sat_kinetics2vector.m

％The Metabolic Networks Toolbox contains functions to create, ％modify, display, and simulate bioche

function [v,names] = sat_kinetics2vector(kinetics)
v=[];
names={};
if isfield(kinetics,'reactions'),
  r = kinetics.reactions;
  for it=1:length(r),
    switch r{it}.type,
      case 'mass-action',                      this_v = [ r{it}.k;    r{it}.km];
      case 'mass-action_rev',                  this_v = [ r{it}.k;    r{it}.km];
      case 'mass-action_irrev',                this_v = [ r{it}.k; ];
      case 'multiple_michaelis_menten_rev',    this_v = [ r{it}.Km_S; r{it}.Km_P;  r{it}.Vm_S;  r{it}.Vm_P];
      case 'multiple_michaelis_menten_irrev',  this_v = [ r{it}.Km_S; r{it}.Vm_S  ];
      case 'michaelis_menten_rev',             this_v = [ r{it}.Vm_S; r{it}.Km_S; r{it}.Vm_P;  r{it}.Km_P ];
      case 'influx',                           this_v = [  r{it}.v_in ];
      case 'efflux',                           this_v = [  r{it}.k_out];
      case 'rev_uni_uni',          this_v = [  r{it}.Pk;  r{it}.Pkm; r{it}.k;  r{it}.km];
      case 'rev_bi_uni',           this_v = [  r{it}.Pk;  r{it}.Pkm; r{it}.k;  r{it}.km];
      case 'rev_uni_bi',           this_v = [  r{it}.Pk;  r{it}.Pkm; r{it}.k;  r{it}.km];
      case 'rev_bi_bi',            this_v = [  r{it}.Pk;  r{it}.Pkm; r{it}.k;  r{it}.km];
      case 'irrev_uni',            this_v = [  r{it}.Pk;  r{it}.k];
      case 'irrev_bi',             this_v = [  r{it}.Pk;  r{it}.k];
    end
    v=[v; this_v];
    names=[names; kinetics.reactions{it}.parameters];
  end
end