7.1.1.3.1.3. pta.sampling.primitives

Abstract base class for sampling over the flux polytope.

7.1.1.3.1.3.1. Module Contents

class pta.sampling.primitives.FluxSpaceSamplingModel(polytope: PolyRound.api.Polytope, reaction_ids: List[str])

Bases: pta.sampling.commons.SamplerInterface

Object holding the information necessary to sample a flux space.

Parameters

• polytope (Polytope) – Polytope object describing the flux space.

• reaction_ids (List[str]) – Identifiers of the reactions in the flux space.

property G(self) → numpy.array

Gets the left-hand side of the constraints of the flux space.

property h(self) → numpy.array

Gets the right-hand side of the constraints of the flux space.

property to_fluxes_transform(self) → Tuple[numpy.array, numpy.array]

Gets the transform from a point in the model to a point in the flux space.

property reaction_ids(self)

Gets the IDs of the reactions in the model.

to_fluxes(self, value: numpy.array) → numpy.array

Transform a point or matrix from the model to the flux space.

Parameters

value (np.array) – Input values.

Returns

The corresponding fluxes.

Return type

np.array

property dimensionality(self) → int

Gets the dimensionality of the flux space.

get_initial_points(self, num_points: int) → numpy.array

Gets initial points for sampling fluxes.

Parameters

• model (UniformSamplingModel) – The model to sample.

• num_points (int) – Number of initial points to generate.

Returns

Array containing the initial points.

Return type

np.array