% txtl_utr_rbs.m - information for standard RBS
% RMM, 8 Sep 2012
%
% This file contains a description of a standard ribosome binding site.
% Calling the function txtl_utr_rbs() will set up the reactions for
% translation with the measured binding rates and translation rates.

% Written by Richard Murray, Sep 2012
%
% Copyright (c) 2012 by California Institute of Technology
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function varargout = txtl_utr_rbs(mode, tube, rna, protein, varargin)

%%%%%%%%%%%%%%%%%%% DRIVER MODE: Setup Species %%%%%%%%%%%%%%%%%%%%%%%%%%%%
if strcmp(mode.add_dna_driver, 'Setup Species')

    utrRbsData = varargin{1};
    defaultBasePairs = {'att', 'anti', 'rbs','spacer';10, 10, 20,200};
    utrRbsData = txtl_setup_default_basepair_length(tube,utrRbsData,defaultBasePairs);
    
    if mode.utr_rbs_flag % ribosome only binds to the RNA if the rbs is present
        RiboBound = ['Ribo:' rna.Name];
        coreSpecies = {'Ribo',RiboBound};
    else
        coreSpecies = {'Ribo'};
    end
    
    % empty cellarray for amount => zero amount
    txtl_addspecies(tube, coreSpecies, cell(1,size(coreSpecies,2)), 'Internal');
    
   
    %TODO! 12/8/12 zoltuz - find out why we need the RiboBound here!
    if mode.utr_rbs_flag
        varargout{1} = sbioselect(tube, 'Name', RiboBound);
        varargout{2} = utrRbsData;
    else
    varargout{1} = utrRbsData;    
    end
    
    

%%%%%%%%%%%%%%%%%%% DRIVER MODE: Setup Reactions %%%%%%%%%%%%%%%%%%%%%%%%%%    
elseif strcmp(mode.add_dna_driver,'Setup Reactions')

    if mode.utr_rbs_flag
        % Set up the binding reaction
        txtl_addreaction(tube,['[' rna.Name '] + Ribo <-> [Ribo:' rna.Name ']'],...
            'MassAction',{'TXTL_UTR_RBS_F',tube.UserData.ReactionConfig.Ribosome_Binding_F;
            'TXTL_UTR_RBS_R',tube.UserData.ReactionConfig.Ribosome_Binding_R});
    end
    

%%%%%%%%%%%%%%%%%%% DRIVER MODE: error handling %%%%%%%%%%%%%%%%%%%%%%%%%%%
else
    error('txtltoolbox:txtl_utr_rbs:undefinedmode', ...
      'The possible modes are ''Setup Species'' and ''Setup Reactions''.');
end    


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