Submodules

bngl_utils

Submodule bngl_utils provides a function to load parameters from a BNGL file.

Methods:

load_bngl_parameters (file_name: str, parameter_overrides: Dict[str, float]=None) -> Dict[str, float]

Load parameters section from a BNGL file and return it as a dictionary name->value.

• file_name: str

  Path to the BNGL file to be loaded.
• 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: 2010_bng_parameter_override/model.py

data_utils

Submodule data_utils provides data loading and manipulation functions.

Methods:

load_dat_file (file_name: str) -> List[List[float]]

Loads a two-column file where the first column is usually time and the second is a

floating point value. Returns a two-column list.

Can be used to load a file with variable rate constants.

• file_name: str

  Path to the .dat file to be loaded.

geometry_utils

Submodule geometry_utils provides several functions to define model geometry. Rather limited for now.

Methods:

create_box (name: str, edge_dimension: float=None, xyz_dimensions: List[float]=None) -> GeometryObject

Creates a GeometryObject in the shape of a cube whose center is at (0, 0, 0).

• name: str

  Name of the created geometry object.
• edge_dimension: float = None

  Specifies length of each edge of the box in um.

  None of x/y/z dimensions can be set.
• xyz_dimensions: List[float] = None

  Specifies x/y/z sizes of the box in um. Parameter edge_dimension must not be set.
  Examples: 1400_rel_site_for_each_it/model.py 1105_point_release_w_create_box_not_cube/model.py

create_icosphere (name: str, radius: float, subdivisions: int) -> GeometryObject

Creates a GeometryObject in the shape of an icosphere whose center is at (0, 0, 0).

• name: str

  Name of the created geometry object.
• radius: float

  Specifies radius of the sphere.
• subdivisions: int

  Number of subdivisions from the initial icosphere.

  The higher this value will be the smoother the icosphere will be.

  Allowed range is between 1 and 8.
  Example: 1110_point_release_w_create_icosphere/model.py

validate_volumetric_mesh (model: Model, geometry_object: GeometryObject)

Checks that the mesh was correctly analyzed, that it has volume and

all edges have neighboring walls.

Must be called after model initialization.

Throws exception with detained message if validation did not pass.

• model: Model

  Model object after initialization.
• geometry_object: GeometryObject

  Geometry object to be checked.

run_utils

Submodule run_utils provides functions used by checkpointing.

Methods:

get_last_checkpoint_dir (seed: int) -> str

Searches the directory checkpoints for the last checkpoint for the given

parameters and returns the directory name if such a directory exists.

Returns empty string if no checkpoint directory was found.

Currently supports only the seed argument.

• seed: int

remove_cwd (paths: List[str]) -> List[str]

Removes all directory names items pointing to the current working directory from a list and

returns a new list.

• paths: List[str]