up

Author: vyudu

src/network_analysis.jl

@@ -928,46 +928,3 @@ function treeweight(t::SimpleDiGraph, g::SimpleDiGraph, distmx::Matrix)
     end
     prod
 end
-
-"""
-    cycles(rs::ReactionSystem)
-
-    Returns the matrix of cycles (or flux vectors), or reaction fluxes at steady state. These correspond to right eigenvectors of the stoichiometric matrix. Equivalent to [`fluxmodebasis`](@ref). 
-"""
-
-function cycles(rs::ReactionSystem) 
-    nps = get_networkproperties(rs)
-    nsm = netstoichmat(rs)
-    !isempty(nps.cyclemat) && return nps.cyclemat
-    nps.cyclemat = cycles(nsm; col_order = nps.col_order)
-    nps.cyclemat
-end
-
-function cycles(nsm::T; col_order = nothing) where {T <: AbstractMatrix}
-
-    # compute the left nullspace over the integers
-    N = MT.nullspace(nsm; col_order)
-
-    # if all coefficients for a cycle are negative, make positive
-    for Nrow in eachcol(N)
-        all(r -> r <= 0, Nrow) && (Nrow .*= -1)
-    end
-
-    # check we haven't overflowed
-    iszero(nsm * N) || error("Calculation of the cycle matrix was inaccurate, "
-          * "likely due to numerical overflow. Please use a larger integer "
-          * "type like Int128 or BigInt for the net stoichiometry matrix.")
-
-    T(N)
-end
-
-"""
-    fluxvectors(rs::ReactionSystem)
-
-    See documentation for [`cycles`](@ref). 
-"""
-
-function fluxmodebasis(rs::ReactionSystem) 
-    cycles(rs)
-end
-