cobamp.nullspace package

Submodules

cobamp.nullspace.nullspace module

cobamp.nullspace.nullspace.compute_nullspace(A, eps=1e-09, left=True)

Computes the nullspace of the matrix A.

Parameters

A: A 2D-ndarray

eps: Tolerance value for 0

left: A boolean value indicating whether the result is the left nullspace (right if False)

cobamp.nullspace.nullspace.nullspace_blocked_reactions(K, tolerance)

Parameters

K: A nullspace matrix as a 2D ndarray

tolerance: Tolerance value for 0

Returns indices of the rows of K where all values are 0

cobamp.nullspace.subset_reduction module

Inspired by Metatool’s code

class cobamp.nullspace.subset_reduction.SubsetReducer

Bases: cobamp.core.transformer.ModelTransformer

ABSOLUTE_BOUNDS = 'SUBSET_REDUCER-ABSOLUTE_BOUNDS'

TO_BLOCK = 'SUBSET_REDUCER-TO_BLOCK'

TO_KEEP_SINGLE = 'SUBSET_REDUCER-TO_KEEP_SINGLE'

get_transform_maps(sub)

reduce(S, lb, ub, keep=(), block=(), absolute_bounds=False)

transform_array(S, lb, ub, properties)

class cobamp.nullspace.subset_reduction.SubsetReducerProperties(keep=None, block=None, absolute_bounds=False, reaction_id_sep='_+_')

Bases: cobamp.utilities.property_management.PropertyDictionary

cobamp.nullspace.subset_reduction.reduce(S, sub, irrev_reduced=None)

Reduces a stoichiometric matrix according to the subset information present in the sub matrix and irrev_reduced.

Parameters

S: Stoichiometric matrix

sub: Subset matrix as computed by <subset_correlation_matrix>

irrev_reduced: Irreversibility vector regarding the subsets.

Returns reduced, reduced_indexes, irrev_reduced

cobamp.nullspace.subset_reduction.subset_candidates(kernel, tol=None)

Computes a matrix of subset candidates from the nullspace of the S matrix

Parameters

kernel: Nullspace of the S matrix

tol: Tolerance to 0.

cobamp.nullspace.subset_reduction.subset_correlation_matrix(S, kernel, irrev, cr, keepSingle=None)

S: Stoichiometric matrix as ndarray

kernel: The nullspace of S

irrev: List of booleans representing irreversible reactions (when True)

cr: The subset candidate matrix, computed using <subset_candidates>

keepSingle: List of reaction indices that will not be compressed.

Returns sub, irrev_sub, irrev_violating_subsets

sub : subset matrix, n-subsets by n-reactions -> numpy.array

irrev_sub : subset reversibilities -> numpy.array of type bool

irrev_violating_subsets : same as sub, but list if empty. Contains subsets discarded due to irreversibility faults

cobamp.nullspace.subset_reduction.subset_reduction(S, irrev, to_remove=[], to_keep_single=[])

Reduces a stoichiometric matrix using nullspace analysis by identifying linearly dependent (enzyme) subsets. These reactions are then compressed.

S: Stoichiometric matrix as an ndarray.

irrev: A boolean array with size equal to the number of columns in the S matrix.

to_remove: A list of indices specifying columns of the S matrix to remove before the compression (usually blocked reactions)

to_keep_single: A list of indices specifying columns of the S matrix not to compress.

Returns rd, sub, irrev_reduced, rdind, irrv_subsets, kept_reactions, kernel, correlation_matrix

rd : compressed stoichiometric matrix -> numpy.array

sub : subset matrix, n-subsets by n-reactions -> numpy.array

irrev_reduced : subset reversibilities -> numpy.array of type bool

rdind : metabolite indices -> numpy.array of type int

irrv_subsets : same as sub, but list if empty

kept_reactions : indexes for reactions used in the network compression

kernel : numpy.array with the right nullspace of S

correlation_matrix : numpy.array with reaction correlation matrix

Module contents