ecoli.library.lattice_utils

Utilities for Lattice Environments

class ecoli.library.lattice_utils.ExchangeAgent(parameters=None)

Bases: Process

defaults: Dict[str, Any]

{'default_exchange': 100, 'max_move': 4, 'mol_ids': []}

next_update(timestep, states)

ports_schema()

ecoli.library.lattice_utils.apply_exchanges(agents, fields, exchanges_path, location_path, n_bins, bounds, bin_volume)

ecoli.library.lattice_utils.count_to_concentration(count, bin_volume)

Convert a molecule count into a concentration.

Parameters should all have units. Returned value will have units.

Parameters:

• count (int) – The number of molecules in the bin.

• bin_volume (float) – The volume of the bin.

Returns:

The concentration of molecule in the bin.

Return type:

float

ecoli.library.lattice_utils.gaussian(deviation, distance)

ecoli.library.lattice_utils.get_bin_site(location, n_bins, bounds)

Get a bin’s indices in the lattice

Parameters:

• location (list) – A list of 2 floats that specify the x and y coordinates of a point inside the desired bin.

• n_bins (list) – A list of 2 ints that specify the number of bins along the x and y axes, respectively.

• bounds (list) – A list of 2 floats that define the dimensions of the lattice environment along the x and y axes, respectively.

Returns:

A 2-tuple of the x and y indices of the bin in the lattice.

Return type:

tuple

ecoli.library.lattice_utils.get_bin_volume(n_bins, bounds, depth)

Get a bin’s volume

Parameters:

• n_bins (list) – A list of 2 ints that specify the number of bins along the x and y axes, respectively.

• bounds (list) – A list of 2 floats that specify the lengths of the environment’s sides in the x and y directions, respectively. In units of microns.

• depth (float) – The depth of the environment, in microns.

Returns:

The volume of each bin in the lattice, in Liters.

Return type:

float

ecoli.library.lattice_utils.make_diffusion_schema(exchanges_path, external_path, location_path, bounds, n_bins, depth, molecule_ids, default_field)

ecoli.library.lattice_utils.make_gradient(gradient, n_bins, size)

Create a gradient from a configuration

Random A random gradient fills the field randomly with each molecule, with values between 0 and the concentrations specified.

Example configuration:

'gradient': {
    'type': 'random',
    'molecules': {
        'mol_id1': 1.0,
        'mol_id2': 2.0
    }},

Uniform

A uniform gradient fills the field evenly with each molecule, at the concentrations specified.

Example configuration:

'gradient': {
    'type': 'uniform',
    'molecules': {
        'mol_id1': 1.0,
        'mol_id2': 2.0
    }},

Gaussian

A gaussian gradient multiplies the base concentration of the given molecule by a gaussian function of distance from center and deviation. Distance is scaled by 1/1000 from microns to millimeters.

Example configuration:

'gradient': {
    'type': 'gaussian',
    'molecules': {
        'mol_id1':{
            'center': [0.25, 0.5],
            'deviation': 30},
        'mol_id2': {
            'center': [0.75, 0.5],
            'deviation': 30}
    }},

Linear

A linear gradient sets a site’s concentration (c) of the given molecule as a function of distance (d) from center and slope (b), and base concentration (a). Distance is scaled by 1/1000 from microns to millimeters.

\[c = a + b * d\]

Example configuration:

'gradient': {
    'type': 'linear',
    'molecules': {
        'mol_id1':{
            'center': [0.0, 0.0],
            'base': 0.1,
            'slope': -10},
        'mol_id2': {
            'center': [1.0, 1.0],
            'base': 0.1,
            'slope': -5}
    }},

Exponential

An exponential gradient sets a site’s concentration (c) of the given molecule as a function of distance (d) from center, with parameters base (b) and scale (a). Distance is scaled by 1/1000 from microns to millimeters. Note: base > 1 makes concentrations increase from the center.

\[c=a*b^d.\]

Example configuration:

'gradient': {
    'type': 'exponential',
    'molecules': {
        'mol_id1':{
            'center': [0.0, 0.0],
            'base': 1+2e-4,
            'scale': 1.0},
        'mol_id2': {
            'center': [1.0, 1.0],
            'base': 1+2e-4,
            'scale' : 0.1}
    }},

Parameters:

• gradient – Configuration dictionary that includes the type key to specify the type of gradient to make.

• n_bins – A list of two elements that specify the number of bins to have along each axis.

• size – A list of two elements that specifies the size of the environment.