graphmix

class graphmix.ChemicalRegistry(uow: ChemicalUnitOfWork | None = None, path: str | None = None)

A registry for storing and retrieving chemical information. Uses a local database to store chemicals, and queries PubChem if a chemical is not found.

Chemical(name: str) → Chemical

__init__(uow: ChemicalUnitOfWork | None = None, path: str | None = None)

add_chemical(chemical: Chemical)

Add a chemical to the local database.

get_chemical(name: str) → Chemical

Get a chemical by name. If the chemical is not found in the local database, query PubChem for the chemical information.

property path: Path

pubchem: PubChemService

uow: ChemicalUnitOfWork

class graphmix.Solution(*, name: str, G: DiGraph = None, components: dict[str, Chemical | Solution] = {})

G: DiGraph

add_entity(entity: Chemical | Solution)

property chemicals: Generator[tuple[str, Chemical], None, None]

components: dict[str, Chemical | Solution]

property composition: Composition

dilute_with(solvent: Chemical | Solution, ratio: float, name: str | None = None) → Solution

in_edges(node: str) → Generator[tuple[str, str, Quantity | float], None, None]

model_computed_fields: ClassVar[dict[str, ComputedFieldInfo]] = {}

A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

model_config: ClassVar[ConfigDict] = {}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

model_fields: ClassVar[dict[str, FieldInfo]] = {'G': FieldInfo(annotation=DiGraph, required=False, default_factory=Annotated[DiGraph, _DiGraphPydanticAnnotation], metadata=[<class 'graphmix.graph.model._DiGraphPydanticAnnotation'>]), 'components': FieldInfo(annotation=dict[str, Union[Chemical, Solution]], required=False, default={}), 'name': FieldInfo(annotation=str, required=True)}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo].

This replaces Model.__fields__ from Pydantic V1.

name: str

with_component(component: Chemical | Solution, concentration: Quantity)

with_components(components: dict[Chemical | Solution, Quantity])

graphmix.plot_graph(G: ~networkx.classes.digraph.DiGraph, node_color: str = '#0d9488', font_color: str = '#ccfbf1', font_size: int = 8, node_size: int = 500, edge_colors: str = '#042f2e', edge_attr: str = 'concentration', line_width: float = 1.1, alpha: float = 0.8, ax: ~matplotlib.axes._axes.Axes = None, layout: ~collections.abc.Callable[[~networkx.classes.digraph.DiGraph], dict] = <function kamada_kawai_layout>) → Axes