Models¶
Core data model classes for representing VCell biomodels.
Biomodel¶
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Model¶
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Species¶
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Compartment¶
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Reaction¶
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Kinetics¶
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KineticsParameter¶
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ModelParameter¶
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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
|
to_cartesian_mesh(mesh_size: tuple[int, int, int] | None = None, resolution: int = 50) -> CartesianMesh
¶
Generate the VCell finite-volume :class:CartesianMesh for this geometry.
Convenience wrapper around :func:pyvcell.vcml.cartesian_mesh_from_geometry;
requires the native and solver extras (libvcell + pyvcell-fvsolver).
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SubVolume¶
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SubVolumeType¶
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SurfaceClass¶
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Image¶
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Application¶
Bases: VcmlNode
get_species_mapping(species_name: str) -> SpeciesMapping
¶
Get a species mapping by name.
set_moving_boundary_front(velocity_x: float | str = 0.0, velocity_y: float | str = 0.0, velocity_z: float | str = 0.0, surface_name: str | None = None) -> FrontVelocity
¶
Declare the prescribed velocity of the moving-boundary front.
The front is the geometry surface that separates the two subvolumes of a
moving-boundary model. The velocity components are VCell expressions in
space (x, y, z), time (t), and the volume species. When
surface_name is omitted, the geometry's single surface class is used.
add_moving_boundary_sim(name: str, duration: float, output_time_step: float, mesh_size: tuple[int, int, int], options: MovingBoundarySolverOptions | None = None) -> Simulation
¶
Add a simulation configured for the Moving Boundary solver.
Equivalent to :meth:add_sim but sets the solver to MovingB and
attaches :class:MovingBoundarySolverOptions (defaults when options
is None). The application must also declare a moving front via
:meth:set_moving_boundary_front.
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Simulation¶
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SpeciesMapping¶
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BoundaryType¶
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SpeciesReference¶
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SpeciesRefType¶
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