network_construct.m

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

%network = network_construct(N,reversible,external_ind,metabolites,actions)
%
%Construct network data structures from stoichiometric matrix
%  network structure has mandatory fields 
%  'metabolites','actions','N','reversible','external'
%  see 'network_structure'
%
%ARGUMENT
% N           stoichiometric matrix
%
%OPTIONAL ARGUMENTS
% metabolites          names of metabolites  (column list of strings)
% actions              names of reactions    (column list of strings)
% reversible           column vector (elements 0,1) indicating reversible actions. default: all reversible
% external_ind indices (vector) of external (=fixed) metabolites.    default: all internal

function n = network_construct(N,reversible,external_ind,metabolites,actions)

if ~exist('reversible','var'), reversible   = ones(size(N,2),1); end
if ~exist('external_ind'),     external_ind = []; end

if ~exist('metabolites'),   
  metabolites = cellstr([repmat('S',size(N,1),1)  num2str((1:size(N,1))')]);
  for i = 1:length(metabolites), metabolites{i}=metabolites{i}(find(metabolites{i}~=' ')); end
end

if ~exist('actions'),   
  actions = cellstr([repmat('E',size(N,2),1)  num2str((1:size(N,2))')]);
  for i = 1:length(actions), actions{i}=actions{i}(find(actions{i}~=' ')); end
end

if size(reversible,1)==1, reversible=reversible'; end

n.metabolites = metabolites;
n.actions     = actions;
n.N           = N;
n.reversible  = reversible;
n.external    = bit_vector(external_ind,size(N,1));
n.external    = (n.external + bit_vector(network_find_ext_metabolites(n),length(n.metabolites)) ) >0;
n.kinetics    = set_kinetics(n);
n             = netgraph_make_graph(n);