Develop

.gitmodules

@@ -52,7 +52,7 @@
 	path = papers
 	url = https://github.com/opencobra/COBRA.papers.git
 	ignore = dirty
-        branch = master
+	branch = master
 [submodule "octave-networks-toolbox"]
 	path = external/analysis/octave-networks-toolbox
 	url = https://github.com/aeolianine/octave-networks-toolbox.git
@@ -77,9 +77,9 @@
 	path = external/base/io/xlread
 	url = https://github.com/tpfau/xlread
         ignore = dirty
-        branch = master
+	branch = master
 [submodule "external/visualization/MatGPT"]
 	path = external/visualization/MatGPT
 	url = https://github.com/toshiakit/MatGPT.git
         ignore = dirty
-        branch = main
+	branch = main

src/analysis/thermo/reactantContribution/waterGibbsEnergyOfFormation.m

@@ -0,0 +1,28 @@
+function dGf0=waterGibbsEnergyOfFormation(T)
+%http://webbook.nist.gov/cgi/cbook.cgi?ID=C7732185&Units=SI&Mask=2#ref-2
+A	=-203.6060;
+B	=1523.290;
+C	=-3196.413;
+D	=2474.455;
+E	=3.855326;
+F	=-256.5478;
+G	=-488.7163;
+H	=-285.8304;
+
+% t = temperature (K) / 1000.
+t=T/1000;
+
+% Cp = heat capacity (J/mol*K)
+%Cp = A + B*t + C*t2 + D*t3 + E/t2
+
+% H° = standard enthalpy (kJ/mol)
+dHf_liquid =	-285.83; % (kJ/mol)
+H = dHf_liquid + A*t + B*((t^2)/2) + C*(t^3)/3 + D*(t^4)/4 - E/t + F - H;
+
+% S° = standard entropy (J/mol*K)
+S = A*log(t) + B*t + C*(t^2)/2 + D*(t^3)/3 - E/(2*t^2) + G;
+% TS° = standard entropy (kJ/mol)
+TS = T*1000*S;
+
+dGf0 = H - TS;
+

src/analysis/topology/getCorrespondingCols.m

@@ -1,15 +1,15 @@
-function restrictedColBool = getCorrespondingCols(S, rowBool, colBool, mode)
+function restrictedColBool = getCorrespondingCols(A, rowBool, colBool, mode)
 % Returns a boolean vector that is true for a subset of the true cols in
 % `colBool` according to whether the cols 'exclusive', 'inclusive', or
 % 'partial' -ly correspond to true entries in `rowBool`
 %
 %
 % USAGE:
 %
-%    restrictedColBool = getCorrespondingCols(S, rowBool, colBool, mode)
+%    restrictedColBool = getCorrespondingCols(A, rowBool, colBool, mode)
 %
 % INPUTS:
-%    S:                    `m x n` stoichiometric matrix
+%    A:                    `m x n` matrix
 %    rowBool:              `m x 1` boolean vector
 %    colBool:              `n x 1` boolean vector
 %    mode:                 'exclusive' or 'inclusive' or 'partial'
@@ -19,7 +19,7 @@
 %
 % EXAMPLE:
 %
-%    S =
+%    A =
 %        -1     0     0     0     0
 %         2    -3     0     0     0
 %         0     4    -5     0     0
@@ -58,34 +58,34 @@
     error('colBool must be a logical vector')
 end
 
-[mlt,nlt]=size(S);
+[mlt,nlt]=size(A);
 
 if length(rowBool)~=mlt
-    error('length of rowBool must equal size(S,1)')
+    error('length of rowBool must equal size(A,1)')
 end
 
 if length(colBool)~=nlt
-    error('length of rowBool must equal size(S,2)')
+    error('length of rowBool must equal size(A,2)')
 end
 
 restrictedColBool=false(nlt,1);
 switch mode
     case 'exclusive'
         %corresponding reactions exclusively involving certain metabolites
-        restrictedColBool(colBool)=    any(S( rowBool,colBool),1)'...
-                                    & ~any(S(~rowBool,colBool),1)';
+        restrictedColBool(colBool)=    any(A( rowBool,colBool),1)'...
+                                    & ~any(A(~rowBool,colBool),1)';
     case 'inclusive'
         %corresponding reactions involving certain metabolites
-        restrictedColBool(colBool)=any(S( rowBool,colBool),1)';
+        restrictedColBool(colBool)=any(A( rowBool,colBool),1)';
 
     case 'partial'
         %metatbolites exclusively involved in certain reactions
-        restrictedColBool(colBool)=    any(S( rowBool,colBool),1)'...
-                                    & ~any(S(~rowBool,colBool),1)';
+        restrictedColBool(colBool)=    any(A( rowBool,colBool),1)'...
+                                    & ~any(A(~rowBool,colBool),1)';
 
         %corresponding reactions involving certain metabolites
         restricedColBool2=false(nlt,1);
-        restricedColBool2(colBool)=any(S( rowBool,colBool),1)';
+        restricedColBool2(colBool)=any(A( rowBool,colBool),1)';
         %difference
         restrictedColBool= restricedColBool2  & ~restrictedColBool;
     otherwise

src/analysis/topology/getCorrespondingRows.m

@@ -1,14 +1,14 @@
-function restricedRowBool = getCorrespondingRows(S, rowBool, colBool, mode)
+function restricedRowBool = getCorrespondingRows(A, rowBool, colBool, mode)
 % Returns a boolean vector that is true for a subset of the true rows in
 % `rowBool` according to whether the rows 'exclusive', 'inclusive', or
 % 'partial' -ly correspond to true entries in `colBool`
 %
 % USAGE:
 %
-%    restricedRowBool = getCorrespondingRows(S, rowBool, colBool, mode)
+%    restricedRowBool = getCorrespondingRows(A, rowBool, colBool, mode)
 %
 % INPUTS:
-%    S:                     `m x n` stoichiometric matrix
+%    A:                     `m x n` matrix
 %    rowBool:               `m x 1` boolean vector
 %    colBool:               `n x 1` boolean vector
 %    mode:                  'exclusive' , 'inclusive' or 'partial'
@@ -18,7 +18,7 @@
 %
 % EXAMPLE:
 %
-%    S =
+%    A =
 %        -1     0     0     0     0
 %         2    -3     0     0     0
 %         0     4    -5     0     0
@@ -62,33 +62,33 @@
     error('colBool must be a logical vector')
 end
 
-[mlt,nlt]=size(S);
+[mlt,nlt]=size(A);
 
 if length(rowBool)~=mlt
-    error('length of rowBool must equal size(S,1)')
+    error('length of rowBool must equal size(A,1)')
 end
 
 if length(colBool)~=nlt
-    error('length of rowBool must equal size(S,2)')
+    error('length of rowBool must equal size(A,2)')
 end
 
 restricedRowBool=false(mlt,1);
 switch mode
     case 'exclusive'
         %metatbolites exclusively involved in certain reactions
-        restricedRowBool(rowBool)=     any(S(rowBool, colBool),2)...
-                                    & ~any(S(rowBool,~colBool),2);
+        restricedRowBool(rowBool)=     any(A(rowBool, colBool),2)...
+                                    & ~any(A(rowBool,~colBool),2);
     case 'inclusive'
         %corresponding reactions involving certain metabolites
-        restricedRowBool(rowBool) = any(S(rowBool, colBool),2);
+        restricedRowBool(rowBool) = any(A(rowBool, colBool),2);
     case 'partial'
         %metatbolites exclusively involved in certain reactions
-        restricedRowBool(rowBool)=     any(S(rowBool, colBool),2)...
-                                    & ~any(S(rowBool,~colBool),2);
+        restricedRowBool(rowBool)=     any(A(rowBool, colBool),2)...
+                                    & ~any(A(rowBool,~colBool),2);
 
         %corresponding reactions involving certain metabolites
         restricedRowBool2=false(mlt,1);
-        restricedRowBool2(rowBool) = any(S(rowBool, colBool),2);
+        restricedRowBool2(rowBool) = any(A(rowBool, colBool),2);
         %difference
         restricedRowBool= restricedRowBool2  & ~restricedRowBool;
    otherwise

src/base/solvers/mosek/parseMskResult.m

@@ -212,8 +212,8 @@
                 accessSolution = 'dontAccess';
         end
     otherwise
-        accessSolution = 'dontAccess';
         origStat = -1;
+        accessSolution = 'dontAccess';
 end
 
 if strcmp(accessSolution,'dontAccess')
@@ -224,7 +224,7 @@
         case {'DUAL_INFEASIBLE_CER','MSK_SOL_STA_DUAL_INFEAS_CER','MSK_SOL_STA_NEAR_DUAL_INFEAS_CER'}
             stat=2; % Unbounded solution
             origStat = [origStat ' & ' res.rcodestr];
-        case {'UNKNOWN','PRIM_ILLPOSED_CER','PRIMAL_ILLPOSED_CER','DUAL_ILLPOSED_CER','PRIM_FEAS','DUAL_FEAS','PRIM_AND_DUAL_FEAS','DUAL_FEASIBLE'}
+        case {'UNKNOWN','PRIM_ILLPOSED_CER','PRIMAL_ILLPOSED_CER','DUAL_ILLPOSED_CER','PRIM_FEAS','DUAL_FEAS','PRIM_AND_DUAL_FEAS','DUAL_FEASIBLE','MSK_RES_ERR_IN_ARGUMENT'}
             stat=-1; %some other problem
             origStat = [origStat ' & ' res.rcodestr];
         otherwise
@@ -233,8 +233,8 @@
             fprintf('%s\n',res.rcode)
             fprintf('%s\n',res.rmsg)
             fprintf('%s\n',res.rcodestr)
-            if strcmp(origStat,'UNKNOWN')
-                origStat = [origStat ' & ' res.rcodestr];
+            if isfield(res,'rcodestr') && ~isempty(res.rcodestr)
+                origStat = res.rcodestr;
             end
     end
 end

src/base/solvers/mosek/setMosekParam.m

@@ -18,8 +18,10 @@
     % A higher level implies that more information is logged.
     switch param.printLevel
         case 0
+            param.MSK_IPAR_LOG = 0;
             echolev = 0;
         case 1
+            param.MSK_IPAR_LOG = 1;
             echolev = 3;
         case 2
             param.MSK_IPAR_WRITE_DATA_PARAM='MSK_ON';