set_sat_kinetics.m

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

function kinetics = set_sat_kinetics(network)

% kinetics = set_sat_kinetics(network)
%
% construct a kinetics field for a metabolic network
% set default kinetics types for all reactions of a network,
% depending on number of substrates and products and reversibility
%
% kinetics         parameters
%
% 'rev_uni_uni'    {'k','km','Pk','Pkm'}
% 'rev_uni_bi'     {'k','km','Pk','Pkm'}
% 'rev_bi_uni'     {'k','km','Pk','Pkm'}
% 'rev_bi_bi'      {'k','km','Pk','Pkm'}
% 'irrev_uni'      {'k','Pk'}
% 'irrev_bi'       {'k','Pk'}
% 'influx'         {'v_in'}
% 'efflux'         {'k_out'}
% 'rev_multiple'   {'k','km','Pk','Pkm'}

kinetics.type='saturated';
kinetics.reactions=cell(length(network.actions),1);

for i=1:length(network.actions)
  kinetics.reactions{i}.type = 'unknown';
  n_in  = sum(network.N(:,i)<0) ;
  n_out = sum(network.N(:,i)>0) ;
  rev   = network.reversible(i);
  
%  switch rev
%    case 1,
%      if n_in == 1 & n_out == 1, kinetics.reactions{i}.type = 'rev_uni_uni'; end
%      if n_in == 1 & n_out == 2, kinetics.reactions{i}.type = 'rev_uni_bi'; end
%      if n_in == 2 & n_out == 1, kinetics.reactions{i}.type = 'rev_bi_uni'; end
%      if n_in == 2 & n_out == 2, kinetics.reactions{i}.type = 'rev_bi_bi'; end
%    case 0,
%      if n_in == 1 , kinetics.reactions{i}.type = 'irrev_uni'; end
%      if n_in == 2 , kinetics.reactions{i}.type = 'irrev_bi'; end
%  end
  
  switch rev,
    case 1,
      kinetics.reactions{i}.type='multiple_michaelis_menten_rev';
    case 0,
     kinetics.reactions{i}.type='multiple_michaelis_menten_irrev';
  end

  if n_in == 0 & n_out > 0, kinetics.reactions{i}.type = 'influx'; end
  if n_in > 0  & n_out == 0, kinetics.reactions{i}.type = 'efflux'; end
  if strcmp(kinetics.reactions{i}.type,'unknown'), 
    kinetics.reactions{i}.type='rev_multiple';
  end

  
  switch kinetics.reactions{i}.type,
    case 'mass-action',
      kinetics.reactions{i}.parameters = {'k','km'}';
      kinetics.reactions{i}.sizes = [1 1]';
    case 'michaelis_menten_rev', 
      kinetics.reactions{i}.parameters = {'Km_S','Km_P','Vm_S','Vm_P'}';
      kinetics.reactions{i}.sizes = [1 1 1 1]';
    case 'multiple_michaelis_menten_rev', 
      kinetics.reactions{i}.parameters = {'Km_S','Km_P','Vm_S','Vm_P'}';
      kinetics.reactions{i}.sizes = [1 1 1 1]';
    case 'multiple_michaelis_menten_irrev', 
      kinetics.reactions{i}.parameters = {'Km_S','Vm_S'}';
      kinetics.reactions{i}.sizes = [1 1]';
    case 'influx', 
      kinetics.reactions{i}.parameters = {'v_in'}'; 
      kinetics.reactions{i}.sizes = [1]';
    case 'efflux', 
      kinetics.reactions{i}.parameters = {'k_out'}';
      kinetics.reactions{i}.sizes = [1]';
    case {'rev_uni_uni'},
      kinetics.reactions{i}.parameters = {'k','km','Pk','Pkm'}';
      kinetics.reactions{i}.sizes = [2 2 1 1]';
    case {'rev_uni_bi'},
      kinetics.reactions{i}.parameters = {'k','km','Pk','Pkm'}';
      kinetics.reactions{i}.sizes = [3 3 1 1]';
    case {'rev_bi_uni'},
      kinetics.reactions{i}.parameters = {'k','km','Pk','Pkm'}';
      kinetics.reactions{i}.sizes = [3 3 1 1]';
    case {'rev_bi_bi'},
      kinetics.reactions{i}.parameters = {'k','km','Pk','Pkm'}';
      kinetics.reactions{i}.sizes = [4 4 1 1]';
    case {'rev_multiple'},
      kinetics.reactions{i}.parameters = {'k','km','Pk','Pkm'}';
      kinetics.reactions{i}.sizes = [2 2 1 1]';
    case {'irrev_uni'},
      kinetics.reactions{i}.parameters = {'k','Pk'}';
      kinetics.reactions{i}.sizes = [2 1]';
    case {'irrev_bi'},
      kinetics.reactions{i}.parameters = {'k','Pk'}';
      kinetics.reactions{i}.sizes = [3 1]';
  end
  for it=1:length(kinetics.reactions{i}.parameters),
    kinetics.reactions{i}=setfield(kinetics.reactions{i},kinetics.reactions{i}.parameters{it}, ...
						 ones(kinetics.reactions{i}.sizes(it),1));
  end
end

%kinetics.used_fwd = ones(length(network.actions),1);
%kinetics.used_bwd = network.reversible;