setParam
Sets parameters for reactions
model a model structure
paramType the type of parameter to set:
'lb' Lower bound
'ub' Upper bound
'eq' Both upper and lower bound (equality constraint)
'obj' Objective coefficient
'rev' Reversibility (only changes the model.rev fields,
does not affect model.lb and model.ub)
'var' Variance around measured bound
'unc' Unconstrained, set lower and upper bound to the
default values (-1000 and 1000, or any other values
that are defined in model.annotation.defaultLB and
.defaultUB)
rxnList a cell array of reaction IDs or a vector with their
corresponding indexes
params a vector of the corresponding values
var percentage of variance around measured value, if 'var' is
set as paramType. Defining 'var' as 5 results in lb and ub
at 97.5% and 102.5% of the provide params value (if params
value is negative, then lb and ub are 102.5% and 97.5%).
model an updated model structure
Usage: model=setParam(model, paramType, rxnList, params)0001 function model=setParam(model, paramType, rxnList, params, var) 0002 % setParam 0003 % Sets parameters for reactions 0004 % 0005 % model a model structure 0006 % paramType the type of parameter to set: 0007 % 'lb' Lower bound 0008 % 'ub' Upper bound 0009 % 'eq' Both upper and lower bound (equality constraint) 0010 % 'obj' Objective coefficient 0011 % 'rev' Reversibility (only changes the model.rev fields, 0012 % does not affect model.lb and model.ub) 0013 % 'var' Variance around measured bound 0014 % 'unc' Unconstrained, set lower and upper bound to the 0015 % default values (-1000 and 1000, or any other values 0016 % that are defined in model.annotation.defaultLB and 0017 % .defaultUB) 0018 % rxnList a cell array of reaction IDs or a vector with their 0019 % corresponding indexes 0020 % params a vector of the corresponding values 0021 % var percentage of variance around measured value, if 'var' is 0022 % set as paramType. Defining 'var' as 5 results in lb and ub 0023 % at 97.5% and 102.5% of the provide params value (if params 0024 % value is negative, then lb and ub are 102.5% and 97.5%). 0025 % 0026 % model an updated model structure 0027 % 0028 % Usage: model=setParam(model, paramType, rxnList, params) 0029 0030 paramType=convertCharArray(paramType); 0031 if ~any(strcmpi(paramType,{'lb','ub','eq','obj','rev','var','unc'})) 0032 EM=['Incorrect parameter type: "' paramType '"']; 0033 dispEM(EM); 0034 end 0035 if isnumeric(rxnList) || islogical(rxnList) 0036 rxnList=model.rxns(rxnList); 0037 else 0038 rxnList=convertCharArray(rxnList); 0039 end 0040 0041 %Allow to set several parameters to the same value 0042 if numel(rxnList)~=numel(params) && numel(params)~=1 0043 EM='The number of parameter values and the number of reactions must be the same'; 0044 dispEM(EM); 0045 end 0046 0047 if length(rxnList)>1 0048 if length(paramType)==1 0049 paramType(1:length(rxnList))=paramType; 0050 end 0051 if length(params)==1 0052 params(1:length(rxnList))=params; 0053 end 0054 end 0055 0056 %Find the indexes for the reactions in rxnList. Do not use getIndexes 0057 %as we do not want to throw errors if matches fail 0058 indexes=zeros(numel(rxnList),1); 0059 0060 for i=1:numel(rxnList) 0061 index=find(strcmp(rxnList{i},model.rxns),1); 0062 if ~isempty(index) 0063 indexes(i)=index; 0064 else 0065 indexes(i)=-1; 0066 EM=['Reaction ' rxnList{i} ' is not present in the reaction list']; 0067 dispEM(EM,false); 0068 end 0069 end 0070 0071 %Remove the reactions that were not found 0072 params(indexes==-1)=[]; 0073 indexes(indexes==-1)=[]; 0074 paramType(indexes==-1)=[]; 0075 %Change the parameters 0076 0077 if ~isempty(indexes) 0078 if contains(paramType,'obj') 0079 model.c=zeros(numel(model.c),1); % parameter is changed, not added 0080 end 0081 for j=1:length(paramType) 0082 if strcmpi(paramType{j},'eq') 0083 model.lb(indexes(j))=params(j); 0084 model.ub(indexes(j))=params(j); 0085 end 0086 if strcmpi(paramType{j},'lb') 0087 model.lb(indexes(j))=params(j); 0088 end 0089 if strcmpi(paramType{j},'ub') 0090 model.ub(indexes(j))=params(j); 0091 end 0092 if strcmpi(paramType{j},'obj') 0093 model.c(indexes(j))=params(j); 0094 end 0095 if strcmpi(paramType{j},'rev') 0096 %Non-zero values are interpreted as reversible 0097 model.rev(indexes(j))=params(j)~=0; 0098 end 0099 if strcmpi(paramType{j},'var') 0100 if params(j) < 0 0101 model.lb(indexes(j)) = params(j) * (1+var/200); 0102 model.ub(indexes(j)) = params(j) * (1-var/200); 0103 else 0104 model.lb(indexes(j)) = params(j) * (1-var/200); 0105 model.ub(indexes(j)) = params(j) * (1+var/200); 0106 end 0107 end 0108 if strcmpi(paramType{j},'unc') 0109 if isfield(model.annotation,'defaultLB') 0110 lb = model.annotation.defaultLB; 0111 else 0112 lb = -1000; 0113 end 0114 if isfield(model.annotation,'defaultUB') 0115 ub = model.annotation.defaultUB; 0116 else 0117 ub = 1000; 0118 end 0119 model.lb(indexes(j)) = lb; 0120 model.ub(indexes(j)) = ub; 0121 end 0122 end 0123 end 0124 end