setParam
Sets parameters for reactions
Input:
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%).
Output:
model an updated model structure
Usage: model = setParam(model, paramType, rxnList, params, var)0001 function model=setParam(model, paramType, rxnList, params, var) 0002 % setParam 0003 % Sets parameters for reactions 0004 % 0005 % Input: 0006 % model a model structure 0007 % paramType the type of parameter to set: 0008 % 'lb' lower bound 0009 % 'ub' upper bound 0010 % 'eq' both upper and lower bound (equality constraint) 0011 % 'obj' objective coefficient 0012 % 'rev' reversibility (only changes the model.rev fields, 0013 % does not affect model.lb and model.ub) 0014 % 'var' variance around measured bound 0015 % 'unc' unconstrained, set lower and upper bound to the 0016 % default values (-1000 and 1000, or any other values 0017 % that are defined in model.annotation.defaultLB and 0018 % .defaultUB) 0019 % rxnList a cell array of reaction IDs or a vector with their 0020 % corresponding indexes 0021 % params a vector of the corresponding values 0022 % var percentage of variance around measured value, if 'var' is 0023 % set as paramType. Defining 'var' as 5 results in lb and ub 0024 % at 97.5% and 102.5% of the provide params value (if params 0025 % value is negative, then lb and ub are 102.5% and 97.5%). 0026 % 0027 % Output: 0028 % model an updated model structure 0029 % 0030 % Usage: model = setParam(model, paramType, rxnList, params, var) 0031 0032 paramType=convertCharArray(paramType); 0033 if ~any(strcmpi(paramType,{'lb','ub','eq','obj','rev','var','unc'})) 0034 EM=['Incorrect parameter type: "' paramType{1} '"']; 0035 dispEM(EM); 0036 end 0037 if isnumeric(rxnList) || islogical(rxnList) 0038 rxnList=model.rxns(rxnList); 0039 else 0040 rxnList=convertCharArray(rxnList); 0041 end 0042 0043 %Allow to set several parameters to the same value 0044 if numel(rxnList)~=numel(params) && numel(params)~=1 0045 EM='The number of parameter values and the number of reactions must be the same'; 0046 dispEM(EM); 0047 end 0048 0049 if length(rxnList)>1 0050 if length(paramType)==1 0051 paramType(1:length(rxnList))=paramType; 0052 end 0053 if length(params)==1 0054 params(1:length(rxnList))=params; 0055 end 0056 end 0057 0058 %Find the indexes for the reactions in rxnList. Do not use getIndexes 0059 %as we do not want to throw errors if matches fail 0060 indexes=zeros(numel(rxnList),1); 0061 0062 for i=1:numel(rxnList) 0063 index=find(strcmp(rxnList{i},model.rxns),1); 0064 if ~isempty(index) 0065 indexes(i)=index; 0066 else 0067 indexes(i)=-1; 0068 EM=['Reaction ' rxnList{i} ' is not present in the reaction list']; 0069 dispEM(EM,false); 0070 end 0071 end 0072 0073 %Remove the reactions that were not found 0074 params(indexes==-1)=[]; 0075 indexes(indexes==-1)=[]; 0076 paramType(indexes==-1)=[]; 0077 %Change the parameters 0078 0079 if ~isempty(indexes) 0080 if contains(paramType,'obj') 0081 model.c=zeros(numel(model.c),1); % parameter is changed, not added 0082 end 0083 for j=1:length(paramType) 0084 if strcmpi(paramType{j},'eq') 0085 model.lb(indexes(j))=params(j); 0086 model.ub(indexes(j))=params(j); 0087 end 0088 if strcmpi(paramType{j},'lb') 0089 model.lb(indexes(j))=params(j); 0090 end 0091 if strcmpi(paramType{j},'ub') 0092 model.ub(indexes(j))=params(j); 0093 end 0094 if strcmpi(paramType{j},'obj') 0095 model.c(indexes(j))=params(j); 0096 end 0097 if strcmpi(paramType{j},'rev') 0098 %Non-zero values are interpreted as reversible 0099 model.rev(indexes(j))=params(j)~=0; 0100 end 0101 if strcmpi(paramType{j},'var') 0102 if params(j) < 0 0103 model.lb(indexes(j)) = params(j) * (1+var/200); 0104 model.ub(indexes(j)) = params(j) * (1-var/200); 0105 else 0106 model.lb(indexes(j)) = params(j) * (1-var/200); 0107 model.ub(indexes(j)) = params(j) * (1+var/200); 0108 end 0109 end 0110 if strcmpi(paramType{j},'unc') 0111 if isfield(model.annotation,'defaultLB') 0112 lb = model.annotation.defaultLB; 0113 else 0114 lb = -1000; 0115 end 0116 if isfield(model.annotation,'defaultUB') 0117 ub = model.annotation.defaultUB; 0118 else 0119 ub = 1000; 0120 end 0121 model.lb(indexes(j)) = lb; 0122 model.ub(indexes(j)) = ub; 0123 end 0124 end 0125 end 0126 end