- sbml - Static variable in class massbalance.Utilities
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- sbmlDocument - Static variable in class massbalance.Utilities
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- sbmlMessage - Static variable in class massbalance.Utilities
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- sbmlThrowable - Static variable in class massbalance.Utilities
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- scope(Set<Vertex>) - Method in class massbalance.MetabolicGraph
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Returns the scope for the given set of seed compounds.
- scope_old(HashSet<Vertex>) - Method in class massbalance.MetabolicGraph
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Deprecated.
- select(String, String, boolean) - Static method in class massbalance.Utilities
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Writes every tenth element from every line of the input file to the output file.
- setDeltaGf(Double) - Method in class massbalance.Vertex
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Sets the deltaGf of a compound.
- setEdgeWeight(DefaultWeightedEdge, double) - Method in class massbalance.MetabolicGraph
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Sets the weight for the edge.
- setName(String) - Method in class massbalance.Vertex
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- setRxnLocation(String) - Method in class massbalance.Vertex
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Sets the reaction locations This string is used by BioCyc/MetaCyc files to annotate transport reactions
and reactions within certain compartments.
- stoichiometricMatrix(String, boolean, boolean, boolean, boolean) - Method in class massbalance.MetabolicGraph
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Exports the sparse stoichiometric matrix of the graph into a tab-separated file.
- substitutability(HashMap<ArrayList<Integer>, EquivalenceClass>, String) - Method in class massbalance.MetabolicGraph
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Calculate the sample space and substitutability class sizes for individual and pair substitutions.
- successorsOf(Vertex) - Method in class massbalance.MetabolicGraph
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Returns the set containing all second successor vertices.
- summary(MetabolicGraph) - Static method in class massbalance.Utilities
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Print the summary statistics for the given graph:
- number of compounds and those containing only CHNOPS
- number of reactions, unbalanced and unannotated reactions
- reversibility of the graph, number of vertices and edges
- sizes of connected and strongly connected components
- switchRandomize(boolean) - Method in class massbalance.MetabolicGraph
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Performs switch-randomization on the graph.