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
map_species(species: Species | str, init_conc: float | str, diff_coef: float, *, force_continuous: bool = False, init_count: float | str | None = None) -> SpeciesMapping
¶
Map a species into this application.
In a stochastic (Application.stochastic) spatial application, species become Smoldyn particles
unless force_continuous is set, which keeps them as PDE fields (a PDE/particle hybrid model).
init_count sets a particle species' initial molecule count instead of init_conc.
get_species_mapping(species_name: str) -> SpeciesMapping
¶
Get a species mapping by name.
add_event(name: str, trigger: str, assignments: dict[str, str | float], delay: str | float | None = None, use_values_from_trigger_time: bool = True) -> Event
¶
Add an event that fires on each rising edge of trigger (a condition such as "S1 < 5.0") and,
after delay if given, sets each variable in assignments to its expression.
add_ode_sim(name: str, duration: float, output_time_step: float, solver: str = COMBINED_SUNDIALS_SOLVER, absolute_tolerance: float = 1e-09, relative_tolerance: float = 1e-07, max_time_step: float = 0.1) -> Simulation
¶
Add a non-spatial simulation for one of VCell's Sundials ODE solvers (CVODE, IDA, or the default
Combined IDA/CVODE, which picks IDA when the math has fast systems), saving every output_time_step.
Run it with :func:pyvcell.vcml.simulate_ode. The application must be non-spatial (geometry dimension 0).
add_hybrid_sim(name: str, duration: float, output_time_step: float, mesh_size: tuple[int, int, int], time_step: float, options: SmoldynSimulationOptions | None = None) -> Simulation
¶
Add a simulation for VCell's spatial PDE/particle hybrid solver (finite volume + Smoldyn).
The application must be stochastic with at least one force_continuous species (the fields)
and at least one particle species. output_time_step should be a multiple of time_step.
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¶
Bases: VcmlNode
A simulation of an application. Output is saved in exactly one of three ways: every output_time_step
(VCML OutputTimeStep), every keep_every solver steps keeping at most keep_at_most points (VCell's
default for its ODE solvers), or at the listed output_times. mesh_size is None for a non-spatial
(compartmental) simulation.
is_ode: bool
property
¶
A non-spatial simulation on one of VCell's Sundials ODE solvers (see :func:pyvcell.vcml.simulate_ode).
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SpeciesMapping¶
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BoundaryType¶
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SpeciesReference¶
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SpeciesRefType¶
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