changeRxns
Modifies the equations of reactions
model a model structure
rxns cell array with reaction ids
equations cell array with equations. Alternatively, it can be a
structure with the fields "mets" and "stoichCoeffs",
in the same fashion as addRxns. E.g.:
equations.mets = {{'met1','met2'},{'met1','met3'}}
equations.stoichCoeffs = {[-1,+2],[-1,+1]}
eqnType double describing how the equation string should be
interpreted
1 - The metabolites are matched to model.mets. New
metabolites (if allowed) are added to
"compartment" (default)
2 - The metabolites are matched to model.metNames and
all metabolites are assigned to "compartment". Any
new metabolites that are added will be assigned
IDs "m1", "m2"... If IDs on the same form are
already used in the model then the numbering will
start from the highest used integer+1
3 - The metabolites are written as
"metNames[compNames]". Only compartments in
model.compNames are allowed. Any
new metabolites that are added will be assigned
IDs "m1", "m2"... If IDs on the same form are
already used in the model then the numbering will
start from the highest used integer+1
compartment a string with the compartment the metabolites should
be placed in when using eqnType=2. Must match
model.compNames (optional when eqnType=1 or eqnType=3)
allowNewMets true if the function is allowed to add new
metabolites. It is highly recommended to first add
any new metabolites with addMets rather than
automatically through this function. addMets supports
more annotation of metabolites, allows for the use of
exchange metabolites, and using it reduces the risk
of parsing errors (optional, default false)
model an updated model structure
NOTE: This function should be used with some care, since it doesn't
care about bounds on the reactions. Changing a irreversible reaction to
a reversible one (or the other way around) will only change the
model.rev field and not the model.lb/model.ub fields. The reaction will
therefore still be having the same reversibility because of the
bounds. Use setParams to change the bounds.
NOTE: When adding metabolites to a compartment where it previously
doesn't exist, the function will copy any available information from
the metabolite in another compartment.
Usage: model=changeRxns(model,rxns,equations,eqnType,compartment,allowNewMets)0001 function model=changeRxns(model,rxns,equations,eqnType,compartment,allowNewMets) 0002 % changeRxns 0003 % Modifies the equations of reactions 0004 % 0005 % model a model structure 0006 % rxns cell array with reaction ids 0007 % equations cell array with equations. Alternatively, it can be a 0008 % structure with the fields "mets" and "stoichCoeffs", 0009 % in the same fashion as addRxns. E.g.: 0010 % equations.mets = {{'met1','met2'},{'met1','met3'}} 0011 % equations.stoichCoeffs = {[-1,+2],[-1,+1]} 0012 % eqnType double describing how the equation string should be 0013 % interpreted 0014 % 1 - The metabolites are matched to model.mets. New 0015 % metabolites (if allowed) are added to 0016 % "compartment" (default) 0017 % 2 - The metabolites are matched to model.metNames and 0018 % all metabolites are assigned to "compartment". Any 0019 % new metabolites that are added will be assigned 0020 % IDs "m1", "m2"... If IDs on the same form are 0021 % already used in the model then the numbering will 0022 % start from the highest used integer+1 0023 % 3 - The metabolites are written as 0024 % "metNames[compNames]". Only compartments in 0025 % model.compNames are allowed. Any 0026 % new metabolites that are added will be assigned 0027 % IDs "m1", "m2"... If IDs on the same form are 0028 % already used in the model then the numbering will 0029 % start from the highest used integer+1 0030 % compartment a string with the compartment the metabolites should 0031 % be placed in when using eqnType=2. Must match 0032 % model.compNames (optional when eqnType=1 or eqnType=3) 0033 % allowNewMets true if the function is allowed to add new 0034 % metabolites. It is highly recommended to first add 0035 % any new metabolites with addMets rather than 0036 % automatically through this function. addMets supports 0037 % more annotation of metabolites, allows for the use of 0038 % exchange metabolites, and using it reduces the risk 0039 % of parsing errors (optional, default false) 0040 % 0041 % model an updated model structure 0042 % 0043 % NOTE: This function should be used with some care, since it doesn't 0044 % care about bounds on the reactions. Changing a irreversible reaction to 0045 % a reversible one (or the other way around) will only change the 0046 % model.rev field and not the model.lb/model.ub fields. The reaction will 0047 % therefore still be having the same reversibility because of the 0048 % bounds. Use setParams to change the bounds. 0049 % 0050 % NOTE: When adding metabolites to a compartment where it previously 0051 % doesn't exist, the function will copy any available information from 0052 % the metabolite in another compartment. 0053 % 0054 % Usage: model=changeRxns(model,rxns,equations,eqnType,compartment,allowNewMets) 0055 0056 if nargin<4 0057 eqnType=1; 0058 end 0059 0060 if nargin<5 0061 compartment=[]; 0062 end 0063 if nargin<6 0064 allowNewMets=false; 0065 end 0066 0067 rxns=convertCharArray(rxns); 0068 compartment=char(compartment); 0069 0070 %Find the indexes of the reactions and throw an error if they aren't all 0071 %found 0072 [I, J]=ismember(rxns,model.rxns); 0073 if ~all(I) 0074 EM='All reaction ids must exist in the model'; 0075 dispEM(EM); 0076 end 0077 0078 %The reactions are changed in the following manner. First create a 0079 %rxns-structure by copying info from the model. Then remove the old 0080 %reactions. Then add the updated ones using addRxns. Lastly, the model is 0081 %reordered to match the original order. This is done like this to make use 0082 %of the advanced parsing of equations that addRxns use. 0083 rxnsToChange.rxns=rxns; 0084 if isfield(equations,'mets') && isfield(equations,'stoichCoeffs') 0085 rxnsToChange.mets=equations.mets; 0086 rxnsToChange.stoichCoeffs=equations.stoichCoeffs; 0087 else 0088 rxnsToChange.equations=convertCharArray(equations); 0089 end 0090 if isfield(model,'rxnNames') 0091 rxnsToChange.rxnNames=model.rxnNames(J); 0092 end 0093 if isfield(model,'lb') 0094 rxnsToChange.lb=model.lb(J); 0095 end 0096 if isfield(model,'ub') 0097 rxnsToChange.ub=model.ub(J); 0098 end 0099 if isfield(model,'c') 0100 rxnsToChange.c=model.c(J); 0101 end 0102 if isfield(model,'eccodes') 0103 rxnsToChange.eccodes=model.eccodes(J); 0104 end 0105 if isfield(model,'subSystems') 0106 rxnsToChange.subSystems=model.subSystems(J); 0107 end 0108 if isfield(model,'rxnComps') 0109 rxnsToChange.rxnComps=model.rxnComps(J); 0110 end 0111 if isfield(model,'grRules') 0112 rxnsToChange.grRules=model.grRules(J); 0113 end 0114 if isfield(model,'rxnFrom') 0115 rxnsToChange.rxnFrom=model.rxnFrom(J); 0116 end 0117 if isfield(model,'rxnScores') 0118 rxnsToChange.rxnScores=model.rxnScores(J); 0119 end 0120 if isfield(model,'rxnMiriams') 0121 rxnsToChange.rxnMiriams=model.rxnMiriams(J); 0122 end 0123 if isfield(model,'rxnNotes') 0124 rxnsToChange.rxnNotes=model.rxnNotes(J); 0125 end 0126 if isfield(model,'rxnReferences') 0127 rxnsToChange.rxnReferences=model.rxnReferences(J); 0128 end 0129 if isfield(model,'rxnConfidenceScores') 0130 rxnsToChange.rxnConfidenceScores=model.rxnConfidenceScores(J); 0131 end 0132 if isfield(model,'rxnDeltaG') 0133 rxnsToChange.rxnDeltaG=model.rxnDeltaG(J); 0134 end 0135 if isfield(model,'pwys') 0136 rxnsToChange.pwys=model.pwys(J); 0137 end 0138 0139 %Calculate the new order of reactions 0140 order=ones(numel(model.rxns),1); 0141 order(J)=0; 0142 order=cumsum(order); 0143 order(J)=order(end)+1:order(end)+numel(rxns); 0144 0145 %Remove the original reactions 0146 model=removeReactions(model,rxns); 0147 0148 model=addRxns(model,rxnsToChange,eqnType,compartment,allowNewMets); 0149 model=permuteModel(model,order,'rxns'); 0150 end