How do you go about creating a file similar to lotka.xml that can be used for Stoichiometry matrices?

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evanma
evanma 2017-2-24
If you have a file for a set of reactions, say a text file in the form
glyc3p[c] + h2o[c] -----> glyc[c] + pi[c]
atp[c] + glyc[c] -----> adp[c] + glyc3p[c] + h[c]
ala-L[m] + glx[m] --- gly[m] + pyr[m]
hcys-L[c] + ser-L[c] -----> cyst-L[c] + h2o[c]
ser-L[c] + thf[c] --- gly[c] + h2o[c] + mlthf[c]
aspsa[c] + h[c] + nadph[c] -----> hom-L[c] + nadp[c]
atp[c] + hom-L[c] -----> adp[c] + h[c] + phom[c]
How can this be converted into a file of the same form as lotka.xml that can be imported and turned into a stoichiometry matrix using commands m1 = sbmlimport('lotka.xml'); and [M,objSpecies,objReactions] = getstoichmatrix(m1) ?

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