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Packages that use ChemRxn | |
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sbrt.kernel.fba | Provides classes and interfaces for creating objects relevant to Flux Balance Analysis. |
sbrt.kernel.fba.proc | Provides classes and interfaces for executing Flux Balance Analysis processes. |
sbrt.shell.mng.fba | Provides classes and interfaces for creating Flux Balance Analysis process managers. |
sbrt.shell.proc.fba | Provides classes for converting FBA-related files of different formats. |
sbrt.shell.text.fba | Provides classes and interfaces for defining formats for objects relevant to Flux Balance Analysis. |
Uses of ChemRxn in sbrt.kernel.fba |
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Subinterfaces of ChemRxn in sbrt.kernel.fba | |
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interface |
ExchangeRxn
This interface is used to represent exchange reactions. |
Classes in sbrt.kernel.fba that implement ChemRxn | |
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class |
AbstractExchangeRxn
This class is a skeleton implementation of ExchangeRxn . |
class |
AbstractRxn
This class is a skeleton implementation of ChemicalRxn. |
class |
IrrevRxn
This class is used to represent irreversible chemical reactions. |
class |
RevExchRxn
This class is used to represent reversible exchange reactions, that is, exchange reactions that can both supply and consume chemical species to and from a chemical system. |
class |
RevRxn
This class is used to represent reversible chemical reactions. |
class |
SinkRxn
This class is used to represent exchange reactions that transport chemicals from a chemical system to its surroundings. |
class |
SourceRxn
This class is used to represent exchange reactions that transport chemicals to a chemical system from its surroundings. |
Methods in sbrt.kernel.fba that return ChemRxn | |
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ChemRxn |
MixedFluxomeV1.getInternalRxn(java.lang.String reactionName)
Returns the internal reaction in this fluxome with the provided name. |
ChemRxn |
MixedFluxome.getInternalRxn(java.lang.String rxnName)
Returns the internal reaction in this fluxome with the provided name. |
ChemRxn |
MixedFluxomeV1.getRxn(java.lang.String reactionName)
Returns the chemical reaction in this fluxome with the provided name. |
ChemRxn |
Fluxome.getRxn(java.lang.String reactionName)
Returns the chemical reaction in this fluxome with the provided name. |
ChemRxn |
IrrevRxnFluxomeV1.getRxn(java.lang.String reactionName)
Returns the chemical reaction in this fluxome with the provided name. |
Methods in sbrt.kernel.fba that return types with arguments of type ChemRxn | |
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java.util.Map<java.lang.String,ChemRxn> |
MixedFluxomeV1.getCatalyzedRxns(java.lang.String catalyst)
Returns all of the internal reactions contained in this fluxome that are catalyzed by the provided catalyst. |
java.util.Map<java.lang.String,? extends ChemRxn> |
CatalyzedFluxome.getCatalyzedRxns(java.lang.String catalyst)
Returns the chemical reactions contained in this fluxome that are catalyzed by the provided catalyst. |
java.util.Map<java.lang.String,ChemRxn> |
MixedFluxomeV1.getInternalRxns()
Returns all of the internal reactions in this fluxome. |
java.util.Map<java.lang.String,? extends ChemRxn> |
Fluxome.getInternalRxns()
Returns the set of all internal chemical reactions contained in this fluxome. |
java.util.Map<java.lang.String,ChemRxn> |
MixedFluxome.getInternalRxns()
Returns all of the internal reactions in this fluxome. |
java.util.Map<java.lang.String,ChemRxn> |
MixedFluxomeV1.getInternalRxns(java.util.Collection<java.lang.String> rxnNames)
Returns the internal reactions whose names appear in the provided collection of reaction names. |
java.util.Map<java.lang.String,ChemRxn> |
MixedFluxome.getInternalRxns(java.util.Collection<java.lang.String> rxnNames)
Returns the internal reactions with the provided names. |
java.util.Map<java.lang.String,ChemRxn> |
MixedFluxomeV1.getRxns()
Returns all chemical reactions contained in this fluxome. |
java.util.Map<java.lang.String,ChemRxn> |
Fluxome.getRxns()
Returns the set of all chemical reactions contained in this fluxome. |
java.util.Map<java.lang.String,ChemRxn> |
IrrevRxnFluxomeV1.getRxns()
Returns all chemical reactions contained in this fluxome. |
java.util.Map<java.lang.String,ChemRxn> |
MixedFluxomeV1.getRxns(java.util.Collection<java.lang.String> rxnNames)
Returns the chemical reactions with the provided names. |
java.util.Map<java.lang.String,ChemRxn> |
Fluxome.getRxns(java.util.Collection<java.lang.String> rxnNames)
Returns the chemical reactions with the provided names. |
java.util.Map<java.lang.String,ChemRxn> |
IrrevRxnFluxomeV1.getRxns(java.util.Collection<java.lang.String> rxnNames)
Returns the chemical reactions with the provided names. |
Methods in sbrt.kernel.fba with parameters of type ChemRxn | |
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static boolean |
RxnComparer.equivChemRxns(ChemRxn rxn1,
ChemRxn rxn2)
Indicates if the provided chemical reactions are stoichiometrically equivalent. |
static boolean |
RxnComparer.reverseChemRxns(ChemRxn rxn1,
ChemRxn rxn2)
Indicates if the provided chemical reactions are the reverse of each other. |
Constructor parameters in sbrt.kernel.fba with type arguments of type ChemRxn | |
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IrrevRxnFluxomeV1(java.util.Map<java.lang.String,? extends ChemRxn> rxns)
Constructs a new irreversible reaction fluxome from the provided internal and exchange reactions. |
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IrrevRxnFluxomeV1(java.util.Map<java.lang.String,? extends ChemRxn> rxns,
java.util.Map<java.lang.String,Or<And<java.lang.String>>> catalysts)
Constructs a new irreversible reaction fluxome from the provided internal and exchange reactions and catalysts. |
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MixedFluxomeV1(java.util.Map<java.lang.String,? extends ChemRxn> rxns)
Constructs a new mixed fluxome from the provided internal and exchange reactions. |
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MixedFluxomeV1(java.util.Map<java.lang.String,? extends ChemRxn> rxns,
java.util.Map<java.lang.String,Or<And<java.lang.String>>> catalysts)
Constructs a new mixed fluxome from the provided internal and exchange reactions and catalysts. |
Uses of ChemRxn in sbrt.kernel.fba.proc |
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Methods in sbrt.kernel.fba.proc that return types with arguments of type ChemRxn | |
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java.util.Map<java.lang.String,ChemRxn> |
RevRxnBreakerProcess.breakRxns(java.util.Map<java.lang.String,ChemRxn> rxns)
Breaks reversible reactions into pairs of irreversible reactions. |
Method parameters in sbrt.kernel.fba.proc with type arguments of type ChemRxn | |
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java.util.Map<java.lang.String,ChemRxn> |
RevRxnBreakerProcess.breakRxns(java.util.Map<java.lang.String,ChemRxn> rxns)
Breaks reversible reactions into pairs of irreversible reactions. |
void |
RevRxnBreakerProcess.run(ResultsManager<java.util.Map<java.lang.String,ChemRxn>> resultsManager)
Breaks the reversible reactions supplied to this process and adds the result to the provided manager. |
void |
RevRxnBreakerProcess.setRxns(java.util.Map<java.lang.String,? extends ChemRxn> rxns)
Sets the reactions for which reversible reactions will be broken. |
Uses of ChemRxn in sbrt.shell.mng.fba |
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Methods in sbrt.shell.mng.fba that return types with arguments of type ChemRxn | |
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static RomoFile<java.lang.String,ChemRxn> |
WwFluxomeReducerManager.getOutputFile(java.lang.String fileName)
Returns a file to which the chemical reactions of a fluxome can be written. |
static RomoFile<java.lang.String,ChemRxn> |
WwFluxomeReducerManager.getOutputFile(java.lang.String fileName,
java.io.PrintWriter out)
Returns a file to which the chemical reactions of a fluxome can be written. |
Uses of ChemRxn in sbrt.shell.proc.fba |
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Methods in sbrt.shell.proc.fba that return types with arguments of type ChemRxn | |
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java.util.Map<java.lang.String,ChemRxn> |
MetatoolInputReader.Results.getCat()
Returns the reactions that are listed in the -CAT
section of the input file. |
Uses of ChemRxn in sbrt.shell.text.fba |
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Methods in sbrt.shell.text.fba that return ChemRxn | |
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ChemRxn |
RevRxnFormatV1.parse(java.lang.String reaction)
Parses the provided string and returns its corresponding chemical reaction. |
ChemRxn |
RxnFormatV1.parse(java.lang.String reaction)
Parses the provided string and returns its corresponding chemical reaction. |
ChemRxn |
IrrevRxnFormatV2.parse(java.lang.String reaction)
Parses the provided string and returns its corresponding chemical reaction. |
ChemRxn |
RevRxnFormatV2.parse(java.lang.String reaction)
Parses the provided string and returns its corresponding chemical reaction. |
ChemRxn |
IrrevRxnFormatV1.parse(java.lang.String reaction)
Parses the provided string and returns its corresponding chemical reaction. |
Methods in sbrt.shell.text.fba that return types with arguments of type ChemRxn | |
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PipeListFormat<ChemRxn> |
IrfFormatV1.getListFormat()
Returns the format used for lists of reactions. |
PipeListFormat<ChemRxn> |
MixedFluxomeFormatV1.getListFormat()
Returns the format used for lists of reactions. |
Methods in sbrt.shell.text.fba with parameters of type ChemRxn | |
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java.lang.String |
RevRxnFormatV1.format(ChemRxn rxn)
Returns a formatted string representation of the provided irreversible chemical reaction. |
java.lang.String |
RxnFormatV1.format(ChemRxn rxn)
Returns a formatted string representation of the provided irreversible chemical reaction. |
java.lang.String |
IrrevRxnFormatV2.format(ChemRxn rxn)
Returns a formatted string representation of the provided irreversible chemical reaction. |
java.lang.String |
RevRxnFormatV2.format(ChemRxn rxn)
Returns a formatted string representation of the provided irreversible chemical reaction. |
java.lang.String |
IrrevRxnFormatV1.format(ChemRxn rxn)
Returns a formatted string representation of the provided irreversible chemical reaction. |
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