printModel
Prints reactions to the screen or to a file
model a model structure
rxnList either a cell array of reaction IDs, a logical vector
with the same number of elements as reactions in the model,
or a vector of indexes to remove (optional, default
model.rxns)
outputString a string that specifies the output of each reaction (optional,
default '%rxnID (%rxnName)\n\t%eqn [%lower %upper]\n')
outputFile a file to save the print-out to (optional, default is output to
the command window)
metaboliteList cell array of metabolite names. Only reactions
involving any of these metabolites will be
printed (optional)
The following codes are available for user-defined output strings:
%rxnID reaction ID
%rxnName reaction name
%lower lower bound
%upper upper bound
%obj objective coefficient
%eqn equation
%element equation using the metabolite formulas rather than
metabolite names
%unbalanced "(*)" if the reaction is unbalanced and "(-)" if it could not
be parsed
%lumped equation where the elemental compositions for the left/right
hand sides are lumped
NOTE: This is just a wrapper function around printFluxes. It is
intended to be used when there is no flux distribution.
Usage: printModel(model,rxnList,outputString,outputFile,metaboliteList)0001 function printModel(model,rxnList,outputString,outputFile,metaboliteList) 0002 % printModel 0003 % Prints reactions to the screen or to a file 0004 % 0005 % model a model structure 0006 % rxnList either a cell array of reaction IDs, a logical vector 0007 % with the same number of elements as reactions in the model, 0008 % or a vector of indexes to remove (optional, default 0009 % model.rxns) 0010 % outputString a string that specifies the output of each reaction (optional, 0011 % default '%rxnID (%rxnName)\n\t%eqn [%lower %upper]\n') 0012 % outputFile a file to save the print-out to (optional, default is output to 0013 % the command window) 0014 % metaboliteList cell array of metabolite names. Only reactions 0015 % involving any of these metabolites will be 0016 % printed (optional) 0017 % 0018 % The following codes are available for user-defined output strings: 0019 % 0020 % %rxnID reaction ID 0021 % %rxnName reaction name 0022 % %lower lower bound 0023 % %upper upper bound 0024 % %obj objective coefficient 0025 % %eqn equation 0026 % %element equation using the metabolite formulas rather than 0027 % metabolite names 0028 % %unbalanced "(*)" if the reaction is unbalanced and "(-)" if it could not 0029 % be parsed 0030 % %lumped equation where the elemental compositions for the left/right 0031 % hand sides are lumped 0032 % 0033 % NOTE: This is just a wrapper function around printFluxes. It is 0034 % intended to be used when there is no flux distribution. 0035 % 0036 % Usage: printModel(model,rxnList,outputString,outputFile,metaboliteList) 0037 0038 if nargin<2 || isempty(rxnList) 0039 rxnList=model.rxns; 0040 elseif ~islogical(rxnList) && ~isnumeric(rxnList) 0041 rxnList=convertCharArray(rxnList); 0042 end 0043 if nargin<3 || isempty(outputString) 0044 outputString='%rxnID (%rxnName)\n\t%eqn [%lower %upper]\n'; 0045 else 0046 outputString=char(outputString); 0047 end 0048 if nargin<4 0049 outputFile=[]; 0050 else 0051 outputFile=char(outputFile); 0052 end 0053 if nargin<5 0054 metaboliteList=[]; 0055 else 0056 metaboliteList=convertCharArray(metaboliteList); 0057 end 0058 0059 I=getIndexes(model,rxnList,'rxns',true)*1.00; %To convert it to "fluxes" 0060 0061 if ~isempty(metaboliteList) 0062 printFluxes(model, I, false, 0.1, outputFile,outputString,metaboliteList); 0063 else 0064 printFluxes(model, I, false, 0.1, outputFile,outputString); 0065 end 0066 end