Models

Core data model classes for representing VCell biomodels.

Biomodel

Bases: VcmlNode

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Model

Bases: VcmlNode

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Species

Bases: VcmlNode

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Compartment

Bases: VcmlNode

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Reaction

Bases: VcmlNode

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Kinetics

Bases: VcmlNode

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KineticsParameter

Bases: Parameter

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ModelParameter

Bases: Parameter

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Geometry

Bases: VcmlNode

to_segmented_image(resolution: int = 50) -> SegmentedImageGeometry

Build a :class:SegmentedImageGeometry from this geometry.

Parameters:

Name	Type	Description	Default
resolution	int	Number of grid points along each axis (analytic geometries only).	50

plot(resolution: int = 50, save_path: str | None = None) -> None

Render the geometry using PyVista.

Parameters:

Name	Type	Description	Default
resolution	int	Number of grid points along each axis.	50
save_path	str | None	If provided, save the figure to this path before showing.	None

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SubVolume

Bases: GeometryClass

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SubVolumeType

Bases: StrEnum

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SurfaceClass

Bases: GeometryClass

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Image

Bases: VcmlNode

ndarray_3d_u8: NDArray3Du8 property

Decompress and return the image as a (Z, Y, X) uint8 array.

from_ndarray_3d_u8(ndarray_3d_u8: NDArray3Du8, name: str) -> Image staticmethod

Create an Image from a (Z, Y, X) uint8 numpy array.

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Application

Bases: VcmlNode

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Simulation

Bases: VcmlNode

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SpeciesMapping

Bases: VcmlNode

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BoundaryType

Bases: StrEnum

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SpeciesReference

Bases: VcmlNode

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SpeciesRefType

Bases: StrEnum

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