Type Definitions

This module defines type aliases and protocols used throughout the package.

Type Aliases

microscopic_gating.types.ArrayLike

Type alias for array-like inputs (numpy arrays, lists, or scalars).

Protocols

class microscopic_gating.types.Isotherm(*args, **kwargs)

Bases: Protocol

Protocol for adsorption isotherms.

Any class implementing this protocol can be used with the gating models, allowing flexible substitution of different adsorption models.

theta(phi)

Calculate occupancy fraction.

Parameters:

phi (ArrayLike) – Bulk concentration.

Returns:

theta – Occupancy fraction in [0, 1], same shape as phi.

Return type:

ArrayLike

__init__(*args, **kwargs)

class microscopic_gating.types.ContactProbability(*args, **kwargs)

Bases: Protocol

Protocol for contact/capture geometry factors.

Implementations provide the mean contact probability <chi> that accounts for geometric constraints on bridge formation.

mean_contact()

Return the mean contact probability.

Returns:

chi_mean – Mean contact probability <chi> in [0, 1].

Return type:

float

__init__(*args, **kwargs)

Data Classes

class microscopic_gating.types.SitePairCount(M, N_acc)

Bases: object

Number of potentially accessible site pairs.

This dataclass encapsulates the combinatorial factor for bridge formation based on available binding sites.

Parameters:

• M (int) – Number of binding sites on the particle.

• N_acc (int) – Number of accessible binding sites on the network (geometry-dependent).

N_pair

Total site pair count, calculated as M * N_acc.

Type:

int

Examples

>>> site_pairs = SitePairCount(M=10, N_acc=5)
>>> site_pairs.N_pair
50

M: int

N_acc: int

__init__(M, N_acc)

Parameters:

• M (int) –

• N_acc (int) –

Return type:

None

Type Hierarchy

The type system is designed for flexibility:

• ArrayLike - Any array-like input (numpy arrays, lists, scalars)

• Isotherm - Protocol for any object with a theta(phi) method

• ContactProbability - Protocol for geometry factors

This allows easy extension with custom isotherms or geometry models.