'], doc='The type of the node.')", 'pk': "QbNumericField('pk', dtype=<class 'int'>, doc='The primary key of the entity')", 'process_type': "QbStrField('process_type', dtype=str | None, doc='The process type of the node')", 'repository_metadata': "QbDictField('repository_metadata', dtype=dict[str, typing.Any], doc='Virtual hierarchy of the file repository')", 'source': "QbDictField('attributes.source', dtype=dict | None, doc='Source of the data')", 'user': "QbNumericField('user', dtype=<class 'int'>, doc='The PK of the user who owns the node')", 'uuid': "QbStrField('uuid', dtype=<class 'uuid.UUID'>, doc='The UUID of the node')"}¶
- schema = <Schema({'c': <class 'str'>, 'e': <class 'str'>, 'g': <class 'str'>, 'o': <class 'str'>, 'x': <class 'str'>, 'cpo': <class 'str'>, 'dhdl': <class 'str'>, 'field': <class 'str'>, 'tpi': <class 'str'>, 'tpid': <class 'str'>, 'eo': <class 'str'>, 'px': <class 'str'>, 'pf': <class 'str'>, 'ro': <class 'str'>, 'ra': <class 'str'>, 'rs': <class 'str'>, 'rt': <class 'str'>, 'mtx': <class 'str'>, 'if': <class 'str'>, 'swap': <class 'str'>, 'xvg': <class 'str'>, 'dd': <class 'str'>, 'ddorder': <class 'str'>, 'npme': <class 'str'>, 'nt': <class 'str'>, 'ntmpi': <class 'str'>, 'ntomp': <class 'str'>, 'ntomp_pme': <class 'str'>, 'pin': <class 'str'>, 'pinoffset': <class 'str'>, 'pinstride': <class 'str'>, 'gpu_id': <class 'str'>, 'gputasks': <class 'str'>, 'ddcheck': <class 'str'>, 'rdd': <class 'str'>, 'rcon': <class 'str'>, 'dlb': <class 'str'>, 'dds': <class 'str'>, 'nb': <class 'str'>, 'nstlist': <class 'str'>, 'tunepme': <class 'str'>, 'pme': <class 'str'>, 'pmefft': <class 'str'>, 'bonded': <class 'str'>, 'update': <class 'str'>, 'v': <class 'str'>, 'pforce': <class 'str'>, 'reprod': <class 'str'>, 'cpt': <class 'str'>, 'cpnum': <class 'str'>, 'append': <class 'str'>, 'nsteps': <class 'str'>, 'maxh': <class 'str'>, 'replex': <class 'str'>, 'nex': <class 'str'>, 'reseed': <class 'str'>}, extra=PREVENT_EXTRA, required=False) object>¶
- validate(parameters_dict)[source]¶
Validate command line options.
Uses the voluptuous package for validation. Find out about allowed keys using:
print(MdrunParameters).schema.schema
- Parameters:
parameters_dict (type) – dictionary with commandline parameters
parameters_dict – dict
- Returns:
validated dictionary
aiida_gromacs.data.pdb2gmx module¶
Data types provided by plugin
Register data types via the “aiida.data” entry point in setup.json.
- class aiida_gromacs.data.pdb2gmx.Pdb2gmxParameters(dict=None, **kwargs)[source]¶
Bases:
DictCommand line options for diff.
This class represents a python dictionary used to pass command line options to the executable.
- class AttributesModel(**data: Any)¶
Bases:
AttributesModel- __abstractmethods__ = frozenset({})¶
- __annotations__ = {}¶
- __class_vars__ = {}¶
The names of the class variables defined on the model.
- __dict__¶
- __module__ = 'aiida_gromacs.data.pdb2gmx'¶
- __private_attributes__ = {'_AIIDA_MINIMAL_MODEL': ModelPrivateAttr()}¶
Metadata about the private attributes of the model.
- __pydantic_complete__ = True¶
Whether model building is completed, or if there are still undefined fields.
- __pydantic_computed_fields__ = {}¶
A dictionary of computed field names and their corresponding [ComputedFieldInfo][pydantic.fields.ComputedFieldInfo] objects.
- __pydantic_core_schema__ = {'cls': <class 'aiida_gromacs.data.pdb2gmx.Pdb2gmxParameters.AttributesModel'>, 'config': {'extra_fields_behavior': 'allow', 'serialize_by_alias': True, 'title': 'Pdb2gmxParametersAttributesModel', 'validate_by_alias': True, 'validate_by_name': True}, 'custom_init': False, 'metadata': {'pydantic_js_functions': [<bound method BaseModel.__get_pydantic_json_schema__ of <class 'aiida_gromacs.data.pdb2gmx.Pdb2gmxParameters.AttributesModel'>>]}, 'post_init': 'model_post_init', 'ref': 'aiida_gromacs.data.pdb2gmx.Pdb2gmxParameters.AttributesModel:109607548531248', 'root_model': False, 'schema': {'computed_fields': [], 'fields': {'source': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'Source of the data'}}, 'schema': {'default': None, 'schema': {'schema': {'keys_schema': {'type': 'any'}, 'type': 'dict', 'values_schema': {'type': 'any'}}, 'type': 'nullable'}, 'type': 'default'}, 'type': 'model-field'}}, 'model_name': 'AttributesModel', 'type': 'model-fields'}, 'type': 'model'}¶
The core schema of the model.
- __pydantic_custom_init__ = False¶
Whether the model has a custom __init__ method.
- __pydantic_decorators__ = DecoratorInfos(validators={}, field_validators={}, root_validators={}, field_serializers={}, model_serializers={}, model_validators={}, computed_fields={})¶
Metadata containing the decorators defined on the model. This replaces Model.__validators__ and Model.__root_validators__ from Pydantic V1.
- __pydantic_extra__¶
A dictionary containing extra values, if [extra][pydantic.config.ConfigDict.extra] is set to ‘allow’.
- __pydantic_extra_info__ = None¶
A wrapper around the __pydantic_extra__ annotation, if explicitly annotated on a model.
This is a private attribute, not meant to be used outside Pydantic.
- __pydantic_fields__ = {'source': FieldInfo(annotation=Union[dict, NoneType], required=False, default=None, description='Source of the data', json_schema_extra={}, metadata=[{'priority': 0}, {'read_only': False}, {'write_only': False}, {'may_be_large': False}])}¶
A dictionary of field names and their corresponding [FieldInfo][pydantic.fields.FieldInfo] objects. This replaces Model.__fields__ from Pydantic V1.
- __pydantic_fields_set__¶
The names of fields explicitly set during instantiation.
- __pydantic_generic_metadata__ = {'args': (), 'origin': None, 'parameters': ()}¶
A dictionary containing metadata about generic Pydantic models.
The origin and args items map to the [__origin__][genericalias.__origin__] and [__args__][genericalias.__args__] attributes of [generic aliases][types-genericalias], and the parameter item maps to the __parameter__ attribute of generic classes.
- __pydantic_post_init__ = 'model_post_init'¶
The name of the post-init method for the model, if defined.
- __pydantic_private__¶
Values of private attributes set on the model instance.
- __pydantic_serializer__ = SchemaSerializer(serializer=PolymorphismTrampoline( PolymorphismTrampoline { class: Py( 0x000063affefeb230, ), serializer: PolymorphismTrampoline( PolymorphismTrampoline { class: Py( 0x000063affefeb230, ), serializer: Model( ModelSerializer { class: Py( 0x000063affefeb230, ), serializer: Fields( GeneralFieldsSerializer { fields: { "source": SerField { key: "source", alias: None, serializer: Some( WithDefault( WithDefaultSerializer { default: Default( Py( 0x00007310e7455800, ), ), serializer: Nullable( NullableSerializer { serializer: Dict( DictSerializer { key_serializer: Any( AnySerializer, ), value_serializer: Any( AnySerializer, ), filter: SchemaFilter { include: None, exclude: None, }, name: "dict[any, any]", }, ), }, ), }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, }, computed_fields: Some( ComputedFields( [], ), ), mode: ModelExtra, extra_serializer: None, filter: SchemaFilter { include: None, exclude: None, }, required_fields: 1, }, ), has_extra: true, root_model: false, name: "AttributesModel", }, ), enabled_from_config: false, }, ), enabled_from_config: false, }, ), definitions=[])¶
The pydantic-core SchemaSerializer used to dump instances of the model.
- __pydantic_setattr_handlers__ = {}¶
__setattr__ handlers. Memoizing the handlers leads to a dramatic performance improvement in __setattr__
- __pydantic_validator__ = SchemaValidator(title="Pdb2gmxParametersAttributesModel", validator=Model( ModelValidator { revalidate: Never, validator: ModelFields( ModelFieldsValidator { fields: [ Field { name: "source", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "source", ), rest: [], }, by_alias: [], }, validator: WithDefault( WithDefaultValidator { default: Default( Py( 0x00007310e7455800, ), ), on_error: Raise, validator: Nullable( NullableValidator { validator: Dict( DictValidator { strict: false, key_validator: Any( AnyValidator, ), value_validator: Any( AnyValidator, ), min_length: None, max_length: None, fail_fast: false, name: "dict[any,any]", }, ), name: "nullable[dict[any,any]]", }, ), validate_default: false, copy_default: false, name: "default[nullable[dict[any,any]]]", undefined: Py( 0x00007310e53bdb90, ), }, ), frozen: false, }, ], model_name: "AttributesModel", extra_behavior: Allow, extras_validator: None, extras_keys_validator: None, strict: false, from_attributes: false, loc_by_alias: true, lookup: LookupTree { inner: { PathItemString( "source", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 0, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, }, }, validate_by_alias: Some( true, ), validate_by_name: Some( true, ), }, ), class: Py( 0x000063affefeb230, ), generic_origin: None, post_init: Some( Py( 0x00007310e2571630, ), ), frozen: false, custom_init: false, root_model: false, undefined: Py( 0x00007310e53bdb90, ), name: "AttributesModel", }, ), definitions=[], cache_strings=True)¶
The pydantic-core SchemaValidator used to validate instances of the model.
- _abc_impl = <_abc._abc_data object>¶
- model_config = {'arbitrary_types_allowed': True, 'defer_build': True, 'extra': 'allow', 'json_encoders': {<class 'datetime.datetime'>: <function OrmModel.<lambda>>}, 'serialize_by_alias': True, 'title': 'Pdb2gmxParametersAttributesModel', 'validate_by_alias': True, 'validate_by_name': True}¶
Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].
- class ReadModel(**data: Any)¶
Bases:
ReadModel- __abstractmethods__ = frozenset({})¶
- __annotations__ = {'attributes': <class 'aiida_gromacs.data.pdb2gmx.Pdb2gmxParameters.AttributesModel'>, 'node_type': typing.Literal['data.gromacs.pdb2gmx.Pdb2gmxParameters.']}¶
- __class_vars__ = {}¶
The names of the class variables defined on the model.
- __dict__¶
- __module__ = 'aiida_gromacs.data.pdb2gmx'¶
- __private_attributes__ = {'_AIIDA_MINIMAL_MODEL': ModelPrivateAttr()}¶
Metadata about the private attributes of the model.
- __pydantic_complete__ = True¶
Whether model building is completed, or if there are still undefined fields.
- __pydantic_computed_fields__ = {}¶
A dictionary of computed field names and their corresponding [ComputedFieldInfo][pydantic.fields.ComputedFieldInfo] objects.
- __pydantic_core_schema__ = {'cls': <class 'aiida_gromacs.data.pdb2gmx.Pdb2gmxParameters.ReadModel'>, 'config': {'extra_fields_behavior': 'forbid', 'serialize_by_alias': True, 'title': 'Pdb2gmxParametersReadModel', 'validate_by_alias': True, 'validate_by_name': True}, 'custom_init': False, 'metadata': {'pydantic_js_functions': [<bound method BaseModel.__get_pydantic_json_schema__ of <class 'aiida_gromacs.data.pdb2gmx.Pdb2gmxParameters.ReadModel'>>]}, 'post_init': 'model_post_init', 'ref': 'aiida_gromacs.data.pdb2gmx.Pdb2gmxParameters.ReadModel:109607548873600', 'root_model': False, 'schema': {'computed_fields': [], 'fields': {'attributes': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'The node attributes', 'examples': [{'attr_key': 'attr_value'}]}}, 'schema': {'cls': <class 'aiida_gromacs.data.pdb2gmx.Pdb2gmxParameters.AttributesModel'>, 'config': {'extra_fields_behavior': 'allow', 'serialize_by_alias': True, 'title': 'Pdb2gmxParametersAttributesModel', 'validate_by_alias': True, 'validate_by_name': True}, 'custom_init': False, 'metadata': {'pydantic_js_functions': [<bound method BaseModel.__get_pydantic_json_schema__ of <class 'aiida_gromacs.data.pdb2gmx.Pdb2gmxParameters.AttributesModel'>>]}, 'post_init': 'model_post_init', 'ref': 'aiida_gromacs.data.pdb2gmx.Pdb2gmxParameters.AttributesModel:109607548531248', 'root_model': False, 'schema': {'computed_fields': [], 'fields': {'source': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'Source of the data'}}, 'schema': {'default': None, 'schema': {'schema': {'keys_schema': {'type': 'any'}, 'type': 'dict', 'values_schema': {'type': 'any'}}, 'type': 'nullable'}, 'type': 'default'}, 'type': 'model-field'}}, 'model_name': 'AttributesModel', 'type': 'model-fields'}, 'type': 'model'}, 'type': 'model-field'}, 'computer': {'metadata': {'pydantic_js_extra': {'readOnly': True}, 'pydantic_js_updates': {'description': 'The PK of the computer', 'examples': [42]}}, 'schema': {'default': None, 'schema': {'schema': {'type': 'int'}, 'type': 'nullable'}, 'type': 'default'}, 'type': 'model-field'}, 'ctime': {'metadata': {'pydantic_js_extra': {'readOnly': True}, 'pydantic_js_updates': {'description': 'The creation time of the node', 'examples': ['2024-01-01T12:00:00+00:00']}}, 'schema': {'microseconds_precision': 'truncate', 'serialization': {'function': <function OrmModel.<lambda>>, 'type': 'function-plain', 'when_used': 'json'}, 'type': 'datetime'}, 'type': 'model-field'}, 'description': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'The node description', 'examples': ['This is my node description.']}}, 'schema': {'default': '', 'schema': {'type': 'str'}, 'type': 'default'}, 'type': 'model-field'}, 'extras': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'The node extras', 'examples': [{'extra_key': 'extra_value'}]}}, 'schema': {'default_factory': <class 'dict'>, 'default_factory_takes_data': False, 'schema': {'keys_schema': {'type': 'str'}, 'type': 'dict', 'values_schema': {'type': 'any'}}, 'type': 'default'}, 'type': 'model-field'}, 'label': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'The node label', 'examples': ['my_node']}}, 'schema': {'default': '', 'schema': {'type': 'str'}, 'type': 'default'}, 'type': 'model-field'}, 'mtime': {'metadata': {'pydantic_js_extra': {'readOnly': True}, 'pydantic_js_updates': {'description': 'The modification time of the node', 'examples': ['2024-01-02T12:00:00+00:00']}}, 'schema': {'microseconds_precision': 'truncate', 'serialization': {'function': <function OrmModel.<lambda>>, 'type': 'function-plain', 'when_used': 'json'}, 'type': 'datetime'}, 'type': 'model-field'}, 'node_type': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'The type of the node.'}}, 'schema': {'expected': ['data.gromacs.pdb2gmx.Pdb2gmxParameters.'], 'type': 'literal'}, 'type': 'model-field'}, 'pk': {'metadata': {'pydantic_js_extra': {'readOnly': True}, 'pydantic_js_updates': {'description': 'The primary key of the entity', 'examples': [42]}}, 'schema': {'type': 'int'}, 'type': 'model-field'}, 'process_type': {'metadata': {'pydantic_js_extra': {'readOnly': True}, 'pydantic_js_updates': {'description': 'The process type of the node', 'examples': ['aiida.calculations:arithmetic.add.']}}, 'schema': {'default': None, 'schema': {'schema': {'type': 'str'}, 'type': 'nullable'}, 'type': 'default'}, 'type': 'model-field'}, 'repository_metadata': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'Virtual hierarchy of the file repository', 'examples': [{'o': {'file.txt': {'k': '<file_hash>'}}}]}}, 'schema': {'default_factory': <class 'dict'>, 'default_factory_takes_data': False, 'schema': {'keys_schema': {'type': 'str'}, 'type': 'dict', 'values_schema': {'type': 'any'}}, 'type': 'default'}, 'type': 'model-field'}, 'user': {'metadata': {'pydantic_js_extra': {'readOnly': True}, 'pydantic_js_updates': {'description': 'The PK of the user who owns the node', 'examples': [7]}}, 'schema': {'type': 'int'}, 'type': 'model-field'}, 'uuid': {'metadata': {'pydantic_js_extra': {'readOnly': True}, 'pydantic_js_updates': {'description': 'The UUID of the node', 'examples': ['123e4567-e89b-12d3-a456-426614174000']}}, 'schema': {'type': 'uuid'}, 'type': 'model-field'}}, 'model_name': 'ReadModel', 'type': 'model-fields'}, 'type': 'model'}¶
The core schema of the model.
- __pydantic_custom_init__ = False¶
Whether the model has a custom __init__ method.
- __pydantic_decorators__ = DecoratorInfos(validators={}, field_validators={}, root_validators={}, field_serializers={}, model_serializers={}, model_validators={}, computed_fields={})¶
Metadata containing the decorators defined on the model. This replaces Model.__validators__ and Model.__root_validators__ from Pydantic V1.
- __pydantic_extra__¶
A dictionary containing extra values, if [extra][pydantic.config.ConfigDict.extra] is set to ‘allow’.
- __pydantic_extra_info__ = None¶
A wrapper around the __pydantic_extra__ annotation, if explicitly annotated on a model.
This is a private attribute, not meant to be used outside Pydantic.
- __pydantic_fields__ = {'attributes': FieldInfo(annotation=Pdb2gmxParameters.AttributesModel, required=True, description='The node attributes', examples=[{'attr_key': 'attr_value'}], json_schema_extra={}, metadata=[{'priority': 0}, {'read_only': False}, {'write_only': False}, {'may_be_large': True}]), 'computer': FieldInfo(annotation=Union[int, NoneType], required=False, default=None, description='The PK of the computer', examples=[42], json_schema_extra={'readOnly': True}, metadata=[{'priority': 0}, {'read_only': True}, {'write_only': False}, {'may_be_large': False}, {'orm_class': <class 'aiida.orm.computers.Computer'>}, {'orm_to_model': <function Node.ReadModel.<lambda>>}]), 'ctime': FieldInfo(annotation=datetime, required=True, description='The creation time of the node', examples=['2024-01-01T12:00:00+00:00'], json_schema_extra={'readOnly': True}, metadata=[{'priority': 0}, {'read_only': True}, {'write_only': False}, {'may_be_large': False}]), 'description': FieldInfo(annotation=str, required=False, default='', description='The node description', examples=['This is my node description.'], json_schema_extra={}, metadata=[{'priority': 0}, {'read_only': False}, {'write_only': False}, {'may_be_large': False}]), 'extras': FieldInfo(annotation=dict[str, Any], required=False, default_factory=dict, description='The node extras', examples=[{'extra_key': 'extra_value'}], json_schema_extra={}, metadata=[{'priority': 0}, {'read_only': False}, {'write_only': False}, {'may_be_large': True}, {'orm_to_model': <function Node.MutableNodeFields.<lambda>>}]), 'label': FieldInfo(annotation=str, required=False, default='', description='The node label', examples=['my_node'], json_schema_extra={}, metadata=[{'priority': 0}, {'read_only': False}, {'write_only': False}, {'may_be_large': False}]), 'mtime': FieldInfo(annotation=datetime, required=True, description='The modification time of the node', examples=['2024-01-02T12:00:00+00:00'], json_schema_extra={'readOnly': True}, metadata=[{'priority': 0}, {'read_only': True}, {'write_only': False}, {'may_be_large': False}]), 'node_type': FieldInfo(annotation=Literal['data.gromacs.pdb2gmx.Pdb2gmxParameters.'], required=True, description='The type of the node.', json_schema_extra={}, metadata=[{'priority': 0}, {'read_only': False}, {'write_only': False}, {'may_be_large': False}]), 'pk': FieldInfo(annotation=int, required=True, description='The primary key of the entity', examples=[42], json_schema_extra={'readOnly': True}, metadata=[{'priority': 0}, {'read_only': True}, {'write_only': False}, {'may_be_large': False}]), 'process_type': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, description='The process type of the node', examples=['aiida.calculations:arithmetic.add.'], json_schema_extra={'readOnly': True}, metadata=[{'priority': 0}, {'read_only': True}, {'write_only': False}, {'may_be_large': False}]), 'repository_metadata': FieldInfo(annotation=dict[str, Any], required=False, default_factory=dict, description='Virtual hierarchy of the file repository', examples=[{'o': {'file.txt': {'k': '<file_hash>'}}}], json_schema_extra={}, metadata=[{'priority': 0}, {'read_only': False}, {'write_only': False}, {'may_be_large': True}, {'orm_to_model': <function Node.WritableFields.<lambda>>}]), 'user': FieldInfo(annotation=int, required=True, description='The PK of the user who owns the node', examples=[7], json_schema_extra={'readOnly': True}, metadata=[{'priority': 0}, {'read_only': True}, {'write_only': False}, {'may_be_large': False}, {'orm_class': <class 'aiida.orm.users.User'>}, {'orm_to_model': <function Node.ReadModel.<lambda>>}]), 'uuid': FieldInfo(annotation=UUID, required=True, description='The UUID of the node', examples=['123e4567-e89b-12d3-a456-426614174000'], json_schema_extra={'readOnly': True}, metadata=[{'priority': 0}, {'read_only': True}, {'write_only': False}, {'may_be_large': False}])}¶
A dictionary of field names and their corresponding [FieldInfo][pydantic.fields.FieldInfo] objects. This replaces Model.__fields__ from Pydantic V1.
- __pydantic_fields_set__¶
The names of fields explicitly set during instantiation.
- __pydantic_generic_metadata__ = {'args': (), 'origin': None, 'parameters': ()}¶
A dictionary containing metadata about generic Pydantic models.
The origin and args items map to the [__origin__][genericalias.__origin__] and [__args__][genericalias.__args__] attributes of [generic aliases][types-genericalias], and the parameter item maps to the __parameter__ attribute of generic classes.
- __pydantic_post_init__ = 'model_post_init'¶
The name of the post-init method for the model, if defined.
- __pydantic_private__¶
Values of private attributes set on the model instance.
- __pydantic_serializer__ = SchemaSerializer(serializer=PolymorphismTrampoline( PolymorphismTrampoline { class: Py( 0x000063afff03eb80, ), serializer: PolymorphismTrampoline( PolymorphismTrampoline { class: Py( 0x000063afff03eb80, ), serializer: Model( ModelSerializer { class: Py( 0x000063afff03eb80, ), serializer: Fields( GeneralFieldsSerializer { fields: { "uuid": SerField { key: "uuid", alias: None, serializer: Some( Uuid( UuidSerializer, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "computer": SerField { key: "computer", alias: None, serializer: Some( WithDefault( WithDefaultSerializer { default: Default( Py( 0x00007310e7455800, ), ), serializer: Nullable( NullableSerializer { serializer: Int( IntSerializer, ), }, ), }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "extras": SerField { key: "extras", alias: None, serializer: Some( WithDefault( WithDefaultSerializer { default: DefaultFactory( Py( 0x00007310e74524a0, ), false, ), serializer: Dict( DictSerializer { key_serializer: Str( StrSerializer, ), value_serializer: Any( AnySerializer, ), filter: SchemaFilter { include: None, exclude: None, }, name: "dict[str, any]", }, ), }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "repository_metadata": SerField { key: "repository_metadata", alias: None, serializer: Some( WithDefault( WithDefaultSerializer { default: DefaultFactory( Py( 0x00007310e74524a0, ), false, ), serializer: Dict( DictSerializer { key_serializer: Str( StrSerializer, ), value_serializer: Any( AnySerializer, ), filter: SchemaFilter { include: None, exclude: None, }, name: "dict[str, any]", }, ), }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "node_type": SerField { key: "node_type", alias: None, serializer: Some( Literal( LiteralSerializer { expected_int: {}, expected_str: { "data.gromacs.pdb2gmx.Pdb2gmxParameters.", }, expected_py: None, name: "literal['data.gromacs.pdb2gmx.Pdb2gmxParameters.']", }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "ctime": SerField { key: "ctime", alias: None, serializer: Some( Function( FunctionPlainSerializer { func: Py( 0x00007310e2355c60, ), name: "plain_function[<lambda>]", function_name: "<lambda>", return_serializer: Any( AnySerializer, ), fallback_serializer: Some( Datetime( DatetimeSerializer { temporal_mode: Iso8601, }, ), ), when_used: Json, is_field_serializer: false, info_arg: false, }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "label": SerField { key: "label", alias: None, serializer: Some( WithDefault( WithDefaultSerializer { default: Default( Py( 0x00007310e7482e40, ), ), serializer: Str( StrSerializer, ), }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "user": SerField { key: "user", alias: None, serializer: Some( Int( IntSerializer, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "description": SerField { key: "description", alias: None, serializer: Some( WithDefault( WithDefaultSerializer { default: Default( Py( 0x00007310e7482e40, ), ), serializer: Str( StrSerializer, ), }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "attributes": SerField { key: "attributes", alias: None, serializer: Some( PolymorphismTrampoline( PolymorphismTrampoline { class: Py( 0x000063affefeb230, ), serializer: Prebuilt( PrebuiltSerializer { schema_serializer: Py( 0x00007310d24a57e0, ), }, ), enabled_from_config: false, }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "pk": SerField { key: "pk", alias: None, serializer: Some( Int( IntSerializer, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "mtime": SerField { key: "mtime", alias: None, serializer: Some( Function( FunctionPlainSerializer { func: Py( 0x00007310e2355c60, ), name: "plain_function[<lambda>]", function_name: "<lambda>", return_serializer: Any( AnySerializer, ), fallback_serializer: Some( Datetime( DatetimeSerializer { temporal_mode: Iso8601, }, ), ), when_used: Json, is_field_serializer: false, info_arg: false, }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "process_type": SerField { key: "process_type", alias: None, serializer: Some( WithDefault( WithDefaultSerializer { default: Default( Py( 0x00007310e7455800, ), ), serializer: Nullable( NullableSerializer { serializer: Str( StrSerializer, ), }, ), }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, }, computed_fields: Some( ComputedFields( [], ), ), mode: SimpleDict, extra_serializer: None, filter: SchemaFilter { include: None, exclude: None, }, required_fields: 13, }, ), has_extra: false, root_model: false, name: "ReadModel", }, ), enabled_from_config: false, }, ), enabled_from_config: false, }, ), definitions=[])¶
The pydantic-core SchemaSerializer used to dump instances of the model.
- __pydantic_setattr_handlers__ = {}¶
__setattr__ handlers. Memoizing the handlers leads to a dramatic performance improvement in __setattr__
- __pydantic_validator__ = SchemaValidator(title="Pdb2gmxParametersReadModel", validator=Model( ModelValidator { revalidate: Never, validator: ModelFields( ModelFieldsValidator { fields: [ Field { name: "pk", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "pk", ), rest: [], }, by_alias: [], }, validator: Int( IntValidator { strict: false, }, ), frozen: false, }, Field { name: "label", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "label", ), rest: [], }, by_alias: [], }, validator: WithDefault( WithDefaultValidator { default: Default( Py( 0x00007310e7482e40, ), ), on_error: Raise, validator: Str( StrValidator { strict: false, coerce_numbers_to_str: false, }, ), validate_default: false, copy_default: false, name: "default[str]", undefined: Py( 0x00007310e53bdb90, ), }, ), frozen: false, }, Field { name: "description", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "description", ), rest: [], }, by_alias: [], }, validator: WithDefault( WithDefaultValidator { default: Default( Py( 0x00007310e7482e40, ), ), on_error: Raise, validator: Str( StrValidator { strict: false, coerce_numbers_to_str: false, }, ), validate_default: false, copy_default: false, name: "default[str]", undefined: Py( 0x00007310e53bdb90, ), }, ), frozen: false, }, Field { name: "extras", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "extras", ), rest: [], }, by_alias: [], }, validator: WithDefault( WithDefaultValidator { default: DefaultFactory( Py( 0x00007310e74524a0, ), false, ), on_error: Raise, validator: Dict( DictValidator { strict: false, key_validator: Str( StrValidator { strict: false, coerce_numbers_to_str: false, }, ), value_validator: Any( AnyValidator, ), min_length: None, max_length: None, fail_fast: false, name: "dict[str,any]", }, ), validate_default: false, copy_default: false, name: "default[dict[str,any]]", undefined: Py( 0x00007310e53bdb90, ), }, ), frozen: false, }, Field { name: "node_type", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "node_type", ), rest: [], }, by_alias: [], }, validator: Literal( LiteralValidator { lookup: LiteralLookup { expected_bool: None, expected_int: None, expected_str: Some( { "data.gromacs.pdb2gmx.Pdb2gmxParameters.": 0, }, ), expected_py_dict: None, expected_py_values: None, expected_py_primitives: Some( Py( 0x00007310d24306c0, ), ), values: [ Py( 0x00007310d2ffd3e0, ), ], }, expected_repr: "'data.gromacs.pdb2gmx.Pdb2gmxParameters.'", name: "literal['data.gromacs.pdb2gmx.Pdb2gmxParameters.']", }, ), frozen: false, }, Field { name: "attributes", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "attributes", ), rest: [], }, by_alias: [], }, validator: Prebuilt( PrebuiltValidator { schema_validator: Py( 0x00007310d24a5870, ), }, ), frozen: false, }, Field { name: "repository_metadata", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "repository_metadata", ), rest: [], }, by_alias: [], }, validator: WithDefault( WithDefaultValidator { default: DefaultFactory( Py( 0x00007310e74524a0, ), false, ), on_error: Raise, validator: Dict( DictValidator { strict: false, key_validator: Str( StrValidator { strict: false, coerce_numbers_to_str: false, }, ), value_validator: Any( AnyValidator, ), min_length: None, max_length: None, fail_fast: false, name: "dict[str,any]", }, ), validate_default: false, copy_default: false, name: "default[dict[str,any]]", undefined: Py( 0x00007310e53bdb90, ), }, ), frozen: false, }, Field { name: "uuid", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "uuid", ), rest: [], }, by_alias: [], }, validator: Uuid( UuidValidator { strict: false, version: None, }, ), frozen: false, }, Field { name: "process_type", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "process_type", ), rest: [], }, by_alias: [], }, validator: WithDefault( WithDefaultValidator { default: Default( Py( 0x00007310e7455800, ), ), on_error: Raise, validator: Nullable( NullableValidator { validator: Str( StrValidator { strict: false, coerce_numbers_to_str: false, }, ), name: "nullable[str]", }, ), validate_default: false, copy_default: false, name: "default[nullable[str]]", undefined: Py( 0x00007310e53bdb90, ), }, ), frozen: false, }, Field { name: "ctime", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "ctime", ), rest: [], }, by_alias: [], }, validator: Datetime( DateTimeValidator { strict: false, constraints: None, microseconds_precision: Truncate, val_temporal_unit: Infer, }, ), frozen: false, }, Field { name: "mtime", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "mtime", ), rest: [], }, by_alias: [], }, validator: Datetime( DateTimeValidator { strict: false, constraints: None, microseconds_precision: Truncate, val_temporal_unit: Infer, }, ), frozen: false, }, Field { name: "computer", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "computer", ), rest: [], }, by_alias: [], }, validator: WithDefault( WithDefaultValidator { default: Default( Py( 0x00007310e7455800, ), ), on_error: Raise, validator: Nullable( NullableValidator { validator: Int( IntValidator { strict: false, }, ), name: "nullable[int]", }, ), validate_default: false, copy_default: false, name: "default[nullable[int]]", undefined: Py( 0x00007310e53bdb90, ), }, ), frozen: false, }, Field { name: "user", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "user", ), rest: [], }, by_alias: [], }, validator: Int( IntValidator { strict: false, }, ), frozen: false, }, ], model_name: "ReadModel", extra_behavior: Forbid, extras_validator: None, extras_keys_validator: None, strict: false, from_attributes: false, loc_by_alias: true, lookup: LookupTree { inner: { PathItemString( "repository_metadata", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 6, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "uuid", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 7, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "process_type", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 8, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "ctime", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 9, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "computer", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 11, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "user", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 12, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "attributes", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 5, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "mtime", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 10, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "label", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 1, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "pk", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 0, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "extras", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 3, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "node_type", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 4, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "description", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 2, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, }, }, validate_by_alias: Some( true, ), validate_by_name: Some( true, ), }, ), class: Py( 0x000063afff03eb80, ), generic_origin: None, post_init: Some( Py( 0x00007310e2571630, ), ), frozen: false, custom_init: false, root_model: false, undefined: Py( 0x00007310e53bdb90, ), name: "ReadModel", }, ), definitions=[], cache_strings=True)¶
The pydantic-core SchemaValidator used to validate instances of the model.
- _abc_impl = <_abc._abc_data object>¶
- attributes: AttributesModel¶
- model_config = {'defer_build': True, 'extra': 'forbid', 'json_encoders': {<class 'datetime.datetime'>: <function OrmModel.<lambda>>}, 'serialize_by_alias': True, 'title': 'Pdb2gmxParametersReadModel', 'validate_by_alias': True, 'validate_by_name': True}¶
Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].
- class WriteModel(**data: Any)¶
Bases:
WriteModel- __abstractmethods__ = frozenset({})¶
- __annotations__ = {'attributes': <class 'aiida_gromacs.data.pdb2gmx.Pdb2gmxParameters.AttributesWriteModel'>, 'description': <class 'str'>, 'extras': dict[str, typing.Any], 'label': <class 'str'>, 'node_type': typing.Literal['data.gromacs.pdb2gmx.Pdb2gmxParameters.'], 'repository_metadata': dict[str, typing.Any]}¶
- __class_vars__ = {}¶
The names of the class variables defined on the model.
- __dict__¶
- __module__ = 'aiida_gromacs.data.pdb2gmx'¶
- __private_attributes__ = {'_AIIDA_MINIMAL_MODEL': ModelPrivateAttr()}¶
Metadata about the private attributes of the model.
- __pydantic_complete__ = True¶
Whether model building is completed, or if there are still undefined fields.
- __pydantic_computed_fields__ = {}¶
A dictionary of computed field names and their corresponding [ComputedFieldInfo][pydantic.fields.ComputedFieldInfo] objects.
- __pydantic_core_schema__ = {'cls': <class 'aiida_gromacs.data.pdb2gmx.Pdb2gmxParameters.WriteModel'>, 'config': {'extra_fields_behavior': 'forbid', 'serialize_by_alias': True, 'title': 'Pdb2gmxParametersWriteModel', 'validate_by_alias': True, 'validate_by_name': True}, 'custom_init': False, 'metadata': {'pydantic_js_functions': [<bound method BaseModel.__get_pydantic_json_schema__ of <class 'aiida_gromacs.data.pdb2gmx.Pdb2gmxParameters.WriteModel'>>]}, 'post_init': 'model_post_init', 'ref': 'aiida_gromacs.data.pdb2gmx.Pdb2gmxParameters.WriteModel:109607548885728', 'root_model': False, 'schema': {'computed_fields': [], 'fields': {'attributes': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'The node attributes', 'examples': [{'attr_key': 'attr_value'}]}}, 'schema': {'cls': <class 'aiida_gromacs.data.pdb2gmx.Pdb2gmxParameters.AttributesWriteModel'>, 'config': {'extra_fields_behavior': 'allow', 'serialize_by_alias': True, 'title': 'Pdb2gmxParametersAttributesWriteModel', 'validate_by_alias': True, 'validate_by_name': True}, 'custom_init': False, 'metadata': {'pydantic_js_functions': [<bound method BaseModel.__get_pydantic_json_schema__ of <class 'aiida_gromacs.data.pdb2gmx.Pdb2gmxParameters.AttributesWriteModel'>>]}, 'post_init': 'model_post_init', 'ref': 'aiida_gromacs.data.pdb2gmx.Pdb2gmxParameters.AttributesWriteModel:109607548883952', 'root_model': False, 'schema': {'computed_fields': [], 'fields': {'source': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'Source of the data'}}, 'schema': {'default': None, 'schema': {'schema': {'keys_schema': {'type': 'any'}, 'type': 'dict', 'values_schema': {'type': 'any'}}, 'type': 'nullable'}, 'type': 'default'}, 'type': 'model-field'}}, 'model_name': 'AttributesWriteModel', 'type': 'model-fields'}, 'type': 'model'}, 'type': 'model-field'}, 'description': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'The node description', 'examples': ['This is my node description.']}}, 'schema': {'default': '', 'schema': {'type': 'str'}, 'type': 'default'}, 'type': 'model-field'}, 'extras': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'The node extras', 'examples': [{'extra_key': 'extra_value'}]}}, 'schema': {'default_factory': <class 'dict'>, 'default_factory_takes_data': False, 'schema': {'keys_schema': {'type': 'str'}, 'type': 'dict', 'values_schema': {'type': 'any'}}, 'type': 'default'}, 'type': 'model-field'}, 'label': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'The node label', 'examples': ['my_node']}}, 'schema': {'default': '', 'schema': {'type': 'str'}, 'type': 'default'}, 'type': 'model-field'}, 'node_type': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'The type of the node.'}}, 'schema': {'expected': ['data.gromacs.pdb2gmx.Pdb2gmxParameters.'], 'type': 'literal'}, 'type': 'model-field'}, 'repository_metadata': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'Virtual hierarchy of the file repository', 'examples': [{'o': {'file.txt': {'k': '<file_hash>'}}}]}}, 'schema': {'default_factory': <class 'dict'>, 'default_factory_takes_data': False, 'schema': {'keys_schema': {'type': 'str'}, 'type': 'dict', 'values_schema': {'type': 'any'}}, 'type': 'default'}, 'type': 'model-field'}}, 'model_name': 'WriteModel', 'type': 'model-fields'}, 'type': 'model'}¶
The core schema of the model.
- __pydantic_custom_init__ = False¶
Whether the model has a custom __init__ method.
- __pydantic_decorators__ = DecoratorInfos(validators={}, field_validators={}, root_validators={}, field_serializers={}, model_serializers={}, model_validators={}, computed_fields={})¶
Metadata containing the decorators defined on the model. This replaces Model.__validators__ and Model.__root_validators__ from Pydantic V1.
- __pydantic_extra__¶
A dictionary containing extra values, if [extra][pydantic.config.ConfigDict.extra] is set to ‘allow’.
- __pydantic_extra_info__ = None¶
A wrapper around the __pydantic_extra__ annotation, if explicitly annotated on a model.
This is a private attribute, not meant to be used outside Pydantic.
- __pydantic_fields__ = {'attributes': FieldInfo(annotation=Pdb2gmxParameters.AttributesWriteModel, required=True, description='The node attributes', examples=[{'attr_key': 'attr_value'}], json_schema_extra={}, metadata=[{'priority': 0}, {'read_only': False}, {'write_only': False}, {'may_be_large': True}]), 'description': FieldInfo(annotation=str, required=False, default='', description='The node description', examples=['This is my node description.'], json_schema_extra={}, metadata=[{'priority': 0}, {'read_only': False}, {'write_only': False}, {'may_be_large': False}]), 'extras': FieldInfo(annotation=dict[str, Any], required=False, default_factory=dict, description='The node extras', examples=[{'extra_key': 'extra_value'}], json_schema_extra={}, metadata=[{'priority': 0}, {'read_only': False}, {'write_only': False}, {'may_be_large': True}, {'orm_to_model': <function Node.MutableNodeFields.<lambda>>}]), 'label': FieldInfo(annotation=str, required=False, default='', description='The node label', examples=['my_node'], json_schema_extra={}, metadata=[{'priority': 0}, {'read_only': False}, {'write_only': False}, {'may_be_large': False}]), 'node_type': FieldInfo(annotation=Literal['data.gromacs.pdb2gmx.Pdb2gmxParameters.'], required=True, description='The type of the node.', json_schema_extra={}, metadata=[{'priority': 0}, {'read_only': False}, {'write_only': False}, {'may_be_large': False}]), 'repository_metadata': FieldInfo(annotation=dict[str, Any], required=False, default_factory=dict, description='Virtual hierarchy of the file repository', examples=[{'o': {'file.txt': {'k': '<file_hash>'}}}], json_schema_extra={}, metadata=[{'priority': 0}, {'read_only': False}, {'write_only': False}, {'may_be_large': True}, {'orm_to_model': <function Node.WritableFields.<lambda>>}])}¶
A dictionary of field names and their corresponding [FieldInfo][pydantic.fields.FieldInfo] objects. This replaces Model.__fields__ from Pydantic V1.
- __pydantic_fields_set__¶
The names of fields explicitly set during instantiation.
- __pydantic_generic_metadata__ = {'args': (), 'origin': None, 'parameters': ()}¶
A dictionary containing metadata about generic Pydantic models.
The origin and args items map to the [__origin__][genericalias.__origin__] and [__args__][genericalias.__args__] attributes of [generic aliases][types-genericalias], and the parameter item maps to the __parameter__ attribute of generic classes.
- __pydantic_post_init__ = 'model_post_init'¶
The name of the post-init method for the model, if defined.
- __pydantic_private__¶
Values of private attributes set on the model instance.
- __pydantic_serializer__ = SchemaSerializer(serializer=PolymorphismTrampoline( PolymorphismTrampoline { class: Py( 0x000063afff041ae0, ), serializer: PolymorphismTrampoline( PolymorphismTrampoline { class: Py( 0x000063afff041ae0, ), serializer: Model( ModelSerializer { class: Py( 0x000063afff041ae0, ), serializer: Fields( GeneralFieldsSerializer { fields: { "repository_metadata": SerField { key: "repository_metadata", alias: None, serializer: Some( WithDefault( WithDefaultSerializer { default: DefaultFactory( Py( 0x00007310e74524a0, ), false, ), serializer: Dict( DictSerializer { key_serializer: Str( StrSerializer, ), value_serializer: Any( AnySerializer, ), filter: SchemaFilter { include: None, exclude: None, }, name: "dict[str, any]", }, ), }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "description": SerField { key: "description", alias: None, serializer: Some( WithDefault( WithDefaultSerializer { default: Default( Py( 0x00007310e7482e40, ), ), serializer: Str( StrSerializer, ), }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "extras": SerField { key: "extras", alias: None, serializer: Some( WithDefault( WithDefaultSerializer { default: DefaultFactory( Py( 0x00007310e74524a0, ), false, ), serializer: Dict( DictSerializer { key_serializer: Str( StrSerializer, ), value_serializer: Any( AnySerializer, ), filter: SchemaFilter { include: None, exclude: None, }, name: "dict[str, any]", }, ), }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "label": SerField { key: "label", alias: None, serializer: Some( WithDefault( WithDefaultSerializer { default: Default( Py( 0x00007310e7482e40, ), ), serializer: Str( StrSerializer, ), }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "attributes": SerField { key: "attributes", alias: None, serializer: Some( PolymorphismTrampoline( PolymorphismTrampoline { class: Py( 0x000063afff0413f0, ), serializer: PolymorphismTrampoline( PolymorphismTrampoline { class: Py( 0x000063afff0413f0, ), serializer: Model( ModelSerializer { class: Py( 0x000063afff0413f0, ), serializer: Fields( GeneralFieldsSerializer { fields: { "source": SerField { key: "source", alias: None, serializer: Some( WithDefault( WithDefaultSerializer { default: Default( Py( 0x00007310e7455800, ), ), serializer: Nullable( NullableSerializer { serializer: Dict( DictSerializer { key_serializer: Any( AnySerializer, ), value_serializer: Any( AnySerializer, ), filter: SchemaFilter { include: None, exclude: None, }, name: "dict[any, any]", }, ), }, ), }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, }, computed_fields: Some( ComputedFields( [], ), ), mode: ModelExtra, extra_serializer: None, filter: SchemaFilter { include: None, exclude: None, }, required_fields: 1, }, ), has_extra: true, root_model: false, name: "AttributesWriteModel", }, ), enabled_from_config: false, }, ), enabled_from_config: false, }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "node_type": SerField { key: "node_type", alias: None, serializer: Some( Literal( LiteralSerializer { expected_int: {}, expected_str: { "data.gromacs.pdb2gmx.Pdb2gmxParameters.", }, expected_py: None, name: "literal['data.gromacs.pdb2gmx.Pdb2gmxParameters.']", }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, }, computed_fields: Some( ComputedFields( [], ), ), mode: SimpleDict, extra_serializer: None, filter: SchemaFilter { include: None, exclude: None, }, required_fields: 6, }, ), has_extra: false, root_model: false, name: "WriteModel", }, ), enabled_from_config: false, }, ), enabled_from_config: false, }, ), definitions=[])¶
The pydantic-core SchemaSerializer used to dump instances of the model.
- __pydantic_setattr_handlers__ = {}¶
__setattr__ handlers. Memoizing the handlers leads to a dramatic performance improvement in __setattr__
- __pydantic_validator__ = SchemaValidator(title="Pdb2gmxParametersWriteModel", validator=Model( ModelValidator { revalidate: Never, validator: ModelFields( ModelFieldsValidator { fields: [ Field { name: "label", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "label", ), rest: [], }, by_alias: [], }, validator: WithDefault( WithDefaultValidator { default: Default( Py( 0x00007310e7482e40, ), ), on_error: Raise, validator: Str( StrValidator { strict: false, coerce_numbers_to_str: false, }, ), validate_default: false, copy_default: false, name: "default[str]", undefined: Py( 0x00007310e53bdb90, ), }, ), frozen: false, }, Field { name: "description", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "description", ), rest: [], }, by_alias: [], }, validator: WithDefault( WithDefaultValidator { default: Default( Py( 0x00007310e7482e40, ), ), on_error: Raise, validator: Str( StrValidator { strict: false, coerce_numbers_to_str: false, }, ), validate_default: false, copy_default: false, name: "default[str]", undefined: Py( 0x00007310e53bdb90, ), }, ), frozen: false, }, Field { name: "extras", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "extras", ), rest: [], }, by_alias: [], }, validator: WithDefault( WithDefaultValidator { default: DefaultFactory( Py( 0x00007310e74524a0, ), false, ), on_error: Raise, validator: Dict( DictValidator { strict: false, key_validator: Str( StrValidator { strict: false, coerce_numbers_to_str: false, }, ), value_validator: Any( AnyValidator, ), min_length: None, max_length: None, fail_fast: false, name: "dict[str,any]", }, ), validate_default: false, copy_default: false, name: "default[dict[str,any]]", undefined: Py( 0x00007310e53bdb90, ), }, ), frozen: false, }, Field { name: "node_type", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "node_type", ), rest: [], }, by_alias: [], }, validator: Literal( LiteralValidator { lookup: LiteralLookup { expected_bool: None, expected_int: None, expected_str: Some( { "data.gromacs.pdb2gmx.Pdb2gmxParameters.": 0, }, ), expected_py_dict: None, expected_py_values: None, expected_py_primitives: Some( Py( 0x00007310d23dbc40, ), ), values: [ Py( 0x00007310d2ffd3e0, ), ], }, expected_repr: "'data.gromacs.pdb2gmx.Pdb2gmxParameters.'", name: "literal['data.gromacs.pdb2gmx.Pdb2gmxParameters.']", }, ), frozen: false, }, Field { name: "attributes", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "attributes", ), rest: [], }, by_alias: [], }, validator: Model( ModelValidator { revalidate: Never, validator: ModelFields( ModelFieldsValidator { fields: [ Field { name: "source", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "source", ), rest: [], }, by_alias: [], }, validator: WithDefault( WithDefaultValidator { default: Default( Py( 0x00007310e7455800, ), ), on_error: Raise, validator: Nullable( NullableValidator { validator: Dict( DictValidator { strict: false, key_validator: Any( AnyValidator, ), value_validator: Any( AnyValidator, ), min_length: None, max_length: None, fail_fast: false, name: "dict[any,any]", }, ), name: "nullable[dict[any,any]]", }, ), validate_default: false, copy_default: false, name: "default[nullable[dict[any,any]]]", undefined: Py( 0x00007310e53bdb90, ), }, ), frozen: false, }, ], model_name: "AttributesWriteModel", extra_behavior: Allow, extras_validator: None, extras_keys_validator: None, strict: false, from_attributes: false, loc_by_alias: true, lookup: LookupTree { inner: { PathItemString( "source", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 0, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, }, }, validate_by_alias: Some( true, ), validate_by_name: Some( true, ), }, ), class: Py( 0x000063afff0413f0, ), generic_origin: None, post_init: Some( Py( 0x00007310e2571630, ), ), frozen: false, custom_init: false, root_model: false, undefined: Py( 0x00007310e53bdb90, ), name: "AttributesWriteModel", }, ), frozen: false, }, Field { name: "repository_metadata", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "repository_metadata", ), rest: [], }, by_alias: [], }, validator: WithDefault( WithDefaultValidator { default: DefaultFactory( Py( 0x00007310e74524a0, ), false, ), on_error: Raise, validator: Dict( DictValidator { strict: false, key_validator: Str( StrValidator { strict: false, coerce_numbers_to_str: false, }, ), value_validator: Any( AnyValidator, ), min_length: None, max_length: None, fail_fast: false, name: "dict[str,any]", }, ), validate_default: false, copy_default: false, name: "default[dict[str,any]]", undefined: Py( 0x00007310e53bdb90, ), }, ), frozen: false, }, ], model_name: "WriteModel", extra_behavior: Forbid, extras_validator: None, extras_keys_validator: None, strict: false, from_attributes: false, loc_by_alias: true, lookup: LookupTree { inner: { PathItemString( "node_type", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 3, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "label", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 0, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "attributes", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 4, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "repository_metadata", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 5, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "description", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 1, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "extras", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 2, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, }, }, validate_by_alias: Some( true, ), validate_by_name: Some( true, ), }, ), class: Py( 0x000063afff041ae0, ), generic_origin: None, post_init: Some( Py( 0x00007310e2571630, ), ), frozen: false, custom_init: false, root_model: false, undefined: Py( 0x00007310e53bdb90, ), name: "WriteModel", }, ), definitions=[], cache_strings=True)¶
The pydantic-core SchemaValidator used to validate instances of the model.
- _abc_impl = <_abc._abc_data object>¶
- attributes: AttributesWriteModel¶
- model_config = {'defer_build': True, 'extra': 'forbid', 'json_encoders': {<class 'datetime.datetime'>: <function OrmModel.<lambda>>}, 'serialize_by_alias': True, 'title': 'Pdb2gmxParametersWriteModel', 'validate_by_alias': True, 'validate_by_name': True}¶
Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].
- _COMPAT_MODEL¶
alias of
Model
- _ConstructorModel¶
alias of
ConstructorModel
- _MODEL_MAP = {'read': <class 'aiida_gromacs.data.pdb2gmx.Pdb2gmxParameters.ReadModel'>, 'write': <class 'aiida_gromacs.data.pdb2gmx.Pdb2gmxParameters.WriteModel'>}¶
- __abstractmethods__ = frozenset({})¶
- __annotations__ = {}¶
- __firstlineno__ = 49¶
- __init__(dict=None, **kwargs)[source]¶
Constructor for the data class
Usage:
Pdb2gmxParameters(dict{'ignore-case': True})- Parameters:
parameters_dict (type) – dictionary with commandline parameters
parameters_dict – dict
- __module__ = 'aiida_gromacs.data.pdb2gmx'¶
- __parameters__ = ()¶
- __static_attributes__ = ()¶
- __str__()[source]¶
String representation of node.
Append values of dictionary to usual representation. E.g.:
uuid: b416cbee-24e8-47a8-8c11-6d668770158b (pk: 590) {'ignore-case': True}
- _abc_impl = <_abc._abc_data object>¶
- _logger = <Logger aiida_gromacs.data.pdb2gmx.Pdb2gmxParameters (WARNING)>¶
- cmdline_params(pdbfile)[source]¶
Synthesize command line parameters.
e.g. [ ‘–ignore-case’, ‘filename1’, ‘filename2’]
- Parameters:
pdbfile (type) – Name of input pdb file
pdbfile – str
- fields = {'attributes': "QbAttributesField('attributes', dtype=<class 'aiida_gromacs.data.pdb2gmx.Pdb2gmxParameters.AttributesModel'>, doc='The node attributes')", 'computer': "QbNumericField('computer', dtype=int | None, doc='The PK of the computer')", 'ctime': "QbNumericField('ctime', dtype=<class 'datetime.datetime'>, doc='The creation time of the node')", 'description': "QbStrField('description', dtype=<class 'str'>, doc='The node description')", 'extras': "QbDictField('extras', dtype=dict[str, typing.Any], doc='The node extras')", 'label': "QbStrField('label', dtype=<class 'str'>, doc='The node label')", 'mtime': "QbNumericField('mtime', dtype=<class 'datetime.datetime'>, doc='The modification time of the node')", 'node_type': "QbStrField('node_type', dtype=typing.Literal['data.gromacs.pdb2gmx.Pdb2gmxParameters.'], doc='The type of the node.')", 'pk': "QbNumericField('pk', dtype=<class 'int'>, doc='The primary key of the entity')", 'process_type': "QbStrField('process_type', dtype=str | None, doc='The process type of the node')", 'repository_metadata': "QbDictField('repository_metadata', dtype=dict[str, typing.Any], doc='Virtual hierarchy of the file repository')", 'source': "QbDictField('attributes.source', dtype=dict | None, doc='Source of the data')", 'user': "QbNumericField('user', dtype=<class 'int'>, doc='The PK of the user who owns the node')", 'uuid': "QbStrField('uuid', dtype=<class 'uuid.UUID'>, doc='The UUID of the node')"}¶
- schema = <Schema({'o': <class 'str'>, 'p': <class 'str'>, 'i': <class 'str'>, 'n': <class 'str'>, 'q': <class 'str'>, 'chainsep': <class 'str'>, 'merge': <class 'str'>, 'ff': <class 'str'>, 'water': <class 'str'>, 'inter': <class 'str'>, 'ss': <class 'str'>, 'ter': <class 'str'>, 'lys': <class 'str'>, 'arg': <class 'str'>, 'asp': <class 'str'>, 'glu': <class 'str'>, 'gln': <class 'str'>, 'his': <class 'str'>, 'angle': <class 'str'>, 'dist': <class 'str'>, 'una': <class 'str'>, 'ignh': <class 'str'>, 'missing': <class 'str'>, 'v': <class 'str'>, 'posrefc': <class 'str'>, 'vsite': <class 'str'>, 'heavyh': <class 'str'>, 'deuterate': <class 'str'>, 'chargegrp': <class 'str'>, 'cmap': <class 'str'>, 'renum': <class 'str'>, 'rtpres': <class 'str'>}, extra=PREVENT_EXTRA, required=False) object>¶
- validate(parameters_dict)[source]¶
Validate command line options.
Uses the voluptuous package for validation. Find out about allowed keys using:
print(Pdb2gmxParameters).schema.schema
- Parameters:
parameters_dict (type) – dictionary with commandline parameters
parameters_dict – dict
- Returns:
validated dictionary
aiida_gromacs.data.plumed_input module¶
Sub class of Data to handle inputs used and outputs that will be produced from commands in the plumed input file.
- class aiida_gromacs.data.plumed_input.PlumedInputData(file: str | Path | IO | None = None, filename: str | Path | None = None, content: str | Path | IO | None = None, **kwargs: Any)[source]¶
Bases:
SinglefileDataClass to find the inputs used and outputs produced from the commands in the plumed input file
- class AttributesModel(**data: Any)¶
Bases:
AttributesModel- __abstractmethods__ = frozenset({})¶
- __annotations__ = {}¶
- __class_vars__ = {'__class_vars__', '__private_attributes__', '__pydantic_complete__', '__pydantic_computed_fields__', '__pydantic_core_schema__', '__pydantic_custom_init__', '__pydantic_decorators__', '__pydantic_extra_info__', '__pydantic_fields__', '__pydantic_generic_metadata__', '__pydantic_parent_namespace__', '__pydantic_post_init__', '__pydantic_root_model__', '__pydantic_serializer__', '__pydantic_setattr_handlers__', '__pydantic_validator__', '__signature__'}¶
The names of the class variables defined on the model.
- __dict__¶
- __module__ = 'aiida_gromacs.data.plumed_input'¶
- __private_attributes__ = {'_AIIDA_MINIMAL_MODEL': ModelPrivateAttr()}¶
Metadata about the private attributes of the model.
- __pydantic_complete__ = True¶
Whether model building is completed, or if there are still undefined fields.
- __pydantic_computed_fields__ = {}¶
A dictionary of computed field names and their corresponding [ComputedFieldInfo][pydantic.fields.ComputedFieldInfo] objects.
- __pydantic_core_schema__ = {'cls': <class 'aiida_gromacs.data.plumed_input.PlumedInputData.AttributesModel'>, 'config': {'extra_fields_behavior': 'forbid', 'serialize_by_alias': True, 'title': 'PlumedInputDataAttributesModel', 'validate_by_alias': True, 'validate_by_name': True}, 'custom_init': False, 'metadata': {'pydantic_js_functions': [<bound method BaseModel.__get_pydantic_json_schema__ of <class 'aiida_gromacs.data.plumed_input.PlumedInputData.AttributesModel'>>]}, 'post_init': 'model_post_init', 'ref': 'aiida_gromacs.data.plumed_input.PlumedInputData.AttributesModel:109607553958784', 'root_model': False, 'schema': {'computed_fields': [], 'fields': {'filename': {'metadata': {'pydantic_js_extra': {'readOnly': True}, 'pydantic_js_updates': {'description': 'The name of the stored file'}}, 'schema': {'type': 'str'}, 'type': 'model-field'}, 'source': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'Source of the data'}}, 'schema': {'default': None, 'schema': {'schema': {'keys_schema': {'type': 'any'}, 'type': 'dict', 'values_schema': {'type': 'any'}}, 'type': 'nullable'}, 'type': 'default'}, 'type': 'model-field'}}, 'model_name': 'AttributesModel', 'type': 'model-fields'}, 'type': 'model'}¶
The core schema of the model.
- __pydantic_custom_init__ = False¶
Whether the model has a custom __init__ method.
- __pydantic_decorators__ = DecoratorInfos(validators={}, field_validators={}, root_validators={}, field_serializers={}, model_serializers={}, model_validators={}, computed_fields={})¶
Metadata containing the decorators defined on the model. This replaces Model.__validators__ and Model.__root_validators__ from Pydantic V1.
- __pydantic_extra__¶
A dictionary containing extra values, if [extra][pydantic.config.ConfigDict.extra] is set to ‘allow’.
- __pydantic_extra_info__ = PydanticExtraInfo(annotation=typing.Optional[typing.Dict[str, typing.Any]], complete=True)¶
A wrapper around the __pydantic_extra__ annotation, if explicitly annotated on a model.
This is a private attribute, not meant to be used outside Pydantic.
- __pydantic_fields__ = {'filename': FieldInfo(annotation=str, required=True, description='The name of the stored file', json_schema_extra={'readOnly': True}, metadata=[{'priority': 0}, {'read_only': True}, {'write_only': False}, {'may_be_large': False}, {'orm_to_model': <function SinglefileData.AttributesModel.<lambda>>}]), 'source': FieldInfo(annotation=Union[dict, NoneType], required=False, default=None, description='Source of the data', json_schema_extra={}, metadata=[{'priority': 0}, {'read_only': False}, {'write_only': False}, {'may_be_large': False}])}¶
A dictionary of field names and their corresponding [FieldInfo][pydantic.fields.FieldInfo] objects. This replaces Model.__fields__ from Pydantic V1.
- __pydantic_fields_set__¶
The names of fields explicitly set during instantiation.
- __pydantic_generic_metadata__ = {'args': (), 'origin': None, 'parameters': ()}¶
A dictionary containing metadata about generic Pydantic models.
The origin and args items map to the [__origin__][genericalias.__origin__] and [__args__][genericalias.__args__] attributes of [generic aliases][types-genericalias], and the parameter item maps to the __parameter__ attribute of generic classes.
- __pydantic_post_init__ = 'model_post_init'¶
The name of the post-init method for the model, if defined.
- __pydantic_private__¶
Values of private attributes set on the model instance.
- __pydantic_serializer__ = SchemaSerializer(serializer=PolymorphismTrampoline( PolymorphismTrampoline { class: Py( 0x000063afff518380, ), serializer: PolymorphismTrampoline( PolymorphismTrampoline { class: Py( 0x000063afff518380, ), serializer: Model( ModelSerializer { class: Py( 0x000063afff518380, ), serializer: Fields( GeneralFieldsSerializer { fields: { "filename": SerField { key: "filename", alias: None, serializer: Some( Str( StrSerializer, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "source": SerField { key: "source", alias: None, serializer: Some( WithDefault( WithDefaultSerializer { default: Default( Py( 0x00007310e7455800, ), ), serializer: Nullable( NullableSerializer { serializer: Dict( DictSerializer { key_serializer: Any( AnySerializer, ), value_serializer: Any( AnySerializer, ), filter: SchemaFilter { include: None, exclude: None, }, name: "dict[any, any]", }, ), }, ), }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, }, computed_fields: Some( ComputedFields( [], ), ), mode: SimpleDict, extra_serializer: None, filter: SchemaFilter { include: None, exclude: None, }, required_fields: 2, }, ), has_extra: false, root_model: false, name: "AttributesModel", }, ), enabled_from_config: false, }, ), enabled_from_config: false, }, ), definitions=[])¶
The pydantic-core SchemaSerializer used to dump instances of the model.
- __pydantic_setattr_handlers__ = {}¶
__setattr__ handlers. Memoizing the handlers leads to a dramatic performance improvement in __setattr__
- __pydantic_validator__ = SchemaValidator(title="PlumedInputDataAttributesModel", validator=Model( ModelValidator { revalidate: Never, validator: ModelFields( ModelFieldsValidator { fields: [ Field { name: "source", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "source", ), rest: [], }, by_alias: [], }, validator: WithDefault( WithDefaultValidator { default: Default( Py( 0x00007310e7455800, ), ), on_error: Raise, validator: Nullable( NullableValidator { validator: Dict( DictValidator { strict: false, key_validator: Any( AnyValidator, ), value_validator: Any( AnyValidator, ), min_length: None, max_length: None, fail_fast: false, name: "dict[any,any]", }, ), name: "nullable[dict[any,any]]", }, ), validate_default: false, copy_default: false, name: "default[nullable[dict[any,any]]]", undefined: Py( 0x00007310e53bdb90, ), }, ), frozen: false, }, Field { name: "filename", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "filename", ), rest: [], }, by_alias: [], }, validator: Str( StrValidator { strict: false, coerce_numbers_to_str: false, }, ), frozen: false, }, ], model_name: "AttributesModel", extra_behavior: Forbid, extras_validator: None, extras_keys_validator: None, strict: false, from_attributes: false, loc_by_alias: true, lookup: LookupTree { inner: { PathItemString( "filename", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 1, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "source", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 0, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, }, }, validate_by_alias: Some( true, ), validate_by_name: Some( true, ), }, ), class: Py( 0x000063afff518380, ), generic_origin: None, post_init: Some( Py( 0x00007310e2571630, ), ), frozen: false, custom_init: false, root_model: false, undefined: Py( 0x00007310e53bdb90, ), name: "AttributesModel", }, ), definitions=[], cache_strings=True)¶
The pydantic-core SchemaValidator used to validate instances of the model.
- _abc_impl = <_abc._abc_data object>¶
- model_config = {'defer_build': True, 'extra': 'forbid', 'json_encoders': {<class 'datetime.datetime'>: <function OrmModel.<lambda>>}, 'serialize_by_alias': True, 'title': 'PlumedInputDataAttributesModel', 'validate_by_alias': True, 'validate_by_name': True}¶
Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].
- class ReadModel(**data: Any)¶
Bases:
ReadModel- __abstractmethods__ = frozenset({})¶
- __annotations__ = {'attributes': <class 'aiida_gromacs.data.plumed_input.PlumedInputData.AttributesModel'>, 'node_type': typing.Literal['data.gromacs.plumed_input.PlumedInputData.']}¶
- __class_vars__ = {'__class_vars__', '__private_attributes__', '__pydantic_complete__', '__pydantic_computed_fields__', '__pydantic_core_schema__', '__pydantic_custom_init__', '__pydantic_decorators__', '__pydantic_extra_info__', '__pydantic_fields__', '__pydantic_generic_metadata__', '__pydantic_parent_namespace__', '__pydantic_post_init__', '__pydantic_root_model__', '__pydantic_serializer__', '__pydantic_setattr_handlers__', '__pydantic_validator__', '__signature__'}¶
The names of the class variables defined on the model.
- __dict__¶
- __module__ = 'aiida_gromacs.data.plumed_input'¶
- __private_attributes__ = {'_AIIDA_MINIMAL_MODEL': ModelPrivateAttr()}¶
Metadata about the private attributes of the model.
- __pydantic_complete__ = True¶
Whether model building is completed, or if there are still undefined fields.
- __pydantic_computed_fields__ = {}¶
A dictionary of computed field names and their corresponding [ComputedFieldInfo][pydantic.fields.ComputedFieldInfo] objects.
- __pydantic_core_schema__ = {'cls': <class 'aiida_gromacs.data.plumed_input.PlumedInputData.ReadModel'>, 'config': {'extra_fields_behavior': 'forbid', 'serialize_by_alias': True, 'title': 'PlumedInputDataReadModel', 'validate_by_alias': True, 'validate_by_name': True}, 'custom_init': False, 'metadata': {'pydantic_js_functions': [<bound method BaseModel.__get_pydantic_json_schema__ of <class 'aiida_gromacs.data.plumed_input.PlumedInputData.ReadModel'>>]}, 'post_init': 'model_post_init', 'ref': 'aiida_gromacs.data.plumed_input.PlumedInputData.ReadModel:109607549810720', 'root_model': False, 'schema': {'computed_fields': [], 'fields': {'attributes': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'The node attributes', 'examples': [{'attr_key': 'attr_value'}]}}, 'schema': {'cls': <class 'aiida_gromacs.data.plumed_input.PlumedInputData.AttributesModel'>, 'config': {'extra_fields_behavior': 'forbid', 'serialize_by_alias': True, 'title': 'PlumedInputDataAttributesModel', 'validate_by_alias': True, 'validate_by_name': True}, 'custom_init': False, 'metadata': {'pydantic_js_functions': [<bound method BaseModel.__get_pydantic_json_schema__ of <class 'aiida_gromacs.data.plumed_input.PlumedInputData.AttributesModel'>>]}, 'post_init': 'model_post_init', 'ref': 'aiida_gromacs.data.plumed_input.PlumedInputData.AttributesModel:109607553958784', 'root_model': False, 'schema': {'computed_fields': [], 'fields': {'filename': {'metadata': {'pydantic_js_extra': {'readOnly': True}, 'pydantic_js_updates': {'description': 'The name of the stored file'}}, 'schema': {'type': 'str'}, 'type': 'model-field'}, 'source': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'Source of the data'}}, 'schema': {'default': None, 'schema': {'schema': {'keys_schema': {'type': 'any'}, 'type': 'dict', 'values_schema': {'type': 'any'}}, 'type': 'nullable'}, 'type': 'default'}, 'type': 'model-field'}}, 'model_name': 'AttributesModel', 'type': 'model-fields'}, 'type': 'model'}, 'type': 'model-field'}, 'computer': {'metadata': {'pydantic_js_extra': {'readOnly': True}, 'pydantic_js_updates': {'description': 'The PK of the computer', 'examples': [42]}}, 'schema': {'default': None, 'schema': {'schema': {'type': 'int'}, 'type': 'nullable'}, 'type': 'default'}, 'type': 'model-field'}, 'ctime': {'metadata': {'pydantic_js_extra': {'readOnly': True}, 'pydantic_js_updates': {'description': 'The creation time of the node', 'examples': ['2024-01-01T12:00:00+00:00']}}, 'schema': {'microseconds_precision': 'truncate', 'serialization': {'function': <function OrmModel.<lambda>>, 'type': 'function-plain', 'when_used': 'json'}, 'type': 'datetime'}, 'type': 'model-field'}, 'description': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'The node description', 'examples': ['This is my node description.']}}, 'schema': {'default': '', 'schema': {'type': 'str'}, 'type': 'default'}, 'type': 'model-field'}, 'extras': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'The node extras', 'examples': [{'extra_key': 'extra_value'}]}}, 'schema': {'default_factory': <class 'dict'>, 'default_factory_takes_data': False, 'schema': {'keys_schema': {'type': 'str'}, 'type': 'dict', 'values_schema': {'type': 'any'}}, 'type': 'default'}, 'type': 'model-field'}, 'label': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'The node label', 'examples': ['my_node']}}, 'schema': {'default': '', 'schema': {'type': 'str'}, 'type': 'default'}, 'type': 'model-field'}, 'mtime': {'metadata': {'pydantic_js_extra': {'readOnly': True}, 'pydantic_js_updates': {'description': 'The modification time of the node', 'examples': ['2024-01-02T12:00:00+00:00']}}, 'schema': {'microseconds_precision': 'truncate', 'serialization': {'function': <function OrmModel.<lambda>>, 'type': 'function-plain', 'when_used': 'json'}, 'type': 'datetime'}, 'type': 'model-field'}, 'node_type': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'The type of the node.'}}, 'schema': {'expected': ['data.gromacs.plumed_input.PlumedInputData.'], 'type': 'literal'}, 'type': 'model-field'}, 'pk': {'metadata': {'pydantic_js_extra': {'readOnly': True}, 'pydantic_js_updates': {'description': 'The primary key of the entity', 'examples': [42]}}, 'schema': {'type': 'int'}, 'type': 'model-field'}, 'process_type': {'metadata': {'pydantic_js_extra': {'readOnly': True}, 'pydantic_js_updates': {'description': 'The process type of the node', 'examples': ['aiida.calculations:arithmetic.add.']}}, 'schema': {'default': None, 'schema': {'schema': {'type': 'str'}, 'type': 'nullable'}, 'type': 'default'}, 'type': 'model-field'}, 'repository_metadata': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'Virtual hierarchy of the file repository', 'examples': [{'o': {'file.txt': {'k': '<file_hash>'}}}]}}, 'schema': {'default_factory': <class 'dict'>, 'default_factory_takes_data': False, 'schema': {'keys_schema': {'type': 'str'}, 'type': 'dict', 'values_schema': {'type': 'any'}}, 'type': 'default'}, 'type': 'model-field'}, 'user': {'metadata': {'pydantic_js_extra': {'readOnly': True}, 'pydantic_js_updates': {'description': 'The PK of the user who owns the node', 'examples': [7]}}, 'schema': {'type': 'int'}, 'type': 'model-field'}, 'uuid': {'metadata': {'pydantic_js_extra': {'readOnly': True}, 'pydantic_js_updates': {'description': 'The UUID of the node', 'examples': ['123e4567-e89b-12d3-a456-426614174000']}}, 'schema': {'type': 'uuid'}, 'type': 'model-field'}}, 'model_name': 'ReadModel', 'type': 'model-fields'}, 'type': 'model'}¶
The core schema of the model.
- __pydantic_custom_init__ = False¶
Whether the model has a custom __init__ method.
- __pydantic_decorators__ = DecoratorInfos(validators={}, field_validators={}, root_validators={}, field_serializers={}, model_serializers={}, model_validators={}, computed_fields={})¶
Metadata containing the decorators defined on the model. This replaces Model.__validators__ and Model.__root_validators__ from Pydantic V1.
- __pydantic_extra__¶
A dictionary containing extra values, if [extra][pydantic.config.ConfigDict.extra] is set to ‘allow’.
- __pydantic_extra_info__ = PydanticExtraInfo(annotation=typing.Optional[typing.Dict[str, typing.Any]], complete=True)¶
A wrapper around the __pydantic_extra__ annotation, if explicitly annotated on a model.
This is a private attribute, not meant to be used outside Pydantic.
- __pydantic_fields__ = {'attributes': FieldInfo(annotation=PlumedInputData.AttributesModel, required=True, description='The node attributes', examples=[{'attr_key': 'attr_value'}], json_schema_extra={}, metadata=[{'priority': 0}, {'read_only': False}, {'write_only': False}, {'may_be_large': True}]), 'computer': FieldInfo(annotation=Union[int, NoneType], required=False, default=None, description='The PK of the computer', examples=[42], json_schema_extra={'readOnly': True}, metadata=[{'priority': 0}, {'read_only': True}, {'write_only': False}, {'may_be_large': False}, {'orm_class': <class 'aiida.orm.computers.Computer'>}, {'orm_to_model': <function Node.ReadModel.<lambda>>}]), 'ctime': FieldInfo(annotation=datetime, required=True, description='The creation time of the node', examples=['2024-01-01T12:00:00+00:00'], json_schema_extra={'readOnly': True}, metadata=[{'priority': 0}, {'read_only': True}, {'write_only': False}, {'may_be_large': False}]), 'description': FieldInfo(annotation=str, required=False, default='', description='The node description', examples=['This is my node description.'], json_schema_extra={}, metadata=[{'priority': 0}, {'read_only': False}, {'write_only': False}, {'may_be_large': False}]), 'extras': FieldInfo(annotation=dict[str, Any], required=False, default_factory=dict, description='The node extras', examples=[{'extra_key': 'extra_value'}], json_schema_extra={}, metadata=[{'priority': 0}, {'read_only': False}, {'write_only': False}, {'may_be_large': True}, {'orm_to_model': <function Node.MutableNodeFields.<lambda>>}]), 'label': FieldInfo(annotation=str, required=False, default='', description='The node label', examples=['my_node'], json_schema_extra={}, metadata=[{'priority': 0}, {'read_only': False}, {'write_only': False}, {'may_be_large': False}]), 'mtime': FieldInfo(annotation=datetime, required=True, description='The modification time of the node', examples=['2024-01-02T12:00:00+00:00'], json_schema_extra={'readOnly': True}, metadata=[{'priority': 0}, {'read_only': True}, {'write_only': False}, {'may_be_large': False}]), 'node_type': FieldInfo(annotation=Literal['data.gromacs.plumed_input.PlumedInputData.'], required=True, description='The type of the node.', json_schema_extra={}, metadata=[{'priority': 0}, {'read_only': False}, {'write_only': False}, {'may_be_large': False}]), 'pk': FieldInfo(annotation=int, required=True, description='The primary key of the entity', examples=[42], json_schema_extra={'readOnly': True}, metadata=[{'priority': 0}, {'read_only': True}, {'write_only': False}, {'may_be_large': False}]), 'process_type': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, description='The process type of the node', examples=['aiida.calculations:arithmetic.add.'], json_schema_extra={'readOnly': True}, metadata=[{'priority': 0}, {'read_only': True}, {'write_only': False}, {'may_be_large': False}]), 'repository_metadata': FieldInfo(annotation=dict[str, Any], required=False, default_factory=dict, description='Virtual hierarchy of the file repository', examples=[{'o': {'file.txt': {'k': '<file_hash>'}}}], json_schema_extra={}, metadata=[{'priority': 0}, {'read_only': False}, {'write_only': False}, {'may_be_large': True}, {'orm_to_model': <function Node.WritableFields.<lambda>>}]), 'user': FieldInfo(annotation=int, required=True, description='The PK of the user who owns the node', examples=[7], json_schema_extra={'readOnly': True}, metadata=[{'priority': 0}, {'read_only': True}, {'write_only': False}, {'may_be_large': False}, {'orm_class': <class 'aiida.orm.users.User'>}, {'orm_to_model': <function Node.ReadModel.<lambda>>}]), 'uuid': FieldInfo(annotation=UUID, required=True, description='The UUID of the node', examples=['123e4567-e89b-12d3-a456-426614174000'], json_schema_extra={'readOnly': True}, metadata=[{'priority': 0}, {'read_only': True}, {'write_only': False}, {'may_be_large': False}])}¶
A dictionary of field names and their corresponding [FieldInfo][pydantic.fields.FieldInfo] objects. This replaces Model.__fields__ from Pydantic V1.
- __pydantic_fields_set__¶
The names of fields explicitly set during instantiation.
- __pydantic_generic_metadata__ = {'args': (), 'origin': None, 'parameters': ()}¶
A dictionary containing metadata about generic Pydantic models.
The origin and args items map to the [__origin__][genericalias.__origin__] and [__args__][genericalias.__args__] attributes of [generic aliases][types-genericalias], and the parameter item maps to the __parameter__ attribute of generic classes.
- __pydantic_post_init__ = 'model_post_init'¶
The name of the post-init method for the model, if defined.
- __pydantic_private__¶
Values of private attributes set on the model instance.
- __pydantic_serializer__ = SchemaSerializer(serializer=PolymorphismTrampoline( PolymorphismTrampoline { class: Py( 0x000063afff123820, ), serializer: PolymorphismTrampoline( PolymorphismTrampoline { class: Py( 0x000063afff123820, ), serializer: Model( ModelSerializer { class: Py( 0x000063afff123820, ), serializer: Fields( GeneralFieldsSerializer { fields: { "pk": SerField { key: "pk", alias: None, serializer: Some( Int( IntSerializer, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "label": SerField { key: "label", alias: None, serializer: Some( WithDefault( WithDefaultSerializer { default: Default( Py( 0x00007310e7482e40, ), ), serializer: Str( StrSerializer, ), }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "description": SerField { key: "description", alias: None, serializer: Some( WithDefault( WithDefaultSerializer { default: Default( Py( 0x00007310e7482e40, ), ), serializer: Str( StrSerializer, ), }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "attributes": SerField { key: "attributes", alias: None, serializer: Some( PolymorphismTrampoline( PolymorphismTrampoline { class: Py( 0x000063afff518380, ), serializer: Prebuilt( PrebuiltSerializer { schema_serializer: Py( 0x00007310d22095a0, ), }, ), enabled_from_config: false, }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "repository_metadata": SerField { key: "repository_metadata", alias: None, serializer: Some( WithDefault( WithDefaultSerializer { default: DefaultFactory( Py( 0x00007310e74524a0, ), false, ), serializer: Dict( DictSerializer { key_serializer: Str( StrSerializer, ), value_serializer: Any( AnySerializer, ), filter: SchemaFilter { include: None, exclude: None, }, name: "dict[str, any]", }, ), }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "node_type": SerField { key: "node_type", alias: None, serializer: Some( Literal( LiteralSerializer { expected_int: {}, expected_str: { "data.gromacs.plumed_input.PlumedInputData.", }, expected_py: None, name: "literal['data.gromacs.plumed_input.PlumedInputData.']", }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "uuid": SerField { key: "uuid", alias: None, serializer: Some( Uuid( UuidSerializer, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "process_type": SerField { key: "process_type", alias: None, serializer: Some( WithDefault( WithDefaultSerializer { default: Default( Py( 0x00007310e7455800, ), ), serializer: Nullable( NullableSerializer { serializer: Str( StrSerializer, ), }, ), }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "extras": SerField { key: "extras", alias: None, serializer: Some( WithDefault( WithDefaultSerializer { default: DefaultFactory( Py( 0x00007310e74524a0, ), false, ), serializer: Dict( DictSerializer { key_serializer: Str( StrSerializer, ), value_serializer: Any( AnySerializer, ), filter: SchemaFilter { include: None, exclude: None, }, name: "dict[str, any]", }, ), }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "ctime": SerField { key: "ctime", alias: None, serializer: Some( Function( FunctionPlainSerializer { func: Py( 0x00007310e2355c60, ), name: "plain_function[<lambda>]", function_name: "<lambda>", return_serializer: Any( AnySerializer, ), fallback_serializer: Some( Datetime( DatetimeSerializer { temporal_mode: Iso8601, }, ), ), when_used: Json, is_field_serializer: false, info_arg: false, }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "mtime": SerField { key: "mtime", alias: None, serializer: Some( Function( FunctionPlainSerializer { func: Py( 0x00007310e2355c60, ), name: "plain_function[<lambda>]", function_name: "<lambda>", return_serializer: Any( AnySerializer, ), fallback_serializer: Some( Datetime( DatetimeSerializer { temporal_mode: Iso8601, }, ), ), when_used: Json, is_field_serializer: false, info_arg: false, }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "computer": SerField { key: "computer", alias: None, serializer: Some( WithDefault( WithDefaultSerializer { default: Default( Py( 0x00007310e7455800, ), ), serializer: Nullable( NullableSerializer { serializer: Int( IntSerializer, ), }, ), }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "user": SerField { key: "user", alias: None, serializer: Some( Int( IntSerializer, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, }, computed_fields: Some( ComputedFields( [], ), ), mode: SimpleDict, extra_serializer: None, filter: SchemaFilter { include: None, exclude: None, }, required_fields: 13, }, ), has_extra: false, root_model: false, name: "ReadModel", }, ), enabled_from_config: false, }, ), enabled_from_config: false, }, ), definitions=[])¶
The pydantic-core SchemaSerializer used to dump instances of the model.
- __pydantic_setattr_handlers__ = {}¶
__setattr__ handlers. Memoizing the handlers leads to a dramatic performance improvement in __setattr__
- __pydantic_validator__ = SchemaValidator(title="PlumedInputDataReadModel", validator=Model( ModelValidator { revalidate: Never, validator: ModelFields( ModelFieldsValidator { fields: [ Field { name: "pk", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "pk", ), rest: [], }, by_alias: [], }, validator: Int( IntValidator { strict: false, }, ), frozen: false, }, Field { name: "label", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "label", ), rest: [], }, by_alias: [], }, validator: WithDefault( WithDefaultValidator { default: Default( Py( 0x00007310e7482e40, ), ), on_error: Raise, validator: Str( StrValidator { strict: false, coerce_numbers_to_str: false, }, ), validate_default: false, copy_default: false, name: "default[str]", undefined: Py( 0x00007310e53bdb90, ), }, ), frozen: false, }, Field { name: "description", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "description", ), rest: [], }, by_alias: [], }, validator: WithDefault( WithDefaultValidator { default: Default( Py( 0x00007310e7482e40, ), ), on_error: Raise, validator: Str( StrValidator { strict: false, coerce_numbers_to_str: false, }, ), validate_default: false, copy_default: false, name: "default[str]", undefined: Py( 0x00007310e53bdb90, ), }, ), frozen: false, }, Field { name: "extras", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "extras", ), rest: [], }, by_alias: [], }, validator: WithDefault( WithDefaultValidator { default: DefaultFactory( Py( 0x00007310e74524a0, ), false, ), on_error: Raise, validator: Dict( DictValidator { strict: false, key_validator: Str( StrValidator { strict: false, coerce_numbers_to_str: false, }, ), value_validator: Any( AnyValidator, ), min_length: None, max_length: None, fail_fast: false, name: "dict[str,any]", }, ), validate_default: false, copy_default: false, name: "default[dict[str,any]]", undefined: Py( 0x00007310e53bdb90, ), }, ), frozen: false, }, Field { name: "node_type", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "node_type", ), rest: [], }, by_alias: [], }, validator: Literal( LiteralValidator { lookup: LiteralLookup { expected_bool: None, expected_int: None, expected_str: Some( { "data.gromacs.plumed_input.PlumedInputData.": 0, }, ), expected_py_dict: None, expected_py_values: None, expected_py_primitives: Some( Py( 0x00007310d22cc300, ), ), values: [ Py( 0x00007310d21ffe10, ), ], }, expected_repr: "'data.gromacs.plumed_input.PlumedInputData.'", name: "literal['data.gromacs.plumed_input.PlumedInputData.']", }, ), frozen: false, }, Field { name: "attributes", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "attributes", ), rest: [], }, by_alias: [], }, validator: Prebuilt( PrebuiltValidator { schema_validator: Py( 0x00007310d2209480, ), }, ), frozen: false, }, Field { name: "repository_metadata", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "repository_metadata", ), rest: [], }, by_alias: [], }, validator: WithDefault( WithDefaultValidator { default: DefaultFactory( Py( 0x00007310e74524a0, ), false, ), on_error: Raise, validator: Dict( DictValidator { strict: false, key_validator: Str( StrValidator { strict: false, coerce_numbers_to_str: false, }, ), value_validator: Any( AnyValidator, ), min_length: None, max_length: None, fail_fast: false, name: "dict[str,any]", }, ), validate_default: false, copy_default: false, name: "default[dict[str,any]]", undefined: Py( 0x00007310e53bdb90, ), }, ), frozen: false, }, Field { name: "uuid", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "uuid", ), rest: [], }, by_alias: [], }, validator: Uuid( UuidValidator { strict: false, version: None, }, ), frozen: false, }, Field { name: "process_type", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "process_type", ), rest: [], }, by_alias: [], }, validator: WithDefault( WithDefaultValidator { default: Default( Py( 0x00007310e7455800, ), ), on_error: Raise, validator: Nullable( NullableValidator { validator: Str( StrValidator { strict: false, coerce_numbers_to_str: false, }, ), name: "nullable[str]", }, ), validate_default: false, copy_default: false, name: "default[nullable[str]]", undefined: Py( 0x00007310e53bdb90, ), }, ), frozen: false, }, Field { name: "ctime", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "ctime", ), rest: [], }, by_alias: [], }, validator: Datetime( DateTimeValidator { strict: false, constraints: None, microseconds_precision: Truncate, val_temporal_unit: Infer, }, ), frozen: false, }, Field { name: "mtime", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "mtime", ), rest: [], }, by_alias: [], }, validator: Datetime( DateTimeValidator { strict: false, constraints: None, microseconds_precision: Truncate, val_temporal_unit: Infer, }, ), frozen: false, }, Field { name: "computer", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "computer", ), rest: [], }, by_alias: [], }, validator: WithDefault( WithDefaultValidator { default: Default( Py( 0x00007310e7455800, ), ), on_error: Raise, validator: Nullable( NullableValidator { validator: Int( IntValidator { strict: false, }, ), name: "nullable[int]", }, ), validate_default: false, copy_default: false, name: "default[nullable[int]]", undefined: Py( 0x00007310e53bdb90, ), }, ), frozen: false, }, Field { name: "user", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "user", ), rest: [], }, by_alias: [], }, validator: Int( IntValidator { strict: false, }, ), frozen: false, }, ], model_name: "ReadModel", extra_behavior: Forbid, extras_validator: None, extras_keys_validator: None, strict: false, from_attributes: false, loc_by_alias: true, lookup: LookupTree { inner: { PathItemString( "extras", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 3, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "node_type", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 4, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "uuid", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 7, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "pk", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 0, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "ctime", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 9, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "process_type", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 8, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "mtime", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 10, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "label", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 1, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "repository_metadata", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 6, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "attributes", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 5, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "computer", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 11, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "user", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 12, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "description", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 2, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, }, }, validate_by_alias: Some( true, ), validate_by_name: Some( true, ), }, ), class: Py( 0x000063afff123820, ), generic_origin: None, post_init: Some( Py( 0x00007310e2571630, ), ), frozen: false, custom_init: false, root_model: false, undefined: Py( 0x00007310e53bdb90, ), name: "ReadModel", }, ), definitions=[], cache_strings=True)¶
The pydantic-core SchemaValidator used to validate instances of the model.
- _abc_impl = <_abc._abc_data object>¶
- attributes: AttributesModel¶
- model_config = {'defer_build': True, 'extra': 'forbid', 'json_encoders': {<class 'datetime.datetime'>: <function OrmModel.<lambda>>}, 'serialize_by_alias': True, 'title': 'PlumedInputDataReadModel', 'validate_by_alias': True, 'validate_by_name': True}¶
Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].
- class WriteModel(**data: Any)¶
Bases:
WriteModel- __abstractmethods__ = frozenset({})¶
- __annotations__ = {'attributes': <class 'aiida_gromacs.data.plumed_input.PlumedInputData.AttributesWriteModel'>, 'description': <class 'str'>, 'extras': dict[str, typing.Any], 'label': <class 'str'>, 'node_type': typing.Literal['data.gromacs.plumed_input.PlumedInputData.'], 'repository_metadata': dict[str, typing.Any]}¶
- __class_vars__ = {'__class_vars__', '__private_attributes__', '__pydantic_complete__', '__pydantic_computed_fields__', '__pydantic_core_schema__', '__pydantic_custom_init__', '__pydantic_decorators__', '__pydantic_extra_info__', '__pydantic_fields__', '__pydantic_generic_metadata__', '__pydantic_parent_namespace__', '__pydantic_post_init__', '__pydantic_root_model__', '__pydantic_serializer__', '__pydantic_setattr_handlers__', '__pydantic_validator__', '__signature__'}¶
The names of the class variables defined on the model.
- __dict__¶
- __module__ = 'aiida_gromacs.data.plumed_input'¶
- __private_attributes__ = {'_AIIDA_MINIMAL_MODEL': ModelPrivateAttr()}¶
Metadata about the private attributes of the model.
- __pydantic_complete__ = True¶
Whether model building is completed, or if there are still undefined fields.
- __pydantic_computed_fields__ = {}¶
A dictionary of computed field names and their corresponding [ComputedFieldInfo][pydantic.fields.ComputedFieldInfo] objects.
- __pydantic_core_schema__ = {'cls': <class 'aiida_gromacs.data.plumed_input.PlumedInputData.WriteModel'>, 'config': {'extra_fields_behavior': 'forbid', 'serialize_by_alias': True, 'title': 'PlumedInputDataWriteModel', 'validate_by_alias': True, 'validate_by_name': True}, 'custom_init': False, 'metadata': {'pydantic_js_functions': [<bound method BaseModel.__get_pydantic_json_schema__ of <class 'aiida_gromacs.data.plumed_input.PlumedInputData.WriteModel'>>]}, 'post_init': 'model_post_init', 'ref': 'aiida_gromacs.data.plumed_input.PlumedInputData.WriteModel:109607553808432', 'root_model': False, 'schema': {'computed_fields': [], 'fields': {'attributes': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'The node attributes', 'examples': [{'attr_key': 'attr_value'}]}}, 'schema': {'cls': <class 'aiida_gromacs.data.plumed_input.PlumedInputData.AttributesWriteModel'>, 'config': {'extra_fields_behavior': 'forbid', 'serialize_by_alias': True, 'title': 'PlumedInputDataAttributesWriteModel', 'validate_by_alias': True, 'validate_by_name': True}, 'custom_init': False, 'metadata': {'pydantic_js_functions': [<bound method BaseModel.__get_pydantic_json_schema__ of <class 'aiida_gromacs.data.plumed_input.PlumedInputData.AttributesWriteModel'>>]}, 'post_init': 'model_post_init', 'ref': 'aiida_gromacs.data.plumed_input.PlumedInputData.AttributesWriteModel:109607550575664', 'root_model': False, 'schema': {'computed_fields': [], 'fields': {'source': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'Source of the data'}}, 'schema': {'default': None, 'schema': {'schema': {'keys_schema': {'type': 'any'}, 'type': 'dict', 'values_schema': {'type': 'any'}}, 'type': 'nullable'}, 'type': 'default'}, 'type': 'model-field'}}, 'model_name': 'AttributesWriteModel', 'type': 'model-fields'}, 'type': 'model'}, 'type': 'model-field'}, 'description': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'The node description', 'examples': ['This is my node description.']}}, 'schema': {'default': '', 'schema': {'type': 'str'}, 'type': 'default'}, 'type': 'model-field'}, 'extras': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'The node extras', 'examples': [{'extra_key': 'extra_value'}]}}, 'schema': {'default_factory': <class 'dict'>, 'default_factory_takes_data': False, 'schema': {'keys_schema': {'type': 'str'}, 'type': 'dict', 'values_schema': {'type': 'any'}}, 'type': 'default'}, 'type': 'model-field'}, 'label': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'The node label', 'examples': ['my_node']}}, 'schema': {'default': '', 'schema': {'type': 'str'}, 'type': 'default'}, 'type': 'model-field'}, 'node_type': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'The type of the node.'}}, 'schema': {'expected': ['data.gromacs.plumed_input.PlumedInputData.'], 'type': 'literal'}, 'type': 'model-field'}, 'repository_metadata': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'Virtual hierarchy of the file repository', 'examples': [{'o': {'file.txt': {'k': '<file_hash>'}}}]}}, 'schema': {'default_factory': <class 'dict'>, 'default_factory_takes_data': False, 'schema': {'keys_schema': {'type': 'str'}, 'type': 'dict', 'values_schema': {'type': 'any'}}, 'type': 'default'}, 'type': 'model-field'}}, 'model_name': 'WriteModel', 'type': 'model-fields'}, 'type': 'model'}¶
The core schema of the model.
- __pydantic_custom_init__ = False¶
Whether the model has a custom __init__ method.
- __pydantic_decorators__ = DecoratorInfos(validators={}, field_validators={}, root_validators={}, field_serializers={}, model_serializers={}, model_validators={}, computed_fields={})¶
Metadata containing the decorators defined on the model. This replaces Model.__validators__ and Model.__root_validators__ from Pydantic V1.
- __pydantic_extra__¶
A dictionary containing extra values, if [extra][pydantic.config.ConfigDict.extra] is set to ‘allow’.
- __pydantic_extra_info__ = PydanticExtraInfo(annotation=typing.Optional[typing.Dict[str, typing.Any]], complete=True)¶
A wrapper around the __pydantic_extra__ annotation, if explicitly annotated on a model.
This is a private attribute, not meant to be used outside Pydantic.
- __pydantic_fields__ = {'attributes': FieldInfo(annotation=PlumedInputData.AttributesWriteModel, required=True, description='The node attributes', examples=[{'attr_key': 'attr_value'}], json_schema_extra={}, metadata=[{'priority': 0}, {'read_only': False}, {'write_only': False}, {'may_be_large': True}]), 'description': FieldInfo(annotation=str, required=False, default='', description='The node description', examples=['This is my node description.'], json_schema_extra={}, metadata=[{'priority': 0}, {'read_only': False}, {'write_only': False}, {'may_be_large': False}]), 'extras': FieldInfo(annotation=dict[str, Any], required=False, default_factory=dict, description='The node extras', examples=[{'extra_key': 'extra_value'}], json_schema_extra={}, metadata=[{'priority': 0}, {'read_only': False}, {'write_only': False}, {'may_be_large': True}, {'orm_to_model': <function Node.MutableNodeFields.<lambda>>}]), 'label': FieldInfo(annotation=str, required=False, default='', description='The node label', examples=['my_node'], json_schema_extra={}, metadata=[{'priority': 0}, {'read_only': False}, {'write_only': False}, {'may_be_large': False}]), 'node_type': FieldInfo(annotation=Literal['data.gromacs.plumed_input.PlumedInputData.'], required=True, description='The type of the node.', json_schema_extra={}, metadata=[{'priority': 0}, {'read_only': False}, {'write_only': False}, {'may_be_large': False}]), 'repository_metadata': FieldInfo(annotation=dict[str, Any], required=False, default_factory=dict, description='Virtual hierarchy of the file repository', examples=[{'o': {'file.txt': {'k': '<file_hash>'}}}], json_schema_extra={}, metadata=[{'priority': 0}, {'read_only': False}, {'write_only': False}, {'may_be_large': True}, {'orm_to_model': <function Node.WritableFields.<lambda>>}])}¶
A dictionary of field names and their corresponding [FieldInfo][pydantic.fields.FieldInfo] objects. This replaces Model.__fields__ from Pydantic V1.
- __pydantic_fields_set__¶
The names of fields explicitly set during instantiation.
- __pydantic_generic_metadata__ = {'args': (), 'origin': None, 'parameters': ()}¶
A dictionary containing metadata about generic Pydantic models.
The origin and args items map to the [__origin__][genericalias.__origin__] and [__args__][genericalias.__args__] attributes of [generic aliases][types-genericalias], and the parameter item maps to the __parameter__ attribute of generic classes.
- __pydantic_post_init__ = 'model_post_init'¶
The name of the post-init method for the model, if defined.
- __pydantic_private__¶
Values of private attributes set on the model instance.
- __pydantic_serializer__ = SchemaSerializer(serializer=PolymorphismTrampoline( PolymorphismTrampoline { class: Py( 0x000063afff4f3830, ), serializer: PolymorphismTrampoline( PolymorphismTrampoline { class: Py( 0x000063afff4f3830, ), serializer: Model( ModelSerializer { class: Py( 0x000063afff4f3830, ), serializer: Fields( GeneralFieldsSerializer { fields: { "attributes": SerField { key: "attributes", alias: None, serializer: Some( PolymorphismTrampoline( PolymorphismTrampoline { class: Py( 0x000063afff1de430, ), serializer: PolymorphismTrampoline( PolymorphismTrampoline { class: Py( 0x000063afff1de430, ), serializer: Model( ModelSerializer { class: Py( 0x000063afff1de430, ), serializer: Fields( GeneralFieldsSerializer { fields: { "source": SerField { key: "source", alias: None, serializer: Some( WithDefault( WithDefaultSerializer { default: Default( Py( 0x00007310e7455800, ), ), serializer: Nullable( NullableSerializer { serializer: Dict( DictSerializer { key_serializer: Any( AnySerializer, ), value_serializer: Any( AnySerializer, ), filter: SchemaFilter { include: None, exclude: None, }, name: "dict[any, any]", }, ), }, ), }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, }, computed_fields: Some( ComputedFields( [], ), ), mode: SimpleDict, extra_serializer: None, filter: SchemaFilter { include: None, exclude: None, }, required_fields: 1, }, ), has_extra: false, root_model: false, name: "AttributesWriteModel", }, ), enabled_from_config: false, }, ), enabled_from_config: false, }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "extras": SerField { key: "extras", alias: None, serializer: Some( WithDefault( WithDefaultSerializer { default: DefaultFactory( Py( 0x00007310e74524a0, ), false, ), serializer: Dict( DictSerializer { key_serializer: Str( StrSerializer, ), value_serializer: Any( AnySerializer, ), filter: SchemaFilter { include: None, exclude: None, }, name: "dict[str, any]", }, ), }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "node_type": SerField { key: "node_type", alias: None, serializer: Some( Literal( LiteralSerializer { expected_int: {}, expected_str: { "data.gromacs.plumed_input.PlumedInputData.", }, expected_py: None, name: "literal['data.gromacs.plumed_input.PlumedInputData.']", }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "repository_metadata": SerField { key: "repository_metadata", alias: None, serializer: Some( WithDefault( WithDefaultSerializer { default: DefaultFactory( Py( 0x00007310e74524a0, ), false, ), serializer: Dict( DictSerializer { key_serializer: Str( StrSerializer, ), value_serializer: Any( AnySerializer, ), filter: SchemaFilter { include: None, exclude: None, }, name: "dict[str, any]", }, ), }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "label": SerField { key: "label", alias: None, serializer: Some( WithDefault( WithDefaultSerializer { default: Default( Py( 0x00007310e7482e40, ), ), serializer: Str( StrSerializer, ), }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "description": SerField { key: "description", alias: None, serializer: Some( WithDefault( WithDefaultSerializer { default: Default( Py( 0x00007310e7482e40, ), ), serializer: Str( StrSerializer, ), }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, }, computed_fields: Some( ComputedFields( [], ), ), mode: SimpleDict, extra_serializer: None, filter: SchemaFilter { include: None, exclude: None, }, required_fields: 6, }, ), has_extra: false, root_model: false, name: "WriteModel", }, ), enabled_from_config: false, }, ), enabled_from_config: false, }, ), definitions=[])¶
The pydantic-core SchemaSerializer used to dump instances of the model.
- __pydantic_setattr_handlers__ = {}¶
__setattr__ handlers. Memoizing the handlers leads to a dramatic performance improvement in __setattr__
- __pydantic_validator__ = SchemaValidator(title="PlumedInputDataWriteModel", validator=Model( ModelValidator { revalidate: Never, validator: ModelFields( ModelFieldsValidator { fields: [ Field { name: "label", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "label", ), rest: [], }, by_alias: [], }, validator: WithDefault( WithDefaultValidator { default: Default( Py( 0x00007310e7482e40, ), ), on_error: Raise, validator: Str( StrValidator { strict: false, coerce_numbers_to_str: false, }, ), validate_default: false, copy_default: false, name: "default[str]", undefined: Py( 0x00007310e53bdb90, ), }, ), frozen: false, }, Field { name: "description", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "description", ), rest: [], }, by_alias: [], }, validator: WithDefault( WithDefaultValidator { default: Default( Py( 0x00007310e7482e40, ), ), on_error: Raise, validator: Str( StrValidator { strict: false, coerce_numbers_to_str: false, }, ), validate_default: false, copy_default: false, name: "default[str]", undefined: Py( 0x00007310e53bdb90, ), }, ), frozen: false, }, Field { name: "extras", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "extras", ), rest: [], }, by_alias: [], }, validator: WithDefault( WithDefaultValidator { default: DefaultFactory( Py( 0x00007310e74524a0, ), false, ), on_error: Raise, validator: Dict( DictValidator { strict: false, key_validator: Str( StrValidator { strict: false, coerce_numbers_to_str: false, }, ), value_validator: Any( AnyValidator, ), min_length: None, max_length: None, fail_fast: false, name: "dict[str,any]", }, ), validate_default: false, copy_default: false, name: "default[dict[str,any]]", undefined: Py( 0x00007310e53bdb90, ), }, ), frozen: false, }, Field { name: "node_type", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "node_type", ), rest: [], }, by_alias: [], }, validator: Literal( LiteralValidator { lookup: LiteralLookup { expected_bool: None, expected_int: None, expected_str: Some( { "data.gromacs.plumed_input.PlumedInputData.": 0, }, ), expected_py_dict: None, expected_py_values: None, expected_py_primitives: Some( Py( 0x00007310d222a880, ), ), values: [ Py( 0x00007310d21ffe10, ), ], }, expected_repr: "'data.gromacs.plumed_input.PlumedInputData.'", name: "literal['data.gromacs.plumed_input.PlumedInputData.']", }, ), frozen: false, }, Field { name: "attributes", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "attributes", ), rest: [], }, by_alias: [], }, validator: Model( ModelValidator { revalidate: Never, validator: ModelFields( ModelFieldsValidator { fields: [ Field { name: "source", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "source", ), rest: [], }, by_alias: [], }, validator: WithDefault( WithDefaultValidator { default: Default( Py( 0x00007310e7455800, ), ), on_error: Raise, validator: Nullable( NullableValidator { validator: Dict( DictValidator { strict: false, key_validator: Any( AnyValidator, ), value_validator: Any( AnyValidator, ), min_length: None, max_length: None, fail_fast: false, name: "dict[any,any]", }, ), name: "nullable[dict[any,any]]", }, ), validate_default: false, copy_default: false, name: "default[nullable[dict[any,any]]]", undefined: Py( 0x00007310e53bdb90, ), }, ), frozen: false, }, ], model_name: "AttributesWriteModel", extra_behavior: Forbid, extras_validator: None, extras_keys_validator: None, strict: false, from_attributes: false, loc_by_alias: true, lookup: LookupTree { inner: { PathItemString( "source", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 0, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, }, }, validate_by_alias: Some( true, ), validate_by_name: Some( true, ), }, ), class: Py( 0x000063afff1de430, ), generic_origin: None, post_init: Some( Py( 0x00007310e2571630, ), ), frozen: false, custom_init: false, root_model: false, undefined: Py( 0x00007310e53bdb90, ), name: "AttributesWriteModel", }, ), frozen: false, }, Field { name: "repository_metadata", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "repository_metadata", ), rest: [], }, by_alias: [], }, validator: WithDefault( WithDefaultValidator { default: DefaultFactory( Py( 0x00007310e74524a0, ), false, ), on_error: Raise, validator: Dict( DictValidator { strict: false, key_validator: Str( StrValidator { strict: false, coerce_numbers_to_str: false, }, ), value_validator: Any( AnyValidator, ), min_length: None, max_length: None, fail_fast: false, name: "dict[str,any]", }, ), validate_default: false, copy_default: false, name: "default[dict[str,any]]", undefined: Py( 0x00007310e53bdb90, ), }, ), frozen: false, }, ], model_name: "WriteModel", extra_behavior: Forbid, extras_validator: None, extras_keys_validator: None, strict: false, from_attributes: false, loc_by_alias: true, lookup: LookupTree { inner: { PathItemString( "description", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 1, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "node_type", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 3, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "label", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 0, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "attributes", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 4, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "extras", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 2, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "repository_metadata", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 5, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, }, }, validate_by_alias: Some( true, ), validate_by_name: Some( true, ), }, ), class: Py( 0x000063afff4f3830, ), generic_origin: None, post_init: Some( Py( 0x00007310e2571630, ), ), frozen: false, custom_init: false, root_model: false, undefined: Py( 0x00007310e53bdb90, ), name: "WriteModel", }, ), definitions=[], cache_strings=True)¶
The pydantic-core SchemaValidator used to validate instances of the model.
- _abc_impl = <_abc._abc_data object>¶
- attributes: AttributesWriteModel¶
- model_config = {'defer_build': True, 'extra': 'forbid', 'json_encoders': {<class 'datetime.datetime'>: <function OrmModel.<lambda>>}, 'serialize_by_alias': True, 'title': 'PlumedInputDataWriteModel', 'validate_by_alias': True, 'validate_by_name': True}¶
Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].
- _COMPAT_MODEL¶
alias of
Model
- _ConstructorModel¶
alias of
ConstructorModel
- _MODEL_MAP = {'read': <class 'aiida_gromacs.data.plumed_input.PlumedInputData.ReadModel'>, 'write': <class 'aiida_gromacs.data.plumed_input.PlumedInputData.WriteModel'>}¶
- __abstractmethods__ = frozenset({})¶
- __annotations__ = {}¶
- __firstlineno__ = 43¶
- __module__ = 'aiida_gromacs.data.plumed_input'¶
- __parameters__ = ()¶
- __static_attributes__ = ()¶
- _abc_impl = <_abc._abc_data object>¶
- _logger = <Logger aiida_gromacs.data.plumed_input.PlumedInputData (WARNING)>¶
- property calculation_inputs_outputs¶
Return the inputs for the plumed calculation job
- fields = {'attributes': "QbAttributesField('attributes', dtype=<class 'aiida_gromacs.data.plumed_input.PlumedInputData.AttributesModel'>, doc='The node attributes')", 'computer': "QbNumericField('computer', dtype=int | None, doc='The PK of the computer')", 'ctime': "QbNumericField('ctime', dtype=<class 'datetime.datetime'>, doc='The creation time of the node')", 'description': "QbStrField('description', dtype=<class 'str'>, doc='The node description')", 'extras': "QbDictField('extras', dtype=dict[str, typing.Any], doc='The node extras')", 'filename': "QbStrField('attributes.filename', dtype=<class 'str'>, doc='The name of the stored file')", 'label': "QbStrField('label', dtype=<class 'str'>, doc='The node label')", 'mtime': "QbNumericField('mtime', dtype=<class 'datetime.datetime'>, doc='The modification time of the node')", 'node_type': "QbStrField('node_type', dtype=typing.Literal['data.gromacs.plumed_input.PlumedInputData.'], doc='The type of the node.')", 'pk': "QbNumericField('pk', dtype=<class 'int'>, doc='The primary key of the entity')", 'process_type': "QbStrField('process_type', dtype=str | None, doc='The process type of the node')", 'repository_metadata': "QbDictField('repository_metadata', dtype=dict[str, typing.Any], doc='Virtual hierarchy of the file repository')", 'source': "QbDictField('attributes.source', dtype=dict | None, doc='Source of the data')", 'user': "QbNumericField('user', dtype=<class 'int'>, doc='The PK of the user who owns the node')", 'uuid': "QbStrField('uuid', dtype=<class 'uuid.UUID'>, doc='The UUID of the node')"}¶
- property inpfile_list¶
Return the list input files used in the plumed script
- property outfile_list¶
Return the list output files to be produced from the plumed script
- aiida_gromacs.data.plumed_input.add_calculation_inputs(subdirs, files)[source]¶
If they exist, add input files for plumed and dirs into the calcjob inputs directory
- Parameters:
subdirs – list of subdirectories that contain input files
files – list of input files
- aiida_gromacs.data.plumed_input.add_calculation_outputs(files)[source]¶
Add outputs from plumed script
- Parameters:
files – list of output files
- aiida_gromacs.data.plumed_input.find_filename_from_string(head, values, filenames)[source]¶
Find any filenames that are in a line of the plumed input file. Some keyword arguments allow for multiple filenames, which are comma separated. Each argument has an ‘=’ after it.
- Parameters:
head – line of plumed input file that doesn’t start with ‘#’
values – list of arguments for a plumed keyword that would produce a file
filenames – list of input/output filenames to append to, that are found in the plumed input
- Returns:
list of filenames found in parsed plumed input file
- Return type:
- aiida_gromacs.data.plumed_input.find_plumed_filenames(keywords, i, line, lines)[source]¶
Find lines that contain a plumed keyword that would require an input/output file
- Parameters:
keywords – dictionary of plumed keywords and their arguments that require an input/output file
i – the parsed line number
line – the currently parsed line
lines – all the lines in the plumed input file
- Returns:
list of filenames found in parsed plumed input file
- Return type:
- aiida_gromacs.data.plumed_input.parse_plumed_input_file(lines)[source]¶
Parse plumed input file and find any instances of reading input files and writing output files. Find the lines that contain the keyword and then find the FILE keyword in the subsequent lines, onces this is found, then stop and carry on with outer loop. If the FILE keyword does not exist, there may be a default filename for some keywords.
- Parameters:
lines – parsed lines from the plumed input file
aiida_gromacs.data.solvate module¶
Data types provided by plugin
Register data types via the “aiida.data” entry point in setup.json.
- class aiida_gromacs.data.solvate.SolvateParameters(dict=None, **kwargs)[source]¶
Bases:
DictCommand line options for diff.
This class represents a python dictionary used to pass command line options to the executable.
- class AttributesModel(**data: Any)¶
Bases:
AttributesModel- __abstractmethods__ = frozenset({})¶
- __annotations__ = {}¶
- __class_vars__ = {}¶
The names of the class variables defined on the model.
- __dict__¶
- __module__ = 'aiida_gromacs.data.solvate'¶
- __private_attributes__ = {'_AIIDA_MINIMAL_MODEL': ModelPrivateAttr()}¶
Metadata about the private attributes of the model.
- __pydantic_complete__ = True¶
Whether model building is completed, or if there are still undefined fields.
- __pydantic_computed_fields__ = {}¶
A dictionary of computed field names and their corresponding [ComputedFieldInfo][pydantic.fields.ComputedFieldInfo] objects.
- __pydantic_core_schema__ = {'cls': <class 'aiida_gromacs.data.solvate.SolvateParameters.AttributesModel'>, 'config': {'extra_fields_behavior': 'allow', 'serialize_by_alias': True, 'title': 'SolvateParametersAttributesModel', 'validate_by_alias': True, 'validate_by_name': True}, 'custom_init': False, 'metadata': {'pydantic_js_functions': [<bound method BaseModel.__get_pydantic_json_schema__ of <class 'aiida_gromacs.data.solvate.SolvateParameters.AttributesModel'>>]}, 'post_init': 'model_post_init', 'ref': 'aiida_gromacs.data.solvate.SolvateParameters.AttributesModel:109607548880560', 'root_model': False, 'schema': {'computed_fields': [], 'fields': {'source': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'Source of the data'}}, 'schema': {'default': None, 'schema': {'schema': {'keys_schema': {'type': 'any'}, 'type': 'dict', 'values_schema': {'type': 'any'}}, 'type': 'nullable'}, 'type': 'default'}, 'type': 'model-field'}}, 'model_name': 'AttributesModel', 'type': 'model-fields'}, 'type': 'model'}¶
The core schema of the model.
- __pydantic_custom_init__ = False¶
Whether the model has a custom __init__ method.
- __pydantic_decorators__ = DecoratorInfos(validators={}, field_validators={}, root_validators={}, field_serializers={}, model_serializers={}, model_validators={}, computed_fields={})¶
Metadata containing the decorators defined on the model. This replaces Model.__validators__ and Model.__root_validators__ from Pydantic V1.
- __pydantic_extra__¶
A dictionary containing extra values, if [extra][pydantic.config.ConfigDict.extra] is set to ‘allow’.
- __pydantic_extra_info__ = None¶
A wrapper around the __pydantic_extra__ annotation, if explicitly annotated on a model.
This is a private attribute, not meant to be used outside Pydantic.
- __pydantic_fields__ = {'source': FieldInfo(annotation=Union[dict, NoneType], required=False, default=None, description='Source of the data', json_schema_extra={}, metadata=[{'priority': 0}, {'read_only': False}, {'write_only': False}, {'may_be_large': False}])}¶
A dictionary of field names and their corresponding [FieldInfo][pydantic.fields.FieldInfo] objects. This replaces Model.__fields__ from Pydantic V1.
- __pydantic_fields_set__¶
The names of fields explicitly set during instantiation.
- __pydantic_generic_metadata__ = {'args': (), 'origin': None, 'parameters': ()}¶
A dictionary containing metadata about generic Pydantic models.
The origin and args items map to the [__origin__][genericalias.__origin__] and [__args__][genericalias.__args__] attributes of [generic aliases][types-genericalias], and the parameter item maps to the __parameter__ attribute of generic classes.
- __pydantic_post_init__ = 'model_post_init'¶
The name of the post-init method for the model, if defined.
- __pydantic_private__¶
Values of private attributes set on the model instance.
- __pydantic_serializer__ = SchemaSerializer(serializer=PolymorphismTrampoline( PolymorphismTrampoline { class: Py( 0x000063afff0406b0, ), serializer: PolymorphismTrampoline( PolymorphismTrampoline { class: Py( 0x000063afff0406b0, ), serializer: Model( ModelSerializer { class: Py( 0x000063afff0406b0, ), serializer: Fields( GeneralFieldsSerializer { fields: { "source": SerField { key: "source", alias: None, serializer: Some( WithDefault( WithDefaultSerializer { default: Default( Py( 0x00007310e7455800, ), ), serializer: Nullable( NullableSerializer { serializer: Dict( DictSerializer { key_serializer: Any( AnySerializer, ), value_serializer: Any( AnySerializer, ), filter: SchemaFilter { include: None, exclude: None, }, name: "dict[any, any]", }, ), }, ), }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, }, computed_fields: Some( ComputedFields( [], ), ), mode: ModelExtra, extra_serializer: None, filter: SchemaFilter { include: None, exclude: None, }, required_fields: 1, }, ), has_extra: true, root_model: false, name: "AttributesModel", }, ), enabled_from_config: false, }, ), enabled_from_config: false, }, ), definitions=[])¶
The pydantic-core SchemaSerializer used to dump instances of the model.
- __pydantic_setattr_handlers__ = {}¶
__setattr__ handlers. Memoizing the handlers leads to a dramatic performance improvement in __setattr__
- __pydantic_validator__ = SchemaValidator(title="SolvateParametersAttributesModel", validator=Model( ModelValidator { revalidate: Never, validator: ModelFields( ModelFieldsValidator { fields: [ Field { name: "source", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "source", ), rest: [], }, by_alias: [], }, validator: WithDefault( WithDefaultValidator { default: Default( Py( 0x00007310e7455800, ), ), on_error: Raise, validator: Nullable( NullableValidator { validator: Dict( DictValidator { strict: false, key_validator: Any( AnyValidator, ), value_validator: Any( AnyValidator, ), min_length: None, max_length: None, fail_fast: false, name: "dict[any,any]", }, ), name: "nullable[dict[any,any]]", }, ), validate_default: false, copy_default: false, name: "default[nullable[dict[any,any]]]", undefined: Py( 0x00007310e53bdb90, ), }, ), frozen: false, }, ], model_name: "AttributesModel", extra_behavior: Allow, extras_validator: None, extras_keys_validator: None, strict: false, from_attributes: false, loc_by_alias: true, lookup: LookupTree { inner: { PathItemString( "source", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 0, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, }, }, validate_by_alias: Some( true, ), validate_by_name: Some( true, ), }, ), class: Py( 0x000063afff0406b0, ), generic_origin: None, post_init: Some( Py( 0x00007310e2571630, ), ), frozen: false, custom_init: false, root_model: false, undefined: Py( 0x00007310e53bdb90, ), name: "AttributesModel", }, ), definitions=[], cache_strings=True)¶
The pydantic-core SchemaValidator used to validate instances of the model.
- _abc_impl = <_abc._abc_data object>¶
- model_config = {'arbitrary_types_allowed': True, 'defer_build': True, 'extra': 'allow', 'json_encoders': {<class 'datetime.datetime'>: <function OrmModel.<lambda>>}, 'serialize_by_alias': True, 'title': 'SolvateParametersAttributesModel', 'validate_by_alias': True, 'validate_by_name': True}¶
Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].
- class ReadModel(**data: Any)¶
Bases:
ReadModel- __abstractmethods__ = frozenset({})¶
- __annotations__ = {'attributes': <class 'aiida_gromacs.data.solvate.SolvateParameters.AttributesModel'>, 'node_type': typing.Literal['data.gromacs.solvate.SolvateParameters.']}¶
- __class_vars__ = {}¶
The names of the class variables defined on the model.
- __dict__¶
- __module__ = 'aiida_gromacs.data.solvate'¶
- __private_attributes__ = {'_AIIDA_MINIMAL_MODEL': ModelPrivateAttr()}¶
Metadata about the private attributes of the model.
- __pydantic_complete__ = True¶
Whether model building is completed, or if there are still undefined fields.
- __pydantic_computed_fields__ = {}¶
A dictionary of computed field names and their corresponding [ComputedFieldInfo][pydantic.fields.ComputedFieldInfo] objects.
- __pydantic_core_schema__ = {'cls': <class 'aiida_gromacs.data.solvate.SolvateParameters.ReadModel'>, 'config': {'extra_fields_behavior': 'forbid', 'serialize_by_alias': True, 'title': 'SolvateParametersReadModel', 'validate_by_alias': True, 'validate_by_name': True}, 'custom_init': False, 'metadata': {'pydantic_js_functions': [<bound method BaseModel.__get_pydantic_json_schema__ of <class 'aiida_gromacs.data.solvate.SolvateParameters.ReadModel'>>]}, 'post_init': 'model_post_init', 'ref': 'aiida_gromacs.data.solvate.SolvateParameters.ReadModel:109607548834800', 'root_model': False, 'schema': {'computed_fields': [], 'fields': {'attributes': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'The node attributes', 'examples': [{'attr_key': 'attr_value'}]}}, 'schema': {'cls': <class 'aiida_gromacs.data.solvate.SolvateParameters.AttributesModel'>, 'config': {'extra_fields_behavior': 'allow', 'serialize_by_alias': True, 'title': 'SolvateParametersAttributesModel', 'validate_by_alias': True, 'validate_by_name': True}, 'custom_init': False, 'metadata': {'pydantic_js_functions': [<bound method BaseModel.__get_pydantic_json_schema__ of <class 'aiida_gromacs.data.solvate.SolvateParameters.AttributesModel'>>]}, 'post_init': 'model_post_init', 'ref': 'aiida_gromacs.data.solvate.SolvateParameters.AttributesModel:109607548880560', 'root_model': False, 'schema': {'computed_fields': [], 'fields': {'source': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'Source of the data'}}, 'schema': {'default': None, 'schema': {'schema': {'keys_schema': {'type': 'any'}, 'type': 'dict', 'values_schema': {'type': 'any'}}, 'type': 'nullable'}, 'type': 'default'}, 'type': 'model-field'}}, 'model_name': 'AttributesModel', 'type': 'model-fields'}, 'type': 'model'}, 'type': 'model-field'}, 'computer': {'metadata': {'pydantic_js_extra': {'readOnly': True}, 'pydantic_js_updates': {'description': 'The PK of the computer', 'examples': [42]}}, 'schema': {'default': None, 'schema': {'schema': {'type': 'int'}, 'type': 'nullable'}, 'type': 'default'}, 'type': 'model-field'}, 'ctime': {'metadata': {'pydantic_js_extra': {'readOnly': True}, 'pydantic_js_updates': {'description': 'The creation time of the node', 'examples': ['2024-01-01T12:00:00+00:00']}}, 'schema': {'microseconds_precision': 'truncate', 'serialization': {'function': <function OrmModel.<lambda>>, 'type': 'function-plain', 'when_used': 'json'}, 'type': 'datetime'}, 'type': 'model-field'}, 'description': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'The node description', 'examples': ['This is my node description.']}}, 'schema': {'default': '', 'schema': {'type': 'str'}, 'type': 'default'}, 'type': 'model-field'}, 'extras': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'The node extras', 'examples': [{'extra_key': 'extra_value'}]}}, 'schema': {'default_factory': <class 'dict'>, 'default_factory_takes_data': False, 'schema': {'keys_schema': {'type': 'str'}, 'type': 'dict', 'values_schema': {'type': 'any'}}, 'type': 'default'}, 'type': 'model-field'}, 'label': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'The node label', 'examples': ['my_node']}}, 'schema': {'default': '', 'schema': {'type': 'str'}, 'type': 'default'}, 'type': 'model-field'}, 'mtime': {'metadata': {'pydantic_js_extra': {'readOnly': True}, 'pydantic_js_updates': {'description': 'The modification time of the node', 'examples': ['2024-01-02T12:00:00+00:00']}}, 'schema': {'microseconds_precision': 'truncate', 'serialization': {'function': <function OrmModel.<lambda>>, 'type': 'function-plain', 'when_used': 'json'}, 'type': 'datetime'}, 'type': 'model-field'}, 'node_type': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'The type of the node.'}}, 'schema': {'expected': ['data.gromacs.solvate.SolvateParameters.'], 'type': 'literal'}, 'type': 'model-field'}, 'pk': {'metadata': {'pydantic_js_extra': {'readOnly': True}, 'pydantic_js_updates': {'description': 'The primary key of the entity', 'examples': [42]}}, 'schema': {'type': 'int'}, 'type': 'model-field'}, 'process_type': {'metadata': {'pydantic_js_extra': {'readOnly': True}, 'pydantic_js_updates': {'description': 'The process type of the node', 'examples': ['aiida.calculations:arithmetic.add.']}}, 'schema': {'default': None, 'schema': {'schema': {'type': 'str'}, 'type': 'nullable'}, 'type': 'default'}, 'type': 'model-field'}, 'repository_metadata': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'Virtual hierarchy of the file repository', 'examples': [{'o': {'file.txt': {'k': '<file_hash>'}}}]}}, 'schema': {'default_factory': <class 'dict'>, 'default_factory_takes_data': False, 'schema': {'keys_schema': {'type': 'str'}, 'type': 'dict', 'values_schema': {'type': 'any'}}, 'type': 'default'}, 'type': 'model-field'}, 'user': {'metadata': {'pydantic_js_extra': {'readOnly': True}, 'pydantic_js_updates': {'description': 'The PK of the user who owns the node', 'examples': [7]}}, 'schema': {'type': 'int'}, 'type': 'model-field'}, 'uuid': {'metadata': {'pydantic_js_extra': {'readOnly': True}, 'pydantic_js_updates': {'description': 'The UUID of the node', 'examples': ['123e4567-e89b-12d3-a456-426614174000']}}, 'schema': {'type': 'uuid'}, 'type': 'model-field'}}, 'model_name': 'ReadModel', 'type': 'model-fields'}, 'type': 'model'}¶
The core schema of the model.
- __pydantic_custom_init__ = False¶
Whether the model has a custom __init__ method.
- __pydantic_decorators__ = DecoratorInfos(validators={}, field_validators={}, root_validators={}, field_serializers={}, model_serializers={}, model_validators={}, computed_fields={})¶
Metadata containing the decorators defined on the model. This replaces Model.__validators__ and Model.__root_validators__ from Pydantic V1.
- __pydantic_extra__¶
A dictionary containing extra values, if [extra][pydantic.config.ConfigDict.extra] is set to ‘allow’.
- __pydantic_extra_info__ = None¶
A wrapper around the __pydantic_extra__ annotation, if explicitly annotated on a model.
This is a private attribute, not meant to be used outside Pydantic.
- __pydantic_fields__ = {'attributes': FieldInfo(annotation=SolvateParameters.AttributesModel, required=True, description='The node attributes', examples=[{'attr_key': 'attr_value'}], json_schema_extra={}, metadata=[{'priority': 0}, {'read_only': False}, {'write_only': False}, {'may_be_large': True}]), 'computer': FieldInfo(annotation=Union[int, NoneType], required=False, default=None, description='The PK of the computer', examples=[42], json_schema_extra={'readOnly': True}, metadata=[{'priority': 0}, {'read_only': True}, {'write_only': False}, {'may_be_large': False}, {'orm_class': <class 'aiida.orm.computers.Computer'>}, {'orm_to_model': <function Node.ReadModel.<lambda>>}]), 'ctime': FieldInfo(annotation=datetime, required=True, description='The creation time of the node', examples=['2024-01-01T12:00:00+00:00'], json_schema_extra={'readOnly': True}, metadata=[{'priority': 0}, {'read_only': True}, {'write_only': False}, {'may_be_large': False}]), 'description': FieldInfo(annotation=str, required=False, default='', description='The node description', examples=['This is my node description.'], json_schema_extra={}, metadata=[{'priority': 0}, {'read_only': False}, {'write_only': False}, {'may_be_large': False}]), 'extras': FieldInfo(annotation=dict[str, Any], required=False, default_factory=dict, description='The node extras', examples=[{'extra_key': 'extra_value'}], json_schema_extra={}, metadata=[{'priority': 0}, {'read_only': False}, {'write_only': False}, {'may_be_large': True}, {'orm_to_model': <function Node.MutableNodeFields.<lambda>>}]), 'label': FieldInfo(annotation=str, required=False, default='', description='The node label', examples=['my_node'], json_schema_extra={}, metadata=[{'priority': 0}, {'read_only': False}, {'write_only': False}, {'may_be_large': False}]), 'mtime': FieldInfo(annotation=datetime, required=True, description='The modification time of the node', examples=['2024-01-02T12:00:00+00:00'], json_schema_extra={'readOnly': True}, metadata=[{'priority': 0}, {'read_only': True}, {'write_only': False}, {'may_be_large': False}]), 'node_type': FieldInfo(annotation=Literal['data.gromacs.solvate.SolvateParameters.'], required=True, description='The type of the node.', json_schema_extra={}, metadata=[{'priority': 0}, {'read_only': False}, {'write_only': False}, {'may_be_large': False}]), 'pk': FieldInfo(annotation=int, required=True, description='The primary key of the entity', examples=[42], json_schema_extra={'readOnly': True}, metadata=[{'priority': 0}, {'read_only': True}, {'write_only': False}, {'may_be_large': False}]), 'process_type': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, description='The process type of the node', examples=['aiida.calculations:arithmetic.add.'], json_schema_extra={'readOnly': True}, metadata=[{'priority': 0}, {'read_only': True}, {'write_only': False}, {'may_be_large': False}]), 'repository_metadata': FieldInfo(annotation=dict[str, Any], required=False, default_factory=dict, description='Virtual hierarchy of the file repository', examples=[{'o': {'file.txt': {'k': '<file_hash>'}}}], json_schema_extra={}, metadata=[{'priority': 0}, {'read_only': False}, {'write_only': False}, {'may_be_large': True}, {'orm_to_model': <function Node.WritableFields.<lambda>>}]), 'user': FieldInfo(annotation=int, required=True, description='The PK of the user who owns the node', examples=[7], json_schema_extra={'readOnly': True}, metadata=[{'priority': 0}, {'read_only': True}, {'write_only': False}, {'may_be_large': False}, {'orm_class': <class 'aiida.orm.users.User'>}, {'orm_to_model': <function Node.ReadModel.<lambda>>}]), 'uuid': FieldInfo(annotation=UUID, required=True, description='The UUID of the node', examples=['123e4567-e89b-12d3-a456-426614174000'], json_schema_extra={'readOnly': True}, metadata=[{'priority': 0}, {'read_only': True}, {'write_only': False}, {'may_be_large': False}])}¶
A dictionary of field names and their corresponding [FieldInfo][pydantic.fields.FieldInfo] objects. This replaces Model.__fields__ from Pydantic V1.
- __pydantic_fields_set__¶
The names of fields explicitly set during instantiation.
- __pydantic_generic_metadata__ = {'args': (), 'origin': None, 'parameters': ()}¶
A dictionary containing metadata about generic Pydantic models.
The origin and args items map to the [__origin__][genericalias.__origin__] and [__args__][genericalias.__args__] attributes of [generic aliases][types-genericalias], and the parameter item maps to the __parameter__ attribute of generic classes.
- __pydantic_post_init__ = 'model_post_init'¶
The name of the post-init method for the model, if defined.
- __pydantic_private__¶
Values of private attributes set on the model instance.
- __pydantic_serializer__ = SchemaSerializer(serializer=PolymorphismTrampoline( PolymorphismTrampoline { class: Py( 0x000063afff0353f0, ), serializer: PolymorphismTrampoline( PolymorphismTrampoline { class: Py( 0x000063afff0353f0, ), serializer: Model( ModelSerializer { class: Py( 0x000063afff0353f0, ), serializer: Fields( GeneralFieldsSerializer { fields: { "user": SerField { key: "user", alias: None, serializer: Some( Int( IntSerializer, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "computer": SerField { key: "computer", alias: None, serializer: Some( WithDefault( WithDefaultSerializer { default: Default( Py( 0x00007310e7455800, ), ), serializer: Nullable( NullableSerializer { serializer: Int( IntSerializer, ), }, ), }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "process_type": SerField { key: "process_type", alias: None, serializer: Some( WithDefault( WithDefaultSerializer { default: Default( Py( 0x00007310e7455800, ), ), serializer: Nullable( NullableSerializer { serializer: Str( StrSerializer, ), }, ), }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "repository_metadata": SerField { key: "repository_metadata", alias: None, serializer: Some( WithDefault( WithDefaultSerializer { default: DefaultFactory( Py( 0x00007310e74524a0, ), false, ), serializer: Dict( DictSerializer { key_serializer: Str( StrSerializer, ), value_serializer: Any( AnySerializer, ), filter: SchemaFilter { include: None, exclude: None, }, name: "dict[str, any]", }, ), }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "node_type": SerField { key: "node_type", alias: None, serializer: Some( Literal( LiteralSerializer { expected_int: {}, expected_str: { "data.gromacs.solvate.SolvateParameters.", }, expected_py: None, name: "literal['data.gromacs.solvate.SolvateParameters.']", }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "mtime": SerField { key: "mtime", alias: None, serializer: Some( Function( FunctionPlainSerializer { func: Py( 0x00007310e2355c60, ), name: "plain_function[<lambda>]", function_name: "<lambda>", return_serializer: Any( AnySerializer, ), fallback_serializer: Some( Datetime( DatetimeSerializer { temporal_mode: Iso8601, }, ), ), when_used: Json, is_field_serializer: false, info_arg: false, }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "uuid": SerField { key: "uuid", alias: None, serializer: Some( Uuid( UuidSerializer, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "label": SerField { key: "label", alias: None, serializer: Some( WithDefault( WithDefaultSerializer { default: Default( Py( 0x00007310e7482e40, ), ), serializer: Str( StrSerializer, ), }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "attributes": SerField { key: "attributes", alias: None, serializer: Some( PolymorphismTrampoline( PolymorphismTrampoline { class: Py( 0x000063afff0406b0, ), serializer: Prebuilt( PrebuiltSerializer { schema_serializer: Py( 0x00007310d206d2d0, ), }, ), enabled_from_config: false, }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "ctime": SerField { key: "ctime", alias: None, serializer: Some( Function( FunctionPlainSerializer { func: Py( 0x00007310e2355c60, ), name: "plain_function[<lambda>]", function_name: "<lambda>", return_serializer: Any( AnySerializer, ), fallback_serializer: Some( Datetime( DatetimeSerializer { temporal_mode: Iso8601, }, ), ), when_used: Json, is_field_serializer: false, info_arg: false, }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "extras": SerField { key: "extras", alias: None, serializer: Some( WithDefault( WithDefaultSerializer { default: DefaultFactory( Py( 0x00007310e74524a0, ), false, ), serializer: Dict( DictSerializer { key_serializer: Str( StrSerializer, ), value_serializer: Any( AnySerializer, ), filter: SchemaFilter { include: None, exclude: None, }, name: "dict[str, any]", }, ), }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "description": SerField { key: "description", alias: None, serializer: Some( WithDefault( WithDefaultSerializer { default: Default( Py( 0x00007310e7482e40, ), ), serializer: Str( StrSerializer, ), }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "pk": SerField { key: "pk", alias: None, serializer: Some( Int( IntSerializer, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, }, computed_fields: Some( ComputedFields( [], ), ), mode: SimpleDict, extra_serializer: None, filter: SchemaFilter { include: None, exclude: None, }, required_fields: 13, }, ), has_extra: false, root_model: false, name: "ReadModel", }, ), enabled_from_config: false, }, ), enabled_from_config: false, }, ), definitions=[])¶
The pydantic-core SchemaSerializer used to dump instances of the model.
- __pydantic_setattr_handlers__ = {}¶
__setattr__ handlers. Memoizing the handlers leads to a dramatic performance improvement in __setattr__
- __pydantic_validator__ = SchemaValidator(title="SolvateParametersReadModel", validator=Model( ModelValidator { revalidate: Never, validator: ModelFields( ModelFieldsValidator { fields: [ Field { name: "pk", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "pk", ), rest: [], }, by_alias: [], }, validator: Int( IntValidator { strict: false, }, ), frozen: false, }, Field { name: "label", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "label", ), rest: [], }, by_alias: [], }, validator: WithDefault( WithDefaultValidator { default: Default( Py( 0x00007310e7482e40, ), ), on_error: Raise, validator: Str( StrValidator { strict: false, coerce_numbers_to_str: false, }, ), validate_default: false, copy_default: false, name: "default[str]", undefined: Py( 0x00007310e53bdb90, ), }, ), frozen: false, }, Field { name: "description", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "description", ), rest: [], }, by_alias: [], }, validator: WithDefault( WithDefaultValidator { default: Default( Py( 0x00007310e7482e40, ), ), on_error: Raise, validator: Str( StrValidator { strict: false, coerce_numbers_to_str: false, }, ), validate_default: false, copy_default: false, name: "default[str]", undefined: Py( 0x00007310e53bdb90, ), }, ), frozen: false, }, Field { name: "extras", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "extras", ), rest: [], }, by_alias: [], }, validator: WithDefault( WithDefaultValidator { default: DefaultFactory( Py( 0x00007310e74524a0, ), false, ), on_error: Raise, validator: Dict( DictValidator { strict: false, key_validator: Str( StrValidator { strict: false, coerce_numbers_to_str: false, }, ), value_validator: Any( AnyValidator, ), min_length: None, max_length: None, fail_fast: false, name: "dict[str,any]", }, ), validate_default: false, copy_default: false, name: "default[dict[str,any]]", undefined: Py( 0x00007310e53bdb90, ), }, ), frozen: false, }, Field { name: "node_type", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "node_type", ), rest: [], }, by_alias: [], }, validator: Literal( LiteralValidator { lookup: LiteralLookup { expected_bool: None, expected_int: None, expected_str: Some( { "data.gromacs.solvate.SolvateParameters.": 0, }, ), expected_py_dict: None, expected_py_values: None, expected_py_primitives: Some( Py( 0x00007310d1e8edc0, ), ), values: [ Py( 0x00007310d3056510, ), ], }, expected_repr: "'data.gromacs.solvate.SolvateParameters.'", name: "literal['data.gromacs.solvate.SolvateParameters.']", }, ), frozen: false, }, Field { name: "attributes", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "attributes", ), rest: [], }, by_alias: [], }, validator: Prebuilt( PrebuiltValidator { schema_validator: Py( 0x00007310d206d6c0, ), }, ), frozen: false, }, Field { name: "repository_metadata", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "repository_metadata", ), rest: [], }, by_alias: [], }, validator: WithDefault( WithDefaultValidator { default: DefaultFactory( Py( 0x00007310e74524a0, ), false, ), on_error: Raise, validator: Dict( DictValidator { strict: false, key_validator: Str( StrValidator { strict: false, coerce_numbers_to_str: false, }, ), value_validator: Any( AnyValidator, ), min_length: None, max_length: None, fail_fast: false, name: "dict[str,any]", }, ), validate_default: false, copy_default: false, name: "default[dict[str,any]]", undefined: Py( 0x00007310e53bdb90, ), }, ), frozen: false, }, Field { name: "uuid", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "uuid", ), rest: [], }, by_alias: [], }, validator: Uuid( UuidValidator { strict: false, version: None, }, ), frozen: false, }, Field { name: "process_type", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "process_type", ), rest: [], }, by_alias: [], }, validator: WithDefault( WithDefaultValidator { default: Default( Py( 0x00007310e7455800, ), ), on_error: Raise, validator: Nullable( NullableValidator { validator: Str( StrValidator { strict: false, coerce_numbers_to_str: false, }, ), name: "nullable[str]", }, ), validate_default: false, copy_default: false, name: "default[nullable[str]]", undefined: Py( 0x00007310e53bdb90, ), }, ), frozen: false, }, Field { name: "ctime", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "ctime", ), rest: [], }, by_alias: [], }, validator: Datetime( DateTimeValidator { strict: false, constraints: None, microseconds_precision: Truncate, val_temporal_unit: Infer, }, ), frozen: false, }, Field { name: "mtime", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "mtime", ), rest: [], }, by_alias: [], }, validator: Datetime( DateTimeValidator { strict: false, constraints: None, microseconds_precision: Truncate, val_temporal_unit: Infer, }, ), frozen: false, }, Field { name: "computer", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "computer", ), rest: [], }, by_alias: [], }, validator: WithDefault( WithDefaultValidator { default: Default( Py( 0x00007310e7455800, ), ), on_error: Raise, validator: Nullable( NullableValidator { validator: Int( IntValidator { strict: false, }, ), name: "nullable[int]", }, ), validate_default: false, copy_default: false, name: "default[nullable[int]]", undefined: Py( 0x00007310e53bdb90, ), }, ), frozen: false, }, Field { name: "user", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "user", ), rest: [], }, by_alias: [], }, validator: Int( IntValidator { strict: false, }, ), frozen: false, }, ], model_name: "ReadModel", extra_behavior: Forbid, extras_validator: None, extras_keys_validator: None, strict: false, from_attributes: false, loc_by_alias: true, lookup: LookupTree { inner: { PathItemString( "process_type", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 8, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "mtime", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 10, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "ctime", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 9, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "description", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 2, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "node_type", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 4, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "repository_metadata", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 6, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "user", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 12, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "extras", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 3, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "computer", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 11, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "label", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 1, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "uuid", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 7, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "pk", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 0, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "attributes", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 5, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, }, }, validate_by_alias: Some( true, ), validate_by_name: Some( true, ), }, ), class: Py( 0x000063afff0353f0, ), generic_origin: None, post_init: Some( Py( 0x00007310e2571630, ), ), frozen: false, custom_init: false, root_model: false, undefined: Py( 0x00007310e53bdb90, ), name: "ReadModel", }, ), definitions=[], cache_strings=True)¶
The pydantic-core SchemaValidator used to validate instances of the model.
- _abc_impl = <_abc._abc_data object>¶
- attributes: AttributesModel¶
- model_config = {'defer_build': True, 'extra': 'forbid', 'json_encoders': {<class 'datetime.datetime'>: <function OrmModel.<lambda>>}, 'serialize_by_alias': True, 'title': 'SolvateParametersReadModel', 'validate_by_alias': True, 'validate_by_name': True}¶
Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].
- class WriteModel(**data: Any)¶
Bases:
WriteModel- __abstractmethods__ = frozenset({})¶
- __annotations__ = {'attributes': <class 'aiida_gromacs.data.solvate.SolvateParameters.AttributesWriteModel'>, 'description': <class 'str'>, 'extras': dict[str, typing.Any], 'label': <class 'str'>, 'node_type': typing.Literal['data.gromacs.solvate.SolvateParameters.'], 'repository_metadata': dict[str, typing.Any]}¶
- __class_vars__ = {}¶
The names of the class variables defined on the model.
- __dict__¶
- __module__ = 'aiida_gromacs.data.solvate'¶
- __private_attributes__ = {'_AIIDA_MINIMAL_MODEL': ModelPrivateAttr()}¶
Metadata about the private attributes of the model.
- __pydantic_complete__ = True¶
Whether model building is completed, or if there are still undefined fields.
- __pydantic_computed_fields__ = {}¶
A dictionary of computed field names and their corresponding [ComputedFieldInfo][pydantic.fields.ComputedFieldInfo] objects.
- __pydantic_core_schema__ = {'cls': <class 'aiida_gromacs.data.solvate.SolvateParameters.WriteModel'>, 'config': {'extra_fields_behavior': 'forbid', 'serialize_by_alias': True, 'title': 'SolvateParametersWriteModel', 'validate_by_alias': True, 'validate_by_name': True}, 'custom_init': False, 'metadata': {'pydantic_js_functions': [<bound method BaseModel.__get_pydantic_json_schema__ of <class 'aiida_gromacs.data.solvate.SolvateParameters.WriteModel'>>]}, 'post_init': 'model_post_init', 'ref': 'aiida_gromacs.data.solvate.SolvateParameters.WriteModel:109607549030128', 'root_model': False, 'schema': {'computed_fields': [], 'fields': {'attributes': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'The node attributes', 'examples': [{'attr_key': 'attr_value'}]}}, 'schema': {'cls': <class 'aiida_gromacs.data.solvate.SolvateParameters.AttributesWriteModel'>, 'config': {'extra_fields_behavior': 'allow', 'serialize_by_alias': True, 'title': 'SolvateParametersAttributesWriteModel', 'validate_by_alias': True, 'validate_by_name': True}, 'custom_init': False, 'metadata': {'pydantic_js_functions': [<bound method BaseModel.__get_pydantic_json_schema__ of <class 'aiida_gromacs.data.solvate.SolvateParameters.AttributesWriteModel'>>]}, 'post_init': 'model_post_init', 'ref': 'aiida_gromacs.data.solvate.SolvateParameters.AttributesWriteModel:109607549036800', 'root_model': False, 'schema': {'computed_fields': [], 'fields': {'source': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'Source of the data'}}, 'schema': {'default': None, 'schema': {'schema': {'keys_schema': {'type': 'any'}, 'type': 'dict', 'values_schema': {'type': 'any'}}, 'type': 'nullable'}, 'type': 'default'}, 'type': 'model-field'}}, 'model_name': 'AttributesWriteModel', 'type': 'model-fields'}, 'type': 'model'}, 'type': 'model-field'}, 'description': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'The node description', 'examples': ['This is my node description.']}}, 'schema': {'default': '', 'schema': {'type': 'str'}, 'type': 'default'}, 'type': 'model-field'}, 'extras': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'The node extras', 'examples': [{'extra_key': 'extra_value'}]}}, 'schema': {'default_factory': <class 'dict'>, 'default_factory_takes_data': False, 'schema': {'keys_schema': {'type': 'str'}, 'type': 'dict', 'values_schema': {'type': 'any'}}, 'type': 'default'}, 'type': 'model-field'}, 'label': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'The node label', 'examples': ['my_node']}}, 'schema': {'default': '', 'schema': {'type': 'str'}, 'type': 'default'}, 'type': 'model-field'}, 'node_type': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'The type of the node.'}}, 'schema': {'expected': ['data.gromacs.solvate.SolvateParameters.'], 'type': 'literal'}, 'type': 'model-field'}, 'repository_metadata': {'metadata': {'pydantic_js_extra': {}, 'pydantic_js_updates': {'description': 'Virtual hierarchy of the file repository', 'examples': [{'o': {'file.txt': {'k': '<file_hash>'}}}]}}, 'schema': {'default_factory': <class 'dict'>, 'default_factory_takes_data': False, 'schema': {'keys_schema': {'type': 'str'}, 'type': 'dict', 'values_schema': {'type': 'any'}}, 'type': 'default'}, 'type': 'model-field'}}, 'model_name': 'WriteModel', 'type': 'model-fields'}, 'type': 'model'}¶
The core schema of the model.
- __pydantic_custom_init__ = False¶
Whether the model has a custom __init__ method.
- __pydantic_decorators__ = DecoratorInfos(validators={}, field_validators={}, root_validators={}, field_serializers={}, model_serializers={}, model_validators={}, computed_fields={})¶
Metadata containing the decorators defined on the model. This replaces Model.__validators__ and Model.__root_validators__ from Pydantic V1.
- __pydantic_extra__¶
A dictionary containing extra values, if [extra][pydantic.config.ConfigDict.extra] is set to ‘allow’.
- __pydantic_extra_info__ = None¶
A wrapper around the __pydantic_extra__ annotation, if explicitly annotated on a model.
This is a private attribute, not meant to be used outside Pydantic.
- __pydantic_fields__ = {'attributes': FieldInfo(annotation=SolvateParameters.AttributesWriteModel, required=True, description='The node attributes', examples=[{'attr_key': 'attr_value'}], json_schema_extra={}, metadata=[{'priority': 0}, {'read_only': False}, {'write_only': False}, {'may_be_large': True}]), 'description': FieldInfo(annotation=str, required=False, default='', description='The node description', examples=['This is my node description.'], json_schema_extra={}, metadata=[{'priority': 0}, {'read_only': False}, {'write_only': False}, {'may_be_large': False}]), 'extras': FieldInfo(annotation=dict[str, Any], required=False, default_factory=dict, description='The node extras', examples=[{'extra_key': 'extra_value'}], json_schema_extra={}, metadata=[{'priority': 0}, {'read_only': False}, {'write_only': False}, {'may_be_large': True}, {'orm_to_model': <function Node.MutableNodeFields.<lambda>>}]), 'label': FieldInfo(annotation=str, required=False, default='', description='The node label', examples=['my_node'], json_schema_extra={}, metadata=[{'priority': 0}, {'read_only': False}, {'write_only': False}, {'may_be_large': False}]), 'node_type': FieldInfo(annotation=Literal['data.gromacs.solvate.SolvateParameters.'], required=True, description='The type of the node.', json_schema_extra={}, metadata=[{'priority': 0}, {'read_only': False}, {'write_only': False}, {'may_be_large': False}]), 'repository_metadata': FieldInfo(annotation=dict[str, Any], required=False, default_factory=dict, description='Virtual hierarchy of the file repository', examples=[{'o': {'file.txt': {'k': '<file_hash>'}}}], json_schema_extra={}, metadata=[{'priority': 0}, {'read_only': False}, {'write_only': False}, {'may_be_large': True}, {'orm_to_model': <function Node.WritableFields.<lambda>>}])}¶
A dictionary of field names and their corresponding [FieldInfo][pydantic.fields.FieldInfo] objects. This replaces Model.__fields__ from Pydantic V1.
- __pydantic_fields_set__¶
The names of fields explicitly set during instantiation.
- __pydantic_generic_metadata__ = {'args': (), 'origin': None, 'parameters': ()}¶
A dictionary containing metadata about generic Pydantic models.
The origin and args items map to the [__origin__][genericalias.__origin__] and [__args__][genericalias.__args__] attributes of [generic aliases][types-genericalias], and the parameter item maps to the __parameter__ attribute of generic classes.
- __pydantic_post_init__ = 'model_post_init'¶
The name of the post-init method for the model, if defined.
- __pydantic_private__¶
Values of private attributes set on the model instance.
- __pydantic_serializer__ = SchemaSerializer(serializer=PolymorphismTrampoline( PolymorphismTrampoline { class: Py( 0x000063afff064ef0, ), serializer: PolymorphismTrampoline( PolymorphismTrampoline { class: Py( 0x000063afff064ef0, ), serializer: Model( ModelSerializer { class: Py( 0x000063afff064ef0, ), serializer: Fields( GeneralFieldsSerializer { fields: { "extras": SerField { key: "extras", alias: None, serializer: Some( WithDefault( WithDefaultSerializer { default: DefaultFactory( Py( 0x00007310e74524a0, ), false, ), serializer: Dict( DictSerializer { key_serializer: Str( StrSerializer, ), value_serializer: Any( AnySerializer, ), filter: SchemaFilter { include: None, exclude: None, }, name: "dict[str, any]", }, ), }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "node_type": SerField { key: "node_type", alias: None, serializer: Some( Literal( LiteralSerializer { expected_int: {}, expected_str: { "data.gromacs.solvate.SolvateParameters.", }, expected_py: None, name: "literal['data.gromacs.solvate.SolvateParameters.']", }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "description": SerField { key: "description", alias: None, serializer: Some( WithDefault( WithDefaultSerializer { default: Default( Py( 0x00007310e7482e40, ), ), serializer: Str( StrSerializer, ), }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "label": SerField { key: "label", alias: None, serializer: Some( WithDefault( WithDefaultSerializer { default: Default( Py( 0x00007310e7482e40, ), ), serializer: Str( StrSerializer, ), }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "attributes": SerField { key: "attributes", alias: None, serializer: Some( PolymorphismTrampoline( PolymorphismTrampoline { class: Py( 0x000063afff066900, ), serializer: PolymorphismTrampoline( PolymorphismTrampoline { class: Py( 0x000063afff066900, ), serializer: Model( ModelSerializer { class: Py( 0x000063afff066900, ), serializer: Fields( GeneralFieldsSerializer { fields: { "source": SerField { key: "source", alias: None, serializer: Some( WithDefault( WithDefaultSerializer { default: Default( Py( 0x00007310e7455800, ), ), serializer: Nullable( NullableSerializer { serializer: Dict( DictSerializer { key_serializer: Any( AnySerializer, ), value_serializer: Any( AnySerializer, ), filter: SchemaFilter { include: None, exclude: None, }, name: "dict[any, any]", }, ), }, ), }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, }, computed_fields: Some( ComputedFields( [], ), ), mode: ModelExtra, extra_serializer: None, filter: SchemaFilter { include: None, exclude: None, }, required_fields: 1, }, ), has_extra: true, root_model: false, name: "AttributesWriteModel", }, ), enabled_from_config: false, }, ), enabled_from_config: false, }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, "repository_metadata": SerField { key: "repository_metadata", alias: None, serializer: Some( WithDefault( WithDefaultSerializer { default: DefaultFactory( Py( 0x00007310e74524a0, ), false, ), serializer: Dict( DictSerializer { key_serializer: Str( StrSerializer, ), value_serializer: Any( AnySerializer, ), filter: SchemaFilter { include: None, exclude: None, }, name: "dict[str, any]", }, ), }, ), ), required: true, serialize_by_alias: Some( true, ), serialization_exclude_if: None, }, }, computed_fields: Some( ComputedFields( [], ), ), mode: SimpleDict, extra_serializer: None, filter: SchemaFilter { include: None, exclude: None, }, required_fields: 6, }, ), has_extra: false, root_model: false, name: "WriteModel", }, ), enabled_from_config: false, }, ), enabled_from_config: false, }, ), definitions=[])¶
The pydantic-core SchemaSerializer used to dump instances of the model.
- __pydantic_setattr_handlers__ = {}¶
__setattr__ handlers. Memoizing the handlers leads to a dramatic performance improvement in __setattr__
- __pydantic_validator__ = SchemaValidator(title="SolvateParametersWriteModel", validator=Model( ModelValidator { revalidate: Never, validator: ModelFields( ModelFieldsValidator { fields: [ Field { name: "label", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "label", ), rest: [], }, by_alias: [], }, validator: WithDefault( WithDefaultValidator { default: Default( Py( 0x00007310e7482e40, ), ), on_error: Raise, validator: Str( StrValidator { strict: false, coerce_numbers_to_str: false, }, ), validate_default: false, copy_default: false, name: "default[str]", undefined: Py( 0x00007310e53bdb90, ), }, ), frozen: false, }, Field { name: "description", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "description", ), rest: [], }, by_alias: [], }, validator: WithDefault( WithDefaultValidator { default: Default( Py( 0x00007310e7482e40, ), ), on_error: Raise, validator: Str( StrValidator { strict: false, coerce_numbers_to_str: false, }, ), validate_default: false, copy_default: false, name: "default[str]", undefined: Py( 0x00007310e53bdb90, ), }, ), frozen: false, }, Field { name: "extras", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "extras", ), rest: [], }, by_alias: [], }, validator: WithDefault( WithDefaultValidator { default: DefaultFactory( Py( 0x00007310e74524a0, ), false, ), on_error: Raise, validator: Dict( DictValidator { strict: false, key_validator: Str( StrValidator { strict: false, coerce_numbers_to_str: false, }, ), value_validator: Any( AnyValidator, ), min_length: None, max_length: None, fail_fast: false, name: "dict[str,any]", }, ), validate_default: false, copy_default: false, name: "default[dict[str,any]]", undefined: Py( 0x00007310e53bdb90, ), }, ), frozen: false, }, Field { name: "node_type", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "node_type", ), rest: [], }, by_alias: [], }, validator: Literal( LiteralValidator { lookup: LiteralLookup { expected_bool: None, expected_int: None, expected_str: Some( { "data.gromacs.solvate.SolvateParameters.": 0, }, ), expected_py_dict: None, expected_py_values: None, expected_py_primitives: Some( Py( 0x00007310d1e90b80, ), ), values: [ Py( 0x00007310d3056510, ), ], }, expected_repr: "'data.gromacs.solvate.SolvateParameters.'", name: "literal['data.gromacs.solvate.SolvateParameters.']", }, ), frozen: false, }, Field { name: "attributes", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "attributes", ), rest: [], }, by_alias: [], }, validator: Model( ModelValidator { revalidate: Never, validator: ModelFields( ModelFieldsValidator { fields: [ Field { name: "source", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "source", ), rest: [], }, by_alias: [], }, validator: WithDefault( WithDefaultValidator { default: Default( Py( 0x00007310e7455800, ), ), on_error: Raise, validator: Nullable( NullableValidator { validator: Dict( DictValidator { strict: false, key_validator: Any( AnyValidator, ), value_validator: Any( AnyValidator, ), min_length: None, max_length: None, fail_fast: false, name: "dict[any,any]", }, ), name: "nullable[dict[any,any]]", }, ), validate_default: false, copy_default: false, name: "default[nullable[dict[any,any]]]", undefined: Py( 0x00007310e53bdb90, ), }, ), frozen: false, }, ], model_name: "AttributesWriteModel", extra_behavior: Allow, extras_validator: None, extras_keys_validator: None, strict: false, from_attributes: false, loc_by_alias: true, lookup: LookupTree { inner: { PathItemString( "source", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 0, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, }, }, validate_by_alias: Some( true, ), validate_by_name: Some( true, ), }, ), class: Py( 0x000063afff066900, ), generic_origin: None, post_init: Some( Py( 0x00007310e2571630, ), ), frozen: false, custom_init: false, root_model: false, undefined: Py( 0x00007310e53bdb90, ), name: "AttributesWriteModel", }, ), frozen: false, }, Field { name: "repository_metadata", lookup_path_collection: LookupPathCollection { by_name: LookupPath { first_item: PathItemString( "repository_metadata", ), rest: [], }, by_alias: [], }, validator: WithDefault( WithDefaultValidator { default: DefaultFactory( Py( 0x00007310e74524a0, ), false, ), on_error: Raise, validator: Dict( DictValidator { strict: false, key_validator: Str( StrValidator { strict: false, coerce_numbers_to_str: false, }, ), value_validator: Any( AnyValidator, ), min_length: None, max_length: None, fail_fast: false, name: "dict[str,any]", }, ), validate_default: false, copy_default: false, name: "default[dict[str,any]]", undefined: Py( 0x00007310e53bdb90, ), }, ), frozen: false, }, ], model_name: "WriteModel", extra_behavior: Forbid, extras_validator: None, extras_keys_validator: None, strict: false, from_attributes: false, loc_by_alias: true, lookup: LookupTree { inner: { PathItemString( "extras", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 2, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "description", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 1, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "label", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 0, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "repository_metadata", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 5, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "node_type", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 3, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, PathItemString( "attributes", ): LookupTreeNode { fields: [ LookupFieldInfo { field_index: 4, lookup_priority: LookupFieldPriority { lookup_type: Both, alias_index: 0, }, }, ], map: {}, list: {}, }, }, }, validate_by_alias: Some( true, ), validate_by_name: Some( true, ), }, ), class: Py( 0x000063afff064ef0, ), generic_origin: None, post_init: Some( Py( 0x00007310e2571630, ), ), frozen: false, custom_init: false, root_model: false, undefined: Py( 0x00007310e53bdb90, ), name: "WriteModel", }, ), definitions=[], cache_strings=True)¶
The pydantic-core SchemaValidator used to validate instances of the model.
- _abc_impl = <_abc._abc_data object>¶
- attributes: AttributesWriteModel¶
- model_config = {'defer_build': True, 'extra': 'forbid', 'json_encoders': {<class 'datetime.datetime'>: <function OrmModel.<lambda>>}, 'serialize_by_alias': True, 'title': 'SolvateParametersWriteModel', 'validate_by_alias': True, 'validate_by_name': True}¶
Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].
- _COMPAT_MODEL¶
alias of
Model
- _ConstructorModel¶
alias of
ConstructorModel
- _MODEL_MAP = {'read': <class 'aiida_gromacs.data.solvate.SolvateParameters.ReadModel'>, 'write': <class 'aiida_gromacs.data.solvate.SolvateParameters.WriteModel'>}¶
- __abstractmethods__ = frozenset({})¶
- __annotations__ = {}¶
- __firstlineno__ = 25¶
- __init__(dict=None, **kwargs)[source]¶
Constructor for the data class
Usage:
SolvateParameters(dict{'ignore-case': True})- Parameters:
parameters_dict (type) – dictionary with commandline parameters
parameters_dict – dict
- __module__ = 'aiida_gromacs.data.solvate'¶
- __parameters__ = ()¶
- __static_attributes__ = ()¶
- __str__()[source]¶
String representation of node.
Append values of dictionary to usual representation. E.g.:
uuid: b416cbee-24e8-47a8-8c11-6d668770158b (pk: 590) {'ignore-case': True}
- _abc_impl = <_abc._abc_data object>¶
- _logger = <Logger aiida_gromacs.data.solvate.SolvateParameters (WARNING)>¶
- cmdline_params(grofile, topfile)[source]¶
Synthesize command line parameters.
e.g. [ ‘–ignore-case’, ‘filename1’, ‘filename2’]
- Parameters:
grofile (type) – Name of input gro file
grofile – str
- fields = {'attributes': "QbAttributesField('attributes', dtype=<class 'aiida_gromacs.data.solvate.SolvateParameters.AttributesModel'>, doc='The node attributes')", 'computer': "QbNumericField('computer', dtype=int | None, doc='The PK of the computer')", 'ctime': "QbNumericField('ctime', dtype=<class 'datetime.datetime'>, doc='The creation time of the node')", 'description': "QbStrField('description', dtype=<class 'str'>, doc='The node description')", 'extras': "QbDictField('extras', dtype=dict[str, typing.Any], doc='The node extras')", 'label': "QbStrField('label', dtype=<class 'str'>, doc='The node label')", 'mtime': "QbNumericField('mtime', dtype=<class 'datetime.datetime'>, doc='The modification time of the node')", 'node_type': "QbStrField('node_type', dtype=typing.Literal['data.gromacs.solvate.SolvateParameters.'], doc='The type of the node.')", 'pk': "QbNumericField('pk', dtype=<class 'int'>, doc='The primary key of the entity')", 'process_type': "QbStrField('process_type', dtype=str | None, doc='The process type of the node')", 'repository_metadata': "QbDictField('repository_metadata', dtype=dict[str, typing.Any], doc='Virtual hierarchy of the file repository')", 'source': "QbDictField('attributes.source', dtype=dict | None, doc='Source of the data')", 'user': "QbNumericField('user', dtype=<class 'int'>, doc='The PK of the user who owns the node')", 'uuid': "QbStrField('uuid', dtype=<class 'uuid.UUID'>, doc='The UUID of the node')"}¶
- schema = <Schema({'cs': <class 'str'>, 'o': <class 'str'>, 'box': <class 'str'>, 'radius': <class 'str'>, 'scale': <class 'str'>, 'shell': <class 'str'>, 'maxsol': <class 'str'>, 'vel': <class 'str'>}, extra=PREVENT_EXTRA, required=False) object>¶
- validate(parameters_dict)[source]¶
Validate command line options.
Uses the voluptuous package for validation. Find out about allowed keys using:
print(SolvateParameters).schema.schema
- Parameters:
parameters_dict (type) – dictionary with commandline parameters
parameters_dict – dict
- Returns:
validated dictionary
Module contents¶
aiida_gromacs
A plugin for using GROMACS with AiiDA for molecular dymanics simulations.