Merge pull request #1630 from rmtfleming/cardOptSept30

king ci test bypass for missing toolbox

external/analysis/StoichTools/molweight.m

@@ -45,6 +45,8 @@
     if isempty(ppds)
         element = @(str, atomicnumber, amu) amu;
 
+        ppds.A  = element('R group',      0,   NaN);%Added by Ronan Fleming
+
         ppds.M  = element('any metal',      0,   NaN);
         ppds.X  = element('any halogen',    0,   NaN);
 

src/analysis/topology/conservedMoieties/generateMoietyMoleculeNetwork.m

@@ -0,0 +1,74 @@
+function MMN = generateMoietyMoleculeNetwork(model,L,moietyFormulae,mbool)
+%Generate a structure to represent a network that associates moieties to molecules
+
+[nMet,~]=size(model.S);
+[nMoieties, nMappedMet] = size(L);
+
+if ~exist('mbool','var')
+    if nMet==nMappedMet
+        mbool=true(nMet,1);
+    else
+        if nMet==nMoieties
+            L=L';
+            [nMoieties, nMappedMet] = size(L);
+        else
+            error('mbool must be provided if the number of columns of L is different from the number of rows of model.S')
+        end
+    end
+else
+    if nMappedMet~=nnz(mbool)
+        if nMoieties==nnz(mbool)
+            L=L';
+            [nMoieties, nMappedMet] = size(L);
+        else
+            error('mbool must have the same number of nonzeros as the number of columns of L')
+        end
+    end
+end
+
+MMN=struct();
+
+MMN.L = L;
+
+%order of the numbers matches the order of the rows of L
+moietyID = zeros(nMoieties,1);
+for i=1:nMoieties
+    moietyID(i) = i;
+end
+
+moietyFormulae = hillformula(moietyFormulae);
+
+isotopeAbundance = 0; %use polyisotopic inexact mass i.e. uses all isotopes of each element weighted by natural abundance 
+generalFormula = 1; %NaN for unknown elements
+[moietyMasses, knownMasses, unknownElements, Ematrix, elements] = getMolecularMass(moietyFormulae,isotopeAbundance,generalFormula);
+
+NumMolecules = sum(L,2);
+
+%table of moiety properties
+MMN.moi = table(moietyID,moietyFormulae,moietyMasses,NumMolecules,'VariableNames',{'Name','Formula','Mass','NumMolecules'});
+
+if 0
+    %     Error using parse_formula>parse_formula_ (line 197)
+    %     Could not parse formula:
+    %     C30H56NO12FULLRCO
+    %     ^^^
+    molFormulae = hillformula(model.metFormulas(mbool));
+else
+    molFormulae = model.metFormulas(mbool);
+end
+
+%order of the numbers matches the order of the columns of L
+molID = zeros(nMappedMet,1);
+for i=1:nMappedMet
+    molID(i) = i;
+end
+
+[molecularMasses, knownMasses, unknownElements, Ematrix, elements] = getMolecularMass(model.metFormulas(mbool),isotopeAbundance,generalFormula);
+
+NumMoieties = sum(L,1)';
+
+%table of molecule properties
+MMN.mol = table(molID,model.mets(mbool),molFormulae,molecularMasses,NumMoieties,'VariableNames',{'Name','Mets','Formula','Mass','NumMoieties'});
+
+end
+