Material

Material

Bases: PrimaryBaseNode

Definition

A Material node is a collection of the identifiers and properties of a chemical, mixture, or substance.

Attributes

attribute	type	example	description	required	vocab
identifier	list[Identifier]		material identifiers	True
component	list[Material]		list of component that make up the mixture
property	list[Property]		material properties
process	Process		process node that made this material
parent_material	Material		material node that this node was copied from
computational_forcefield	Computation Forcefield		computation forcefield	Conditional
keyword	list[str]	[thermoplastic, homopolymer, linear, polyolefins]	words that classify the material		True
notes	str	"my awesome notes"	miscellaneous information, or custom data structure		True

Navigating to Material

Materials can be easily found on the CRIPT home screen in the under the navigation within the Materials link

Available Sub-Objects for Material

• Identifier
• Property
• Computational_forcefield

Example

water, brine (water + NaCl), polystyrene, polyethylene glycol hydrogels, vulcanized polyisoprene, mcherry (protein), and mica

Warnings

Material names

Material names Must be unique within a Project

  {
     "node":["Material"],
     "name":"my unique material name",
     "uid":"_:9679ff12-f9b4-41f4-be95-080b78fa71fd",
     "uuid":"9679ff12-f9b4-41f4-be95-080b78fa71fd"
     "bigsmiles":"[H]{[>][<]C(C[>])c1ccccc1[]}",
  }

Source code in src/cript/nodes/primary_nodes/material.py

class Material(PrimaryBaseNode):
    """
    ## Definition
    A [Material node](https://pubs.acs.org/doi/suppl/10.1021/acscentsci.3c00011/suppl_file/oc3c00011_si_001.pdf#page=10)
    is a collection of the identifiers and properties of a chemical, mixture, or substance.

    ## Attributes
    | attribute                 | type                                                                 | example                                           | description                                         | required    | vocab |
    |---------------------------|----------------------------------------------------------------------|---------------------------------------------------|-----------------------------------------------------|-------------|-------|
    | identifier                | list[Identifier]                                                     |                                                   | material identifiers                                | True        |       |
    | component                 | list[[Material](./)]                                                 |                                                   | list of component that make up the mixture          |             |       |
    | property                  | list[[Property](../../subobjects/property)]                          |                                                   | material properties                                 |             |       |
    | process                   | [Process](../process)                                                |                                                   | process node that made this material                |             |       |
    | parent_material           | [Material](./)                                                       |                                                   | material node that this node was copied from        |             |       |
    | computational_forcefield  | [Computation  Forcefield](../../subobjects/computational_forcefield) |                                                   | computation forcefield                              | Conditional |       |
    | keyword                   | list[str]                                                            | [thermoplastic, homopolymer, linear, polyolefins] | words that classify the material                    |             | True  |
    | notes                     | str                                                                  | "my awesome notes"                                | miscellaneous information, or custom data structure |             | True  |

    ## Navigating to Material
    Materials can be easily found on the [CRIPT](https://app.criptapp.org) home screen in the
    under the navigation within the [Materials link](https://app.criptapp.org/material/)

    ## Available Sub-Objects for Material
    * [Identifier](../../subobjects/identifier)
    * [Property](../../subobjects/property)
    * [Computational_forcefield](../../subobjects/computational_forcefield)

    Example
    -------
     water, brine (water + NaCl), polystyrene, polyethylene glycol hydrogels, vulcanized polyisoprene, mcherry (protein), and mica


    Warnings
    -------
    !!! warning "Material names"
        Material names Must be unique within a [Project](../project)

    ```json
      {
         "node":["Material"],
         "name":"my unique material name",
         "uid":"_:9679ff12-f9b4-41f4-be95-080b78fa71fd",
         "uuid":"9679ff12-f9b4-41f4-be95-080b78fa71fd"
         "bigsmiles":"[H]{[>][<]C(C[>])c1ccccc1[]}",
      }
    ```
    """

    @dataclass(frozen=True)
    class JsonAttributes(PrimaryBaseNode.JsonAttributes):
        """
        all Material attributes
        """

        # identifier sub-object for the material
        identifier: List[Dict[str, str]] = field(default_factory=dict)  # type: ignore
        # TODO add proper typing in future, using Any for now to avoid circular import error
        component: List["Material"] = field(default_factory=list)
        process: Optional[Process] = None
        property: List[Any] = field(default_factory=list)
        parent_material: Optional["Material"] = None
        computational_forcefield: Optional[Any] = None
        keyword: List[str] = field(default_factory=list)

    _json_attrs: JsonAttributes = JsonAttributes()

    @beartype
    def __init__(
        self,
        name: str,
        identifier: List[Dict[str, str]],
        component: Optional[List["Material"]] = None,
        process: Optional[Process] = None,
        property: Optional[List[Any]] = None,
        parent_material: Optional["Material"] = None,
        computational_forcefield: Optional[Any] = None,
        keyword: Optional[List[str]] = None,
        notes: str = "",
        **kwargs
    ):
        """
        create a material node

        Examples
        --------
        >>> import cript
        >>> my_material = cript.Material(
        ...     name="my component material 1",
        ...     identifier=[{"amino_acid": "component 1 alternative name"}],
        ... )

        Parameters
        ----------
        name: str
        identifier: List[Dict[str, str]]
        component: List["Material"], default=None
        property: Optional[Process], default=None
        process: List[Process], default=None
        parent_material: "Material", default=None
        computational_forcefield: ComputationalForcefield, default=None
        keyword: List[str], default=None

        Returns
        -------
        None
            Instantiate a material node
        """

        super().__init__(name=name, notes=notes, **kwargs)

        if component is None:
            component = []

        if property is None:
            property = []

        if keyword is None:
            keyword = []

        self._json_attrs = replace(
            self._json_attrs,
            name=name,
            identifier=identifier,
            component=component,
            process=process,
            property=property,
            parent_material=parent_material,
            computational_forcefield=computational_forcefield,
            keyword=keyword,
        )

    @property
    @beartype
    def identifier(self) -> List[Dict[str, str]]:
        """
        get the identifiers for this material

        Examples
        --------
        >>> import cript
        >>> my_material = cript.Material(
        ...     name="my component material 1",
        ...     identifier=[{"smiles": "component 1 smiles"}],
        ... )
        >>> my_material.identifier = [{"smiles": "my material alternative name"}]

        [material identifier key](https://app.criptapp.org/vocab/material_identifier_key)
        must come from CRIPT controlled vocabulary

        Returns
        -------
        List[Dict[str, str]]
            list of dictionary that has identifiers for this material
        """
        return self._json_attrs.identifier.copy()

    @identifier.setter
    @beartype
    def identifier(self, new_identifier_list: List[Dict[str, str]]) -> None:
        """
        set the list of identifiers for this material

        the identifier keys must come from the
        material identifiers keyword within the CRIPT controlled vocabulary

        Parameters
        ----------
        new_identifier_list: List[Dict[str, str]]

        Returns
        -------
        None
        """
        new_attrs = replace(self._json_attrs, identifier=new_identifier_list)
        self._update_json_attrs_if_valid(new_attrs)

    @property
    @beartype
    def component(self) -> List["Material"]:
        """
        list of components ([material nodes](./)) that make up this material

        Examples
        ---------
        >>> import cript
        >>> my_components = [
        ...     cript.Material(
        ...         name="my component material 1",
        ...         identifier=[{"smiles": "my material smiles"}],
        ...     ),
        ...     cript.Material(
        ...         name="my component material 2",
        ...         identifier=[{"vendor": "my material vendor"}],
        ...     ),
        ... ]
        >>> my_mixed_material = cript.Material(
        ...     name="my material",
        ...     component=my_components,
        ...     identifier=[{"bigsmiles": "123456"}]
        ... )

        Returns
        -------
        List[Material]
            list of component that make up this material
        """
        return self._json_attrs.component

    @component.setter
    @beartype
    def component(self, new_component_list: List["Material"]) -> None:
        """
        set the list of component (material nodes) that make up this material

        Parameters
        ----------
        new_component_list: List["Material"]

        Returns
        -------
        None
        """
        new_attrs = replace(self._json_attrs, component=new_component_list)
        self._update_json_attrs_if_valid(new_attrs)

    @property
    @beartype
    def parent_material(self) -> Optional["Material"]:
        """
        List of parent materials

        Returns
        -------
        List["Material"]
            list of parent materials
        """
        return self._json_attrs.parent_material

    @parent_material.setter
    @beartype
    def parent_material(self, new_parent_material: Optional["Material"]) -> None:
        """
        set the [parent materials](./) for this material

        Parameters
        ----------
        new_parent_material: "Material"

        Returns
        -------
        None
        """

        new_attrs = replace(self._json_attrs, parent_material=new_parent_material)
        self._update_json_attrs_if_valid(new_attrs)

    @property
    @beartype
    def computational_forcefield(self) -> Any:
        """
        list of [computational_forcefield](../../subobjects/computational_forcefield) for this material node

        Examples
        --------
        >>> import cript
        >>> my_material = cript.Material(
        ...     name="my component material 1", identifier=[{"smiles": "my smiles"}]
        ... )
        >>> my_computational_forcefield = cript.ComputationalForcefield(
        ...     key="opls_aa",
        ...     building_block="atom",
        ... )
        >>> my_material.computational_forcefield = my_computational_forcefield

        Returns
        -------
        List[ComputationForcefield]
            list of computational_forcefield that created this material
        """
        return self._json_attrs.computational_forcefield

    @computational_forcefield.setter
    @beartype
    def computational_forcefield(self, new_computational_forcefield_list: Any) -> None:
        """
        sets the list of computational forcefields for this material

        Parameters
        ----------
        new_computation_forcefield_list: List[ComputationalForcefield]

        Returns
        -------
        None
        """
        new_attrs = replace(self._json_attrs, computational_forcefield=new_computational_forcefield_list)
        self._update_json_attrs_if_valid(new_attrs)

    @property
    @beartype
    def keyword(self) -> List[str]:
        """
        List of keyword for this material

        the material keyword must come from the
        [CRIPT controlled vocabulary](https://app.criptapp.org/vocab/material_keyword)

        Examples
        --------
        >>> import cript
        >>> my_material = cript.Material(
        ... name="my material", identifier=[{"inchi": "my material inchi"}]
        ... )
        >>> my_material.keyword = ["acetylene", "acrylate", "alternating"]

        Returns
        -------
        List[str]
            list of material keyword
        """
        return self._json_attrs.keyword

    @keyword.setter
    @beartype
    def keyword(self, new_keyword_list: List[str]) -> None:
        """
        set the keyword for this material

        the material keyword must come from the CRIPT controlled vocabulary

        Parameters
        ----------
        new_keyword_list

        Returns
        -------
        None
        """
        new_attrs = replace(self._json_attrs, keyword=new_keyword_list)
        self._update_json_attrs_if_valid(new_attrs)

    @property
    @beartype
    def process(self) -> Optional[Process]:
        return self._json_attrs.process  # type: ignore

    @process.setter
    def process(self, new_process: Process) -> None:
        new_attrs = replace(self._json_attrs, process=new_process)
        self._update_json_attrs_if_valid(new_attrs)

    @property
    def property(self) -> List[Any]:
        """
        list of material [property](../../subobjects/property)

        Examples
        --------
        >>> import cript
        >>> my_material = cript.Material(
        ...     name="my component material 1",
        ...     identifier=[{"smiles": "component 1 smiles"}],
        ... )
        >>> my_property = cript.Property(key="modulus_shear", type="min", value=1.23, unit="gram")
        >>> my_material.property = [my_property]

        Returns
        -------
        List[Property]
            list of property that define this material
        """
        return self._json_attrs.property.copy()

    @property.setter
    @beartype
    def property(self, new_property_list: List[Any]) -> None:
        """
        set the list of properties for this material

        Parameters
        ----------
        new_property_list: List[Property]

        Returns
        -------
        None
        """
        new_attrs = replace(self._json_attrs, property=new_property_list)
        self._update_json_attrs_if_valid(new_attrs)

    @classmethod
    @beartype
    def _from_json(cls, json_dict: Dict):
        """
        Create a new instance of a node from a JSON representation.

        Parameters
        ----------
        json_dict : Dict
            A JSON dictionary representing a node

        Returns
        -------
        node
            A new instance of a node.

        Notes
        -----
        required fields in JSON:
        * `name`: The name of the node

        optional fields in JSON:
        * `identifier`: A list of material identifiers.
            * If the `identifier` property is not present in the JSON dictionary,
            it will be set to an empty list.
        """
        from cript.nodes.util.material_deserialization import (
            _deserialize_flattened_material_identifiers,
        )

        json_dict = _deserialize_flattened_material_identifiers(json_dict)

        return super()._from_json(json_dict)

component: List[Material] property writable

list of components (material nodes) that make up this material

Examples:

>>> import cript
>>> my_components = [
...     cript.Material(
...         name="my component material 1",
...         identifier=[{"smiles": "my material smiles"}],
...     ),
...     cript.Material(
...         name="my component material 2",
...         identifier=[{"vendor": "my material vendor"}],
...     ),
... ]
>>> my_mixed_material = cript.Material(
...     name="my material",
...     component=my_components,
...     identifier=[{"bigsmiles": "123456"}]
... )

Returns:

Type	Description
List[Material]	list of component that make up this material

computational_forcefield: Any property writable

list of computational_forcefield for this material node

Examples:

>>> import cript
>>> my_material = cript.Material(
...     name="my component material 1", identifier=[{"smiles": "my smiles"}]
... )
>>> my_computational_forcefield = cript.ComputationalForcefield(
...     key="opls_aa",
...     building_block="atom",
... )
>>> my_material.computational_forcefield = my_computational_forcefield

Returns:

Type	Description
List[ComputationForcefield]	list of computational_forcefield that created this material

identifier: List[Dict[str, str]] property writable

get the identifiers for this material

Examples:

>>> import cript
>>> my_material = cript.Material(
...     name="my component material 1",
...     identifier=[{"smiles": "component 1 smiles"}],
... )
>>> my_material.identifier = [{"smiles": "my material alternative name"}]

material identifier key must come from CRIPT controlled vocabulary

Returns:

Type	Description
List[Dict[str, str]]	list of dictionary that has identifiers for this material

keyword: List[str] property writable

List of keyword for this material

the material keyword must come from the CRIPT controlled vocabulary

Examples:

>>> import cript
>>> my_material = cript.Material(
... name="my material", identifier=[{"inchi": "my material inchi"}]
... )
>>> my_material.keyword = ["acetylene", "acrylate", "alternating"]

Returns:

Type	Description
List[str]	list of material keyword

parent_material: Optional[Material] property writable

List of parent materials

Returns:

Type	Description
List[Material]	list of parent materials

property: List[Any] property writable

list of material property

Examples:

>>> import cript
>>> my_material = cript.Material(
...     name="my component material 1",
...     identifier=[{"smiles": "component 1 smiles"}],
... )
>>> my_property = cript.Property(key="modulus_shear", type="min", value=1.23, unit="gram")
>>> my_material.property = [my_property]

Returns:

Type	Description
List[Property]	list of property that define this material

JsonAttributes dataclass

Bases: JsonAttributes

all Material attributes

Source code in src/cript/nodes/primary_nodes/material.py

@dataclass(frozen=True)
class JsonAttributes(PrimaryBaseNode.JsonAttributes):
    """
    all Material attributes
    """

    # identifier sub-object for the material
    identifier: List[Dict[str, str]] = field(default_factory=dict)  # type: ignore
    # TODO add proper typing in future, using Any for now to avoid circular import error
    component: List["Material"] = field(default_factory=list)
    process: Optional[Process] = None
    property: List[Any] = field(default_factory=list)
    parent_material: Optional["Material"] = None
    computational_forcefield: Optional[Any] = None
    keyword: List[str] = field(default_factory=list)

__init__(name, identifier, component=None, process=None, property=None, parent_material=None, computational_forcefield=None, keyword=None, notes='', **kwargs)

create a material node

Examples:

>>> import cript
>>> my_material = cript.Material(
...     name="my component material 1",
...     identifier=[{"amino_acid": "component 1 alternative name"}],
... )

Parameters:

Name	Type	Description	Default
name	str		required
identifier	List[Dict[str, str]]		required
component	Optional[List[Material]]		None
property	Optional[List[Any]]		None
process	Optional[Process]		None
parent_material	Optional[Material]		None
computational_forcefield	Optional[Any]		None
keyword	Optional[List[str]]		None

Returns:

Type	Description
None	Instantiate a material node

Source code in src/cript/nodes/primary_nodes/material.py

@beartype
def __init__(
    self,
    name: str,
    identifier: List[Dict[str, str]],
    component: Optional[List["Material"]] = None,
    process: Optional[Process] = None,
    property: Optional[List[Any]] = None,
    parent_material: Optional["Material"] = None,
    computational_forcefield: Optional[Any] = None,
    keyword: Optional[List[str]] = None,
    notes: str = "",
    **kwargs
):
    """
    create a material node

    Examples
    --------
    >>> import cript
    >>> my_material = cript.Material(
    ...     name="my component material 1",
    ...     identifier=[{"amino_acid": "component 1 alternative name"}],
    ... )

    Parameters
    ----------
    name: str
    identifier: List[Dict[str, str]]
    component: List["Material"], default=None
    property: Optional[Process], default=None
    process: List[Process], default=None
    parent_material: "Material", default=None
    computational_forcefield: ComputationalForcefield, default=None
    keyword: List[str], default=None

    Returns
    -------
    None
        Instantiate a material node
    """

    super().__init__(name=name, notes=notes, **kwargs)

    if component is None:
        component = []

    if property is None:
        property = []

    if keyword is None:
        keyword = []

    self._json_attrs = replace(
        self._json_attrs,
        name=name,
        identifier=identifier,
        component=component,
        process=process,
        property=property,
        parent_material=parent_material,
        computational_forcefield=computational_forcefield,
        keyword=keyword,
    )