% txtl_protein_tetR.m - protein information for tetR
% RMM, 9 Sep 2012
%
% This file contains a description of the protein produced by tetR.
% Calling the function txtl_protein_tetR() will set up the reactions for
% sequestration by the inducer aTc.

% Written by Richard Murray, 9 Sep 2012
%
% Copyright (c) 2012 by California Institute of Technology
% All rights reserved.
%
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% modification, are permitted provided that the following conditions are
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%
%   1. Redistributions of source code must retain the above copyright
%      notice, this list of conditions and the following disclaimer.
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%   2. Redistributions in binary form must reproduce the above copyright 
%      notice, this list of conditions and the following disclaimer in the 
%      documentation and/or other materials provided with the distribution.
%
%   3. The name of the author may not be used to endorse or promote products 
%      derived from this software without specific prior written permission.
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function varargout = txtl_protein_tetR2(mode, tube, protein, varargin)
% in 'setup Species' mode, it returns an array of gene lengths, having
% added defaults in places where the lengths are missing. 

% importing the corresponding parameters
paramObj = txtl_component_config('tetRtoggleSwitch'); 


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

    geneData = varargin{1};
    defaultBasePairs = {'tetR','lva','terminator';
        paramObj.Gene_Length,paramObj.LVA_tag_Length,paramObj.Terminator_Length};
    geneData = txtl_setup_default_basepair_length(tube,geneData,...
        defaultBasePairs);
    
    varargout{1} = geneData;
    
    % it is possible that this file is called while 'protein tetR' 
    % (with maybe lva, terminator) is not present (for instance, if protein
    % tetRdimer is added using txtl_addspecies. That is why it is necessary
    % to add 'protein tetR' if it is not present ----> actually maybe its
    % not needed! addspecies takes care of it!
    
    coreSpecies = {'aTc'};
    % empty cellarray for amount => zero amount
    txtl_addspecies(tube, coreSpecies, cell(1,size(coreSpecies,2)), 'Internal');
 
    % call other functions in 'Setup Species' mode
    txtl_dimerize(mode, tube,protein);
   
%%%%%%%%%%%%%%%%%%% DRIVER MODE: Setup Reactions %%%%%%%%%%%%%%%%%%%%%%%%%%    
elseif strcmp(mode.add_dna_driver, 'Setup Reactions')
    [~,listOfSpecies] = getstoichmatrix(tube);
  
    % Set up the binding reaction for all protein variants
    matchStr = regexp(listOfSpecies,'(^protein tetR2.*dimer$)','tokens','once'); 
    listOftetRdimer = vertcat(matchStr{:});

    for k = 1:size(listOftetRdimer,1)
        txtl_addreaction(tube, ...
         ['[' listOftetRdimer{k} '] + 2 aTc <-> [2 aTc:' listOftetRdimer{k} ']'],...
         'MassAction',{'TXTL_INDUCER_TETR_ATC_F',paramObj.Protein_Inducer_Forward;...
                       'TXTL_INDUCER_TETR_ATC_R',paramObj.Protein_Inducer_Reverse});
    end

    % degrade the aTc inducer
     txtl_addreaction(tube,'aTc -> null',...
      'MassAction',{'TXTL_INDUCER_DEGRADATION_ATC',paramObj.Inducer_Degradation});

    % set up a reaction for protein dimerization
    txtl_dimerize(mode, tube,protein, ...
        [paramObj.Dimmerization_Forward, paramObj.Dimmerization_Reverse]);
    
%%%%%%%%%%%%%%%%%%% DRIVER MODE: error handling %%%%%%%%%%%%%%%%%%%%%%%%%%%
else
    error('txtltoolbox:txtl_protein_tetR:undefinedmode', ...
      'The possible modes are ''Setup Species'' and ''Setup Reactions''.');
end



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