Added getElementalMatrix function

opencobra · Mar 25, 2015 · 519527e · 519527e
1 parent 65b137e
commit 519527e
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Showing 2 changed files with 31 additions and 12 deletions.
diff --git a/Toolbox/Core.m b/Toolbox/Core.m
@@ -1366,21 +1366,35 @@
 Options[elementallyBalancedQ]={"ElementalComposition"->{},"RemoveExchanges"->True};
 elementallyBalancedQ::notBalanced="The following reactions are not balanced: `1`.";
 elementallyBalancedQ[model_MASSmodel,opts:OptionsPattern[]]:=Module[{balancing,exclude},
-If[OptionValue["RemoveExchanges"],
-exclude=model["Exchanges"];,
-exclude={};
-];
-balancing=Thread[Rule[model["Reactions"],Expand/@((model["Species"]/.Dispatch[updateRules[model["ElementalComposition"],OptionValue["ElementalComposition"]]]).model["Stoichiometry"])]];
-balancing=DeleteCases[balancing,r_Rule/;MemberQ[exclude,r[[1]]]];
-If[
-(Round[Total[balancing[[All,2]]]]==0.),
-True,
-Message[elementallyBalancedQ::notBalanced,SlideView[Rule@@@Cases[balancing,r_Rule/;Round[r[[2]]]=!=0],AppearanceElements->All]];False]
+	If[OptionValue["RemoveExchanges"],
+		exclude=model["Exchanges"];,
+		exclude={};
+	];
+	balancing=Thread[Rule[model["Reactions"],Expand/@((model["Species"]/.Dispatch[updateRules[model["ElementalComposition"],OptionValue["ElementalComposition"]]]).model["Stoichiometry"])]];
+	balancing=DeleteCases[balancing,r_Rule/;MemberQ[exclude,r[[1]]]];
+	If[
+		(Round[Total[balancing[[All,2]]]]==0.),
+		True,
+		Message[elementallyBalancedQ::notBalanced,SlideView[Rule@@@Cases[balancing,r_Rule/;Round[r[[2]]]=!=0],AppearanceElements->All]];
+			False
+	]
 ];
 
 
 
 
+Options[getElementalMatrix]={"TableForm"->True};
+getElementalMatrix[model_MASSmodel,opts:OptionsPattern[]]:=Module[{elemList,elements,matrix},
+	elemList=List/@(model["Species"]/.model["ElementalComposition"])/.Plus->Sequence;
+	elements=DeleteDuplicates@Flatten[elemList/._?NumericQ->1];
+	matrix=Flatten/@Table[Cases[#,(x_*elem|elem)]&/@elemList/.{}->{0},{elem,elements}]/._String->1;
+	If[OptionValue[TableForm]==True,
+		Framed@TableForm[matrix,TableHeadings->{elements,model["Species"]}],
+		{elements,matrix}
+	]
+];
+
+
 (*Gevorgyan,A.,Poolman,M.G.,& Fell,D.A.(2008).Detection of stoichiometric inconsistencies in biomolecular models Bioinformatics (Oxford,England),24(19),2245\[Dash]2251. doi:10.1093/bioinformatics/btn425*)
 
 Options[stoichiometricallyConsistentQ]={"Solver"->LinearProgramming};

diff --git a/Toolbox/UsageStrings.m b/Toolbox/UsageStrings.m
@@ -4,7 +4,7 @@
 (*Usage strings*)
 
 
-(* ::Subsection:: *)
+(* ::Subsection::Closed:: *)
 (*Options*)
 
 
@@ -368,7 +368,7 @@
 subModel::usage="subModel[model, {rxn1, rxn2, ...}] will extract a sub-model consisting of the specified reactions.";
 
 
-(* ::Subsection::Closed:: *)
+(* ::Subsection:: *)
 (*QC/QA*)
 
 
@@ -378,9 +378,14 @@
 elementallyBalancedQ::usage="Checks if provided model is elementally balanced.";
 
 
+getElementalMatrix::usage="getElementalMatrix[model] displays a formatted elemental matrix for the model. Use TableForm->False for the raw matrix.";
+
+
 stoichiometricallyConsistentQ::usage="Checks the stochiometric consistency of provide matrix or model (see Gevorgyan, A., Poolman, M. G., & Fell, D. A. (2008). Detection of stoichiometric inconsistencies in biomolecular models Bioinformatics (Oxford, England), 24(19), 2245\[Dash]2251. doi:10.1093/bioinformatics/btn425).";
 
 
+
+
 (* ::Subsection::Closed:: *)
 (*Chemoinformatics*)