Instantiation¶

InitialSurfaceRelease¶

Defines molecules to be released onto a SurfaceRegion right when simulation starts

Attributes:¶

complex: Complex¶

Defines the species of the molecule that will be released.

number_to_release: int¶

Number of molecules to be released onto a region,

only one of number_to_release and density can be set.

- default argument value in constructor: None

density: float¶

Density of molecules to be released onto a region,

only one of number_to_release and density can be set.

- default argument value in constructor: None

Instantiation¶

Container used to hold instantiation-related model data. Instantiation is usually specific for each model, defines the geometry and initial setup of molecule releases.

Example: pymcell4/1250_organelle_move

Attributes:¶

release_sites: List[ReleaseSite]¶

List of release sites to be included in the model.

- default argument value in constructor: None

geometry_objects: List[GeometryObject]¶

List of geometry objects to be included in the model.

- default argument value in constructor: None

checkpointed_molecules: List[BaseChkptMol]¶

Used when resuming simulation from a checkpoint.

- default argument value in constructor: None

Methods:¶

add_release_site (s: ReleaseSite)¶

Adds a reference to the release site s to the list of release sites.

s: ReleaseSite

find_release_site (name: str) -> ReleaseSite¶

Finds a release site by its name, returns None if no such release site is present.

name: str

add_geometry_object (o: GeometryObject)¶

Adds a reference to the geometry object o to the list of geometry objects.

o: GeometryObject

find_geometry_object (name: str) -> GeometryObject¶

Finds a geometry object by its name, returns None if no such geometry object is present.

name: str

find_volume_compartment_object (name: str) -> GeometryObject¶

Finds a geometry object by its name, the geometry object must be a BNGL compartment.

Returns None if no such geometry object is present.

name: str

find_surface_compartment_object (name: str) -> GeometryObject¶

Finds a geometry object that is a BNGL compartment and its surface name is name.

Returns None if no such geometry object is present.

name: str

load_bngl_compartments_and_seed_species (file_name: str, default_release_region: Region=None, parameter_overrides: Dict[str, float]=None)¶

First loads section compartments and for each 3D compartment that does not

already exist as a geometry object in this Instantiation object, creates a

box with compartment’s volume and also sets its 2D (membrane) compartment name.

When multiple identical geometry objects are added to the final Model object,

only one copy is left so one can merge multiple Instantiation objects that created

compartments assuming that their volume is the same.

Then loads section seed species from a BNGL file and creates release sites according to it.

All elementary molecule types used in the seed species section must be already defined in subsystem.

If an item in the BNGL seed species section does not have its compartment set,

the argument default_region must be set and the molecules are then released into or onto the

default_region.

file_name: str

Path to the BNGL file.
default_release_region: Region = None

Used as region for releases for seed species that have no compartments specified.
parameter_overrides: Dict[str, float] = None

For each key k in the parameter_overrides, if it is defined in the BNGL’s parameters section,

its value is ignored and instead value parameter_overrides[k] is used.

Example: 2100_gradual_bngl_load/model.py

MoleculeReleaseInfo¶

Defines a pair (molecule, location). Used in ReleaseSite when its shape is Shape.LIST.

Attributes:¶

complex: Complex¶

Complex instance defining the molecule that will be released.

Orientation of the complex instance is used to define orientation of the released molecule,

when Orientation.DEFAULT is set, volume molecules are released with Orientation.NONE and

surface molecules are released with Orientation.UP.

Compartment must not be set because this specific release definition states the location.

location: List[float]¶

3D position where the molecule will be released.

If a molecule has a 2D diffusion constant, it will be

placed on the surface closest to the coordinate given.

Argument must have exactly three floating point values [x, y, z].

ReleasePattern¶

Defines a release pattern that specifies repeating molecule releases. Can be used by a ReleaseSite.

Attributes:¶

name: str¶

Name of the release pattern.

- default argument value in constructor: None

release_interval: float¶

During a train of releases, release molecules after every t seconds.

Default is to release only once.

- default argument value in constructor: TIME_INFINITY

train_duration: float¶

The train of releases lasts for t seconds before turning off.

Default is to never turn off.

- default argument value in constructor: TIME_INFINITY

train_interval: float¶

A new train of releases happens every t seconds.

Default is to never have a new train.

The train interval must not be shorter than the train duration.

- default argument value in constructor: TIME_INFINITY

number_of_trains: int¶

Repeat the release process for n trains of releases. Default is one train.

For unlimited number of trains use a constant NUMBER_OF_TRAINS_UNLIMITED.

- default argument value in constructor: 1

ReleaseSite¶

Defines a release site that specifies where, when and how should molecules be released.

Example: 1100_point_release/model.py

Attributes:¶

name: str¶

Name of the release site

complex: Complex¶

Defines the species of the molecule that will be released. Not used for the LIST shape.

Must be set when molecule_list is empty and unset when molecule_list is not empty.

Orientation of the complex instance is used to define orientation of the released molecule,

when Orientation.DEFAULT is set, volume molecules are released with Orientation.NONE and

surface molecules are released with Orientation.UP.

When compartment is specified and region is not set, this sets shape to Shape.COMPARTMENT and

the molecules are released into the compartment.

When this is a release of volume molecules, and both compartment and region are set,

this sets shape to Shape.REGION_EXPR and the target region is the intersection

of the region and the compartment.

- default argument value in constructor: None

molecule_list: List[MoleculeReleaseInfo]¶

Used for LIST shape release mode.

Only one of number_to_release, density, concentration or molecule_list can be set.

- default argument value in constructor: None

release_time: float¶

Specifies time in seconds when the release event is executed.

In case when a release pattern is used, this is the time of the first release.

Equivalent to MDL’s RELEASE_PATTERN command DELAY.

- default argument value in constructor: 0

release_pattern: ReleasePattern¶

Use the release pattern to define schedule of releases.

The default is to release the specified number of molecules at the set release_time.

- default argument value in constructor: None

shape: Shape¶

Defines how the molecules shoudl be released.

Set automatically for these cases to the following values:

region is set - Shape.REGION_EXPR,

region is not set and complex uses a compartment - Shape.COMPARTMENT,

molecule_list is set - Shape.LIST,

location is set - Shape.SPHERICAL.

- default argument value in constructor: Shape.UNSET

region: Region¶

Defines a volume or surface region where to release molecules.

Setting it sets shape to Shape.REGION_EXPR.

When this is a release of volume molecules, and both compartment and region are set,

this sets shape to Shape.REGION_EXPR and the target region is the intersection

of the region and the compartment.

- default argument value in constructor: None

location: List[float]¶

Defines center of a sphere where to release molecules.

Setting it sets shape to Shape.SPHERICAL.

- default argument value in constructor: None

site_diameter: float¶

For a geometrical release site, this releases molecules uniformly within

a radius r computed as site_diameter/2.

Used only when shape is Shape.SPHERICAL.

Maximum one of site_diameter or site_radius may be set.

- default argument value in constructor: 0

site_radius: float¶

For a geometrical release site, this releases molecules uniformly within

a radius site_radius.

Used only when shape is Shape.SPHERICAL.

Maximum one of site_diameter or site_radius may be set.

- default argument value in constructor: None

number_to_release: float¶

Sets number of molecules to release. Cannot be set when shape is Shape.LIST.

Only one of number_to_release, density, concentration or molecule_list can be set.

Value is truncated (floored) to an integer.

- default argument value in constructor: None

density: float¶

Unit is molecules per square micron (for surfaces).

Only one of number_to_release, density, concentration or molecule_list can be set.

Cannot be set when shape is Shape.LIST.

- default argument value in constructor: None

concentration: float¶

Unit is molar (moles per liter) for volumes.

Only one of number_to_release, density, concentration or molecule_list can be set.

Cannot be set when shape is Shape.LIST.

- default argument value in constructor: None

release_probability: float¶

This release does not occur every time, but rather with probability p.

Either the whole release occurs or none of it does; the probability does not

apply molecule-by-molecule. release_probability must be in the interval [0, 1].

- default argument value in constructor: 1