Computational Forcefield

ComputationalForcefield

Bases: UUIDBaseNode

Definition

A Computational Forcefield Subobject is a mathematical model that describes the forces between atoms and molecules. It is used in computational chemistry and molecular dynamics simulations to predict the behavior of materials. Forcefields are typically based on experimental data or quantum mechanical calculations, and they are often used to study the properties of materials such as their structure, dynamics, and reactivity.

Attributes

attribute	type	example	description	required	vocab
key	str	CHARMM27	type of forcefield	True	True
building_block	str	atom	type of building block	True	True
coarse_grained_mapping	str	SC3 beads in MARTINI forcefield	atom to beads mapping
implicit_solvent	str	water	Name of implicit solvent
source	str	package in GROMACS	source of forcefield
description	str	OPLS forcefield with partial charges calculated via the LBCC algorithm	description of the forcefield and any modifications that have been added
data	Data		details of mapping schema and forcefield parameters
citation	list[Citation]		reference to a book, paper, or scholarly work

Can be Added To Primary Node:

• Material node

JSON Representation

{
    "node": ["ComputationalForcefield"],
    "key": "opls_aa",
    "building_block": "atom",
    "coarse_grained_mapping": "atom -> atom",
    "implicit_solvent": "no implicit solvent",
    "source": "local LigParGen installation",
    "description": "this is a test forcefield",
    "data": {
        "node":["Data"],
        "name":"my data name",
        "type":"afm_amp",
        "file":[
            {
                "node":["File"],
                "type":"calibration",
                "source":"https://criptapp.org",
                "extension":".csv",
                "data_dictionary":"my file's data dictionary"
            }
        ]
    },
    "citation": {
        "node": ["Citation"],
        "type": "reference"
        "reference": {
            "node": ["Reference"],
            "type": "journal_article",
            "title": "Multi-architecture Monte-Carlo (MC) simulation of soft coarse-grained polymeric materials: SOft coarse grained Monte-Carlo Acceleration (SOMA)",
            "author": ["Ludwig Schneider", "Marcus Müller"],
            "journal": "Computer Physics Communications",
            "publisher": "Elsevier",
            "year": 2019,
            "pages": [463, 476],
            "doi": "10.1016/j.cpc.2018.08.011",
            "issn": "0010-4655",
            "website": "https://www.sciencedirect.com/science/article/pii/S0010465518303072",
        }
}

Source code in src/cript/nodes/subobjects/computational_forcefield.py

class ComputationalForcefield(UUIDBaseNode):
    """
    ## Definition
    A [Computational Forcefield Subobject](https://pubs.acs.org/doi/suppl/10.1021/acscentsci.3c00011/suppl_file/oc3c00011_si_001.pdf#page=23)
    is a mathematical model that describes the forces between atoms and molecules.
    It is used in computational chemistry and molecular dynamics simulations to predict the behavior of materials.
    Forcefields are typically based on experimental data or quantum mechanical calculations,
    and they are often used to study the properties of materials such as their structure, dynamics, and reactivity.

    ## Attributes
    | attribute              | type           | example                                                                | description                                                              | required | vocab |
    |------------------------|----------------|------------------------------------------------------------------------|--------------------------------------------------------------------------|----------|-------|
    | key                    | str            | CHARMM27                                                               | type of forcefield                                                       | True     | True  |
    | building_block         | str            | atom                                                                   | type of building block                                                   | True     | True  |
    | coarse_grained_mapping | str            | SC3 beads in MARTINI forcefield                                        | atom to beads mapping                                                    |          |       |
    | implicit_solvent       | str            | water                                                                  | Name of implicit solvent                                                 |          |       |
    | source                 | str            | package in GROMACS                                                     | source of forcefield                                                     |          |       |
    | description            | str            | OPLS forcefield with partial charges calculated via the LBCC algorithm | description of the forcefield and any modifications that have been added |          |       |
    | data                   | Data           |                                                                        | details of mapping schema and forcefield parameters                      |          |       |
    | citation               | list[Citation] |                                                                        | reference to a book, paper, or scholarly work                            |          |       |


    ## Can be Added To Primary Node:
    * Material node

    ## JSON Representation
    ```json
    {
        "node": ["ComputationalForcefield"],
        "key": "opls_aa",
        "building_block": "atom",
        "coarse_grained_mapping": "atom -> atom",
        "implicit_solvent": "no implicit solvent",
        "source": "local LigParGen installation",
        "description": "this is a test forcefield",
        "data": {
            "node":["Data"],
            "name":"my data name",
            "type":"afm_amp",
            "file":[
                {
                    "node":["File"],
                    "type":"calibration",
                    "source":"https://criptapp.org",
                    "extension":".csv",
                    "data_dictionary":"my file's data dictionary"
                }
            ]
        },
        "citation": {
            "node": ["Citation"],
            "type": "reference"
            "reference": {
                "node": ["Reference"],
                "type": "journal_article",
                "title": "Multi-architecture Monte-Carlo (MC) simulation of soft coarse-grained polymeric materials: SOft coarse grained Monte-Carlo Acceleration (SOMA)",
                "author": ["Ludwig Schneider", "Marcus Müller"],
                "journal": "Computer Physics Communications",
                "publisher": "Elsevier",
                "year": 2019,
                "pages": [463, 476],
                "doi": "10.1016/j.cpc.2018.08.011",
                "issn": "0010-4655",
                "website": "https://www.sciencedirect.com/science/article/pii/S0010465518303072",
            }
    }


    ```

    """

    @dataclass(frozen=True)
    class JsonAttributes(UUIDBaseNode.JsonAttributes):
        key: str = ""
        building_block: str = ""
        coarse_grained_mapping: str = ""
        implicit_solvent: str = ""
        source: str = ""
        description: str = ""
        data: List[Union[Data, UIDProxy]] = field(default_factory=list)
        citation: List[Union[Citation, UIDProxy]] = field(default_factory=list)

    _json_attrs: JsonAttributes = JsonAttributes()

    @beartype
    def __init__(
        self,
        key: str,
        building_block: str,
        coarse_grained_mapping: str = "",
        implicit_solvent: str = "",
        source: str = "",
        description: str = "",
        data: Optional[List[Union[Data, UIDProxy]]] = None,
        citation: Optional[List[Union[Citation, UIDProxy]]] = None,
        **kwargs
    ):
        """
        instantiate a computational_forcefield subobject

        Parameters
        ----------
        key : str
            type of forcefield key must come from
            [CRIPT Controlled Vocabulary](https://app.criptapp.org/vocab/computational_forcefield_key)
        building_block : str
            type of computational_forcefield building_block must come from
            [CRIPT Controlled Vocabulary](https://app.criptapp.org/vocab/building_block)
        coarse_grained_mapping : str, optional
            atom to beads mapping, by default ""
        implicit_solvent : str, optional
            Name of implicit solvent, by default ""
        source : str, optional
            source of forcefield, by default ""
        description : str, optional
            description of the forcefield and any modifications that have been added, by default ""
        data : List[Data], optional
            details of mapping schema and forcefield parameters, by default None
        citation : Union[List[Citation], None], optional
            reference to a book, paper, or scholarly work, by default None


        Examples
        --------
        >>> import cript
        >>> my_computational_forcefield = cript.ComputationalForcefield(
        ...     key="opls_aa",
        ...     building_block="atom",
        ... )

        Returns
        -------
        None
            Instantiate a computational_forcefield subobject
        """
        if citation is None:
            citation = []
        super().__init__(**kwargs)

        if data is None:
            data = []

        new_json_attrs = replace(
            self._json_attrs,
            key=key,
            building_block=building_block,
            coarse_grained_mapping=coarse_grained_mapping,
            implicit_solvent=implicit_solvent,
            source=source,
            description=description,
            data=data,
            citation=citation,
        )
        self._update_json_attrs_if_valid(new_json_attrs)

    @property
    @beartype
    def key(self) -> str:
        """
        type of forcefield

        Computational_Forcefield key must come from
        [CRIPT Controlled Vocabulary](https://app.criptapp.org/vocab/computational_forcefield_key)

        Examples
        --------
        >>> import cript
        >>> my_computational_forcefield = cript.ComputationalForcefield(
        ...     key="opls_aa",
        ...     building_block="atom",
        ... )
        >>> my_computational_forcefield.key = "amber"

        Returns
        -------
        str
            type of forcefield
        """
        return self._json_attrs.key

    @key.setter
    @beartype
    def key(self, new_key: str) -> None:
        """
        set key for this computational_forcefield

        Parameters
        ----------
        new_key : str
            computational_forcefield key

        Returns
        -------
        None
        """
        new_attrs = replace(self._json_attrs, key=new_key)
        self._update_json_attrs_if_valid(new_attrs)

    @property
    @beartype
    def building_block(self) -> str:
        """
        type of building block

        Computational_Forcefield building_block must come from
        [CRIPT Controlled Vocabulary](https://app.criptapp.org/vocab/building_block)

        Examples
        --------
        >>> import cript
        >>> my_computational_forcefield = cript.ComputationalForcefield(
        ...     key="opls_aa",
        ...     building_block="atom",
        ... )
        >>> my_computational_forcefield.building_block = "non_atomistic"

        Returns
        -------
        str
            type of building block
        """
        return self._json_attrs.building_block

    @building_block.setter
    @beartype
    def building_block(self, new_building_block: str) -> None:
        """
        type of building block

        Parameters
        ----------
        new_building_block : str
            new type of building block

        Returns
        -------
        None
        """
        new_attrs = replace(self._json_attrs, building_block=new_building_block)
        self._update_json_attrs_if_valid(new_attrs)

    @property
    @beartype
    def coarse_grained_mapping(self) -> str:
        """
        atom to beads mapping

        Examples
        --------
        >>> import cript
        >>> my_computational_forcefield = cript.ComputationalForcefield(
        ...     key="opls_aa",
        ...     building_block="atom",
        ... )
        >>> my_computational_forcefield.coarse_grained_mapping = "SC3 beads in MARTINI forcefield"

        Returns
        -------
        str
            coarse_grained_mapping
        """
        return self._json_attrs.coarse_grained_mapping

    @coarse_grained_mapping.setter
    @beartype
    def coarse_grained_mapping(self, new_coarse_grained_mapping: str) -> None:
        """
        atom to beads mapping

        Parameters
        ----------
        new_coarse_grained_mapping : str
            new coarse_grained_mapping

        Returns
        -------
        None
        """
        new_attrs = replace(self._json_attrs, coarse_grained_mapping=new_coarse_grained_mapping)
        self._update_json_attrs_if_valid(new_attrs)

    @property
    @beartype
    def implicit_solvent(self) -> str:
        """
        Name of implicit solvent

        Examples
        --------
        >>> import cript
        >>> my_computational_forcefield = cript.ComputationalForcefield(
        ...     key="opls_aa",
        ...     building_block="atom",
        ... )
        >>> my_computational_forcefield.implicit_solvent = "water"

        Returns
        -------
        str
            _description_
        """
        return self._json_attrs.implicit_solvent

    @implicit_solvent.setter
    @beartype
    def implicit_solvent(self, new_implicit_solvent: str) -> None:
        """
        set the implicit_solvent

        Parameters
        ----------
        new_implicit_solvent : str
            new implicit_solvent
        """
        new_attrs = replace(self._json_attrs, implicit_solvent=new_implicit_solvent)
        self._update_json_attrs_if_valid(new_attrs)

    @property
    @beartype
    def source(self) -> str:
        """
        source of forcefield

        Examples
        --------
        >>> import cript
        >>> my_computational_forcefield = cript.ComputationalForcefield(
        ...     key="opls_aa",
        ...     building_block="atom",
        ... )
        >>> my_computational_forcefield.source = "package in GROMACS"

        Returns
        -------
        str
            source of forcefield
        """
        return self._json_attrs.source

    @source.setter
    @beartype
    def source(self, new_source: str) -> None:
        """
        set the computational_forcefield

        Parameters
        ----------
        new_source : str
            new source of forcefield
        """
        new_attrs = replace(self._json_attrs, source=new_source)
        self._update_json_attrs_if_valid(new_attrs)

    @property
    @beartype
    def description(self) -> str:
        """
        description of the forcefield and any modifications that have been added

        Examples
        --------
        >>> import cript
        >>> my_computational_forcefield = cript.ComputationalForcefield(
        ...     key="opls_aa",
        ...     building_block="atom",
        ... )
        >>> my_computational_forcefield.description = "OPLS forcefield with partial charges calculated via the LBCC algorithm"

        Returns
        -------
        str
            description of the forcefield and any modifications that have been added
        """
        return self._json_attrs.description

    @description.setter
    @beartype
    def description(self, new_description: str) -> None:
        """
        set this computational_forcefields description

        Parameters
        ----------
        new_description : str
            new computational_forcefields description

        Returns
        -------
        None
        """
        new_attrs = replace(self._json_attrs, description=new_description)
        self._update_json_attrs_if_valid(new_attrs)

    @property
    @beartype
    def data(self) -> List[Union[Data, UIDProxy]]:
        """
        details of mapping schema and forcefield parameters

        Examples
        --------
        >>> import cript
        >>> my_computational_forcefield = cript.ComputationalForcefield(
        ...     key="opls_aa",
        ...     building_block="atom",
        ... )
        >>> my_file = cript.File(
        ...     name="my file node name",
        ...     source="https://pubs.acs.org/doi/suppl/10.1021/acscentsci.3c00011/suppl_file/oc3c00011_si_001.pdf",
        ...     type="calibration",
        ...     extension=".pdf",
        ... )
        >>> my_data = cript.Data(
        ...     name="my data node name",
        ...     type="afm_amp",
        ...     file=[my_file],
        ... )
        >>> my_computational_forcefield.data = [my_data]

        Returns
        -------
        List[Data]
            list of data nodes for this computational_forcefield subobject
        """
        return self._json_attrs.data.copy()

    @data.setter
    @beartype
    def data(self, new_data: List[Union[Data, UIDProxy]]) -> None:
        """
        set the data attribute of this computational_forcefield node

        Parameters
        ----------
        new_data : List[Data]
            new list of data nodes

        Returns
        -------
        None
        """
        new_attrs = replace(self._json_attrs, data=new_data)
        self._update_json_attrs_if_valid(new_attrs)

    @property
    @beartype
    def citation(self) -> List[Union[Citation, UIDProxy]]:
        """
        reference to a book, paper, or scholarly work

        Examples
        --------
        >>> import cript
        >>> my_computational_forcefield = cript.ComputationalForcefield(
        ...     key="opls_aa",
        ...     building_block="atom",
        ... )
        >>> title = (
        ...     "Multi-architecture Monte-Carlo (MC) simulation of soft coarse-grained polymeric materials: "
        ...     "SOft coarse grained Monte-Carlo Acceleration (SOMA)"
        ... )
        >>> my_reference = cript.Reference(
        ...     "journal_article",
        ...     title=title,
        ...     author=["Ludwig Schneider", "Marcus Müller"],
        ...     journal="Computer Physics Communications",
        ...     publisher="Elsevier",
        ...     year=2019,
        ...     pages=[463, 476],
        ...     doi="10.1016/j.cpc.2018.08.011",
        ...     issn="0010-4655",
        ...     website="https://www.sciencedirect.com/science/article/pii/S0010465518303072",
        ... )
        >>> my_citation = cript.Citation(type="reference", reference=my_reference)
        >>> my_computational_forcefield.citation = [my_citation]

        Returns
        -------
        List[Citation]
            computational_forcefield list of citations
        """
        return self._json_attrs.citation.copy()

    @citation.setter
    @beartype
    def citation(self, new_citation: List[Union[Citation, UIDProxy]]) -> None:
        """
        set the citation subobject of the computational_forcefield subobject

        Parameters
        ----------
        new_citation : List[Citation]
            new citation subobject
        """
        new_attrs = replace(self._json_attrs, citation=new_citation)
        self._update_json_attrs_if_valid(new_attrs)

__init__(key, building_block, coarse_grained_mapping='', implicit_solvent='', source='', description='', data=None, citation=None, **kwargs)

instantiate a computational_forcefield subobject

Parameters:

Name	Type	Description	Default
key	str	type of forcefield key must come from CRIPT Controlled Vocabulary	required
building_block	str	type of computational_forcefield building_block must come from CRIPT Controlled Vocabulary	required
coarse_grained_mapping	str	atom to beads mapping, by default ""	''
implicit_solvent	str	Name of implicit solvent, by default ""	''
source	str	source of forcefield, by default ""	''
description	str	description of the forcefield and any modifications that have been added, by default ""	''
data	List[Data]	details of mapping schema and forcefield parameters, by default None	None
citation	Union[List[Citation], None]	reference to a book, paper, or scholarly work, by default None	None

Examples:

>>> import cript
>>> my_computational_forcefield = cript.ComputationalForcefield(
...     key="opls_aa",
...     building_block="atom",
... )

Returns:

Type	Description
None	Instantiate a computational_forcefield subobject

Source code in src/cript/nodes/subobjects/computational_forcefield.py

@beartype
def __init__(
    self,
    key: str,
    building_block: str,
    coarse_grained_mapping: str = "",
    implicit_solvent: str = "",
    source: str = "",
    description: str = "",
    data: Optional[List[Union[Data, UIDProxy]]] = None,
    citation: Optional[List[Union[Citation, UIDProxy]]] = None,
    **kwargs
):
    """
    instantiate a computational_forcefield subobject

    Parameters
    ----------
    key : str
        type of forcefield key must come from
        [CRIPT Controlled Vocabulary](https://app.criptapp.org/vocab/computational_forcefield_key)
    building_block : str
        type of computational_forcefield building_block must come from
        [CRIPT Controlled Vocabulary](https://app.criptapp.org/vocab/building_block)
    coarse_grained_mapping : str, optional
        atom to beads mapping, by default ""
    implicit_solvent : str, optional
        Name of implicit solvent, by default ""
    source : str, optional
        source of forcefield, by default ""
    description : str, optional
        description of the forcefield and any modifications that have been added, by default ""
    data : List[Data], optional
        details of mapping schema and forcefield parameters, by default None
    citation : Union[List[Citation], None], optional
        reference to a book, paper, or scholarly work, by default None


    Examples
    --------
    >>> import cript
    >>> my_computational_forcefield = cript.ComputationalForcefield(
    ...     key="opls_aa",
    ...     building_block="atom",
    ... )

    Returns
    -------
    None
        Instantiate a computational_forcefield subobject
    """
    if citation is None:
        citation = []
    super().__init__(**kwargs)

    if data is None:
        data = []

    new_json_attrs = replace(
        self._json_attrs,
        key=key,
        building_block=building_block,
        coarse_grained_mapping=coarse_grained_mapping,
        implicit_solvent=implicit_solvent,
        source=source,
        description=description,
        data=data,
        citation=citation,
    )
    self._update_json_attrs_if_valid(new_json_attrs)

building_block(new_building_block)

type of building block

Parameters:

Name	Type	Description	Default
new_building_block	str	new type of building block	required

Returns:

Type	Description
None

Source code in src/cript/nodes/subobjects/computational_forcefield.py

@building_block.setter
@beartype
def building_block(self, new_building_block: str) -> None:
    """
    type of building block

    Parameters
    ----------
    new_building_block : str
        new type of building block

    Returns
    -------
    None
    """
    new_attrs = replace(self._json_attrs, building_block=new_building_block)
    self._update_json_attrs_if_valid(new_attrs)

citation(new_citation)

set the citation subobject of the computational_forcefield subobject

Parameters:

Name	Type	Description	Default
new_citation	List[Citation]	new citation subobject	required

Source code in src/cript/nodes/subobjects/computational_forcefield.py

@citation.setter
@beartype
def citation(self, new_citation: List[Union[Citation, UIDProxy]]) -> None:
    """
    set the citation subobject of the computational_forcefield subobject

    Parameters
    ----------
    new_citation : List[Citation]
        new citation subobject
    """
    new_attrs = replace(self._json_attrs, citation=new_citation)
    self._update_json_attrs_if_valid(new_attrs)

coarse_grained_mapping(new_coarse_grained_mapping)

atom to beads mapping

Parameters:

Name	Type	Description	Default
new_coarse_grained_mapping	str	new coarse_grained_mapping	required

Returns:

Type	Description
None

Source code in src/cript/nodes/subobjects/computational_forcefield.py

@coarse_grained_mapping.setter
@beartype
def coarse_grained_mapping(self, new_coarse_grained_mapping: str) -> None:
    """
    atom to beads mapping

    Parameters
    ----------
    new_coarse_grained_mapping : str
        new coarse_grained_mapping

    Returns
    -------
    None
    """
    new_attrs = replace(self._json_attrs, coarse_grained_mapping=new_coarse_grained_mapping)
    self._update_json_attrs_if_valid(new_attrs)

data(new_data)

set the data attribute of this computational_forcefield node

Parameters:

Name	Type	Description	Default
new_data	List[Data]	new list of data nodes	required

Returns:

Type	Description
None

Source code in src/cript/nodes/subobjects/computational_forcefield.py

@data.setter
@beartype
def data(self, new_data: List[Union[Data, UIDProxy]]) -> None:
    """
    set the data attribute of this computational_forcefield node

    Parameters
    ----------
    new_data : List[Data]
        new list of data nodes

    Returns
    -------
    None
    """
    new_attrs = replace(self._json_attrs, data=new_data)
    self._update_json_attrs_if_valid(new_attrs)

description(new_description)

set this computational_forcefields description

Parameters:

Name	Type	Description	Default
new_description	str	new computational_forcefields description	required

Returns:

Type	Description
None

Source code in src/cript/nodes/subobjects/computational_forcefield.py

@description.setter
@beartype
def description(self, new_description: str) -> None:
    """
    set this computational_forcefields description

    Parameters
    ----------
    new_description : str
        new computational_forcefields description

    Returns
    -------
    None
    """
    new_attrs = replace(self._json_attrs, description=new_description)
    self._update_json_attrs_if_valid(new_attrs)

implicit_solvent(new_implicit_solvent)

set the implicit_solvent

Parameters:

Name	Type	Description	Default
new_implicit_solvent	str	new implicit_solvent	required

Source code in src/cript/nodes/subobjects/computational_forcefield.py

@implicit_solvent.setter
@beartype
def implicit_solvent(self, new_implicit_solvent: str) -> None:
    """
    set the implicit_solvent

    Parameters
    ----------
    new_implicit_solvent : str
        new implicit_solvent
    """
    new_attrs = replace(self._json_attrs, implicit_solvent=new_implicit_solvent)
    self._update_json_attrs_if_valid(new_attrs)

key(new_key)

set key for this computational_forcefield

Parameters:

Name	Type	Description	Default
new_key	str	computational_forcefield key	required

Returns:

Type	Description
None

Source code in src/cript/nodes/subobjects/computational_forcefield.py

@key.setter
@beartype
def key(self, new_key: str) -> None:
    """
    set key for this computational_forcefield

    Parameters
    ----------
    new_key : str
        computational_forcefield key

    Returns
    -------
    None
    """
    new_attrs = replace(self._json_attrs, key=new_key)
    self._update_json_attrs_if_valid(new_attrs)

source(new_source)

set the computational_forcefield

Parameters:

Name	Type	Description	Default
new_source	str	new source of forcefield	required

Source code in src/cript/nodes/subobjects/computational_forcefield.py

@source.setter
@beartype
def source(self, new_source: str) -> None:
    """
    set the computational_forcefield

    Parameters
    ----------
    new_source : str
        new source of forcefield
    """
    new_attrs = replace(self._json_attrs, source=new_source)
    self._update_json_attrs_if_valid(new_attrs)