- initSBML(String) - Static method in class massbalance.Utilities
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Checks if there is SBML support, then validates and returns
the SBMLDocument.
- isAdjacent(Vertex, Vertex) - Method in class massbalance.MetabolicGraph
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Tests if compound c1 is adjacent to compound c2, i.e., if there is a reaction which
has c1 as a substrate and c2 as a product.
- isConnected(ArrayList<String>, ArrayList<String>, ArrayList<Boolean>) - Method in class massbalance.MetabolicGraph
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Tests whether the given compounds are connected via paths with the given
reversibilities.
- isCyclic(Vertex, boolean) - Method in class massbalance.MetabolicGraph
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Determines whether the given reaction is a cyclic reaction,
i.e., the substrates and products are identical and have equal weights.
- isDuplicate(Vertex) - Method in class massbalance.MetabolicGraph
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Returns the first found duplicate reaction.
- isHydrogen(int[]) - Static method in class massbalance.Properties
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Determines whether the given mass vector represents
hydrogen (H).
- isNeighbour(Vertex, Vertex) - Method in class massbalance.MetabolicGraph
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Tests if the two compounds are neighbours, i.e., if they are connected
by a substrate-product or product-substrate relationship.
- isPath(ArrayList<String>, boolean) - Method in class massbalance.MetabolicGraph
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Checks if the given intermediary compounds are adjacent in any compartment.
- isPhosphate(int[]) - Static method in class massbalance.Properties
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Returns the type of phosphate represented by the mass or -1, if the mass does not represent
any phosphate form.
- isReachable(Vertex, Vertex, HashSet<Vertex>) - Method in class massbalance.MetabolicGraph
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Test if compound c2 is reachable from compound c1, i.e.,
if there exists a directed path from c1 to c2.
- isReversed() - Method in class massbalance.Vertex
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Returns true, if the vertex is the reversed part of a reversible reaction, false otherwise.
- isReversible() - Method in class massbalance.MetabolicGraph
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Indicates whether the graph is reversible, i.e., for each reaction a reversed
reaction is added implicitly, which converts the products into the substrates.