setProtPoolSize

 setProtPoolSize
   Sets the limit of the total protein usage in the model.

 Input:
   model           an ecModel in GECKO 3 format (with ecModel.ec structure)
   Ptot            Total cellular protein content in g/gDCW. If not
                   specified, the value will be read from the model
                   adapter. If not specified in model adapter, 0.5 g/gDCW
                   is assumed.
   f               Estimated fraction of enzymes in the model. If not
                   specified, the value will be read from the model
                   adapter. If not specified in model adapter, 0.5 is
                   assumed.
   sigma           Estimated saturation factor. If not specified, the
                   value will be read from the model adapter. If not
                   specified in model adapter, 0.5 is assumed.
   modelAdapter    a loaded model adapter (Optional, will otherwise use the
                   default model adapter).

 Output:
   model           ecModel with protein pool constraint set

 Usage: model = setProtPoolSize(model, Ptot, f, sigma, modelAdapter)

0001 function model = setProtPoolSize(model, Ptot, f, sigma, modelAdapter)
0002 % setProtPoolSize
0003 %   Sets the limit of the total protein usage in the model.
0004 %
0005 % Input:
0006 %   model           an ecModel in GECKO 3 format (with ecModel.ec structure)
0007 %   Ptot            Total cellular protein content in g/gDCW. If not
0008 %                   specified, the value will be read from the model
0009 %                   adapter. If not specified in model adapter, 0.5 g/gDCW
0010 %                   is assumed.
0011 %   f               Estimated fraction of enzymes in the model. If not
0012 %                   specified, the value will be read from the model
0013 %                   adapter. If not specified in model adapter, 0.5 is
0014 %                   assumed.
0015 %   sigma           Estimated saturation factor. If not specified, the
0016 %                   value will be read from the model adapter. If not
0017 %                   specified in model adapter, 0.5 is assumed.
0018 %   modelAdapter    a loaded model adapter (Optional, will otherwise use the
0019 %                   default model adapter).
0020 %
0021 % Output:
0022 %   model           ecModel with protein pool constraint set
0023 %
0024 % Usage: model = setProtPoolSize(model, Ptot, f, sigma, modelAdapter)
0025 
0026 if nargin < 5 || isempty(modelAdapter)
0027     modelAdapter = ModelAdapterManager.getDefault();
0028     if isempty(modelAdapter) && (nargin<2 || isempty(Ptot) || isempty(f) || isempty(sigma))
0029         error('Either send in a modelAdapter or set the default model adapter in the ModelAdapterManager.')
0030     end
0031 end
0032 
0033 if nargin<4 || isempty(sigma)
0034     sigma = modelAdapter.getParameters().sigma;
0035 end
0036 if nargin<3 || isempty(f)
0037     f = modelAdapter.getParameters().f;
0038 end
0039 if nargin<2 || isempty(Ptot)
0040     Ptot = modelAdapter.getParameters().Ptot;
0041 end
0042 
0043 model.lb(strcmp(model.rxns, 'prot_pool_exchange')) = -(Ptot*f*sigma*1000);
0044 end
0045