Index

A

addAssociation() (cbmpy.CBModel.GeneProteinAssociation method) (cbmpy.CBModel.Parameter method) addCompartment() (cbmpy.CBModel.Model method) addFluxAsActiveObjective() (in module cbmpy.CBTools) addFluxBound() (cbmpy.CBModel.Model method) addFluxObjective() (cbmpy.CBModel.Objective method) addGene() (cbmpy.CBModel.Model method) addGeneref() (cbmpy.CBModel.GeneProteinAssociation method) addGenesFromAnnotations() (in module cbmpy.CBTools) addGPRAssociation() (cbmpy.CBModel.Model method) addGroup() (cbmpy.CBModel.Model method) addIDorgURI() (cbmpy.CBDataStruct.MIRIAMannotation method) addMember() (cbmpy.CBModel.Group method) addMIRIAMannotation() (cbmpy.CBDataStruct.MIRIAMannotation method) (cbmpy.CBModel.Fbase method) (cbmpy.CBModel.Model method) addMIRIAMuri() (cbmpy.CBModel.Fbase method) addModelCreator() (cbmpy.CBModel.Model method) addObjective() (cbmpy.CBModel.Model method) addParameter() (cbmpy.CBModel.Model method)

addReaction() (cbmpy.CBModel.Model method) addReagent() (cbmpy.CBModel.Reaction method) addSharedMIRIAMannotation() (cbmpy.CBModel.Group method) addSinkReaction() (in module cbmpy.CBTools) addSourceReaction() (in module cbmpy.CBTools) addSpecies() (cbmpy.CBModel.Model method) addStoichToFBAModel() (in module cbmpy.CBTools) addUserConstraint() (cbmpy.CBModel.Model method) AnalyseK() (cbmpy.PyscesStoich.Stoich method) AnalyseL() (cbmpy.PyscesStoich.Stoich method) assertRank2() (cbmpy.PyscesStoich.MathArrayFunc method) assignAllSharedPropertiesToMembers() (cbmpy.CBModel.Group method) assignSharedAnnotationToMembers() (cbmpy.CBModel.Group method) assignSharedMIRIAMannotationToMembers() (cbmpy.CBModel.Group method) assignSharedNotesToMembers() (cbmpy.CBModel.Group method) assignSharedSBOtermsToMembers() (cbmpy.CBModel.Group method)

B

BackSubstitution() (cbmpy.PyscesStoich.Stoich method) buildEvalFunc() (cbmpy.CBModel.GeneProteinAssociation method) BuildHformatFluxBounds() (in module cbmpy.CBWrite) BuildLPConstraints() (in module cbmpy.CBWrite) BuildLPConstraintsMath() (in module cbmpy.CBWrite)

BuildLPConstraintsRelaxed() (in module cbmpy.CBWrite) BuildLPConstraintsStrict() (in module cbmpy.CBWrite) BuildLPFluxBounds() (in module cbmpy.CBWrite) BuildLPUserConstraints() (in module cbmpy.CBWrite) buildStoichMatrix() (cbmpy.CBModel.Model method)

C

castCopyAndTranspose() (cbmpy.PyscesStoich.MathArrayFunc method) cbmpy._multicoreenvfva (module) cbmpy._multicorefva (module) cbmpy.CBCommon (module) cbmpy.CBConfig (module) cbmpy.CBCPLEX (module) cbmpy.CBDataStruct (module) cbmpy.CBGLPK (module) cbmpy.CBGUI (module) cbmpy.CBModel (module) cbmpy.CBModelTools (module) cbmpy.CBMultiCore (module) cbmpy.CBMultiEnv (module) cbmpy.CBNetDB (module) cbmpy.CBPlot (module) cbmpy.CBQt4 (module) cbmpy.CBRead (module) cbmpy.CBReadtxt (module) cbmpy.CBSolver (module) cbmpy.CBTools (module) cbmpy.CBWrite (module) cbmpy.CBWx (module) cbmpy.CBXML (module) cbmpy.miriamids (module) cbmpy.PyscesStoich (module) changeAllFluxBoundsWithValue() (cbmpy.CBModel.Model method) changeId() (cbmpy.CBModel.Reaction method) checkChemFormula() (in module cbmpy.CBCommon) checkEntity() (cbmpy.CBDataStruct.MIRIAMannotation method) checkEntityPattern() (cbmpy.CBDataStruct.MIRIAMannotation method) checkEntryInColumn() (cbmpy.CBNetDB.DBTools method) checkExchangeReactions() (in module cbmpy.CBTools) checkFluxBoundConsistency() (in module cbmpy.CBTools) checkId() (cbmpy.CBDataStruct.MIRIAMannotation method) (in module cbmpy.CBCommon) checkIds() (in module cbmpy.CBTools) checkProducibility() (in module cbmpy.CBTools) checkProducibilityMetabolites() (in module cbmpy.CBTools) checkProducibilityReactions() (in module cbmpy.CBTools) checkReactionBalanceElemental() (in module cbmpy.CBTools) checkSuffixes() (in module cbmpy.CBTools) circlePoints() (in module cbmpy.CBWx) clone() (cbmpy.CBModel.Fbase method) (cbmpy.CBModel.Group method) (cbmpy.CBModel.Model method) Close() (cbmpy.CBNetDB.RESTClient method) closeDB() (cbmpy.CBNetDB.DBTools method) ComboGen (class in cbmpy.CBCommon) commonType() (cbmpy.PyscesStoich.MathArrayFunc method) Compartment (class in cbmpy.CBModel) Connect() (cbmpy.CBNetDB.RESTClient method) connectSQLiteDB() (cbmpy.CBNetDB.DBTools method) containsReactions() (cbmpy.CBModel.Compartment method) containsSpecies() (cbmpy.CBModel.Compartment method) convertExcelToFloat() (in module cbmpy.CBWrite)

convertFloatToExcel() (in module cbmpy.CBWrite) cplx_analyzeModel() (in module cbmpy.CBCPLEX) cplx_constructLPfromFBA() (in module cbmpy.CBCPLEX) cplx_fixConSense() (in module cbmpy.CBCPLEX) cplx_FluxVariabilityAnalysis() (in module cbmpy.CBCPLEX) cplx_func_GetCPXandPresolve() (in module cbmpy.CBCPLEX) cplx_func_SetObjectiveFunctionAsConstraint() (in module cbmpy.CBCPLEX) cplx_getCPLEXModelFromLP() (in module cbmpy.CBCPLEX) cplx_getDualValues() (in module cbmpy.CBCPLEX) cplx_getModelFromLP() (in module cbmpy.CBCPLEX) cplx_getModelFromObj() (in module cbmpy.CBCPLEX) cplx_getOptimalSolution() (in module cbmpy.CBCPLEX) cplx_getOptimalSolution2() (in module cbmpy.CBCPLEX) cplx_getReducedCosts() (in module cbmpy.CBCPLEX) cplx_getSensitivities() (in module cbmpy.CBCPLEX) cplx_getShadowPrices() (in module cbmpy.CBCPLEX) cplx_getSolutionStatus() (in module cbmpy.CBCPLEX) cplx_MinimizeNumActiveFluxes() (in module cbmpy.CBCPLEX) cplx_MinimizeSumOfAbsFluxes() (in module cbmpy.CBCPLEX) cplx_MultiFluxVariabilityAnalysis() (in module cbmpy.CBCPLEX) cplx_runInputScan() (in module cbmpy.CBCPLEX) cplx_setFBAsolutionToModel() (in module cbmpy.CBCPLEX) cplx_setMIPGapTolerance() (in module cbmpy.CBCPLEX) cplx_setObjective() (in module cbmpy.CBCPLEX) cplx_setObjective2() (in module cbmpy.CBCPLEX) cplx_setOutputStreams() (in module cbmpy.CBCPLEX) cplx_setSolutionStatusToModel() (in module cbmpy.CBCPLEX) cplx_singleGeneScan() (in module cbmpy.CBCPLEX) cplx_SolveMILP() (in module cbmpy.CBCPLEX) cplx_WriteFVAtoCSV() (in module cbmpy.CBCPLEX) cplx_writeLPsolution() (in module cbmpy.CBCPLEX) cplx_writeLPtoLPTfile() (in module cbmpy.CBCPLEX) createAssociationAndGeneRefs() (cbmpy.CBModel.GeneProteinAssociation method) createCompartment() (cbmpy.CBModel.Model method) createDBTable() (cbmpy.CBNetDB.DBTools method) createFluxObjectives() (cbmpy.CBModel.Objective method) createGeneAssociationsFromAnnotations() (cbmpy.CBModel.Model method) createGeneProteinAssociation() (cbmpy.CBModel.Model method) createGroup() (cbmpy.CBModel.Model method) createObjectiveFunction() (cbmpy.CBModel.Model method) createReaction() (cbmpy.CBModel.Model method) (in module cbmpy.CBQt4) createReactionBounds() (cbmpy.CBModel.Model method) createReactionLowerBound() (cbmpy.CBModel.Model method) createReactionReagent() (cbmpy.CBModel.Model method) createReactionUpperBound() (cbmpy.CBModel.Model method) createReagent() (cbmpy.CBModel.Reaction method) createSingleGeneEffectMap() (cbmpy.CBModel.Model method) createSpecies() (cbmpy.CBModel.Model method) createTempFileName() (in module cbmpy.CBTools) createZipArchive() (in module cbmpy.CBTools) current_version() (in module cbmpy.CBConfig) current_version_tuple() (in module cbmpy.CBConfig)

D

DBTools (class in cbmpy.CBNetDB) deactivateReaction() (cbmpy.CBModel.Reaction method) deleteAllFluxBoundsWithValue() (cbmpy.CBModel.Model method) deleteAllFluxObjectives() (cbmpy.CBModel.Objective method) deleteAnnotation() (cbmpy.CBModel.Fbase method) deleteAssociation() (cbmpy.CBModel.Parameter method) deleteBoundsForReactionId() (cbmpy.CBModel.Model method) deleteGeneref() (cbmpy.CBModel.GeneProteinAssociation method) deleteGroup() (cbmpy.CBModel.Model method) deleteMember() (cbmpy.CBModel.Group method)

deleteMIRIAMannotation() (cbmpy.CBDataStruct.MIRIAMannotation method) (cbmpy.CBModel.Fbase method) deleteNonReactingSpecies() (cbmpy.CBModel.Model method) deleteObjective() (cbmpy.CBModel.Model method) deleteReactionAndBounds() (cbmpy.CBModel.Model method) deleteReagentWithSpeciesRef() (cbmpy.CBModel.Reaction method) deleteSpecies() (cbmpy.CBModel.Model method) deSerialize() (in module cbmpy.CBTools) deSerializeFromDisk() (in module cbmpy.CBTools) dumpTableToCSV() (cbmpy.CBNetDB.DBTools method) dumpTableToTxt() (cbmpy.CBNetDB.DBTools method)

E

emptyUndelete() (cbmpy.CBModel.Model method) evalAssociation() (cbmpy.CBModel.GeneProteinAssociation method) executeSQL() (cbmpy.CBNetDB.DBTools method) exportArray2CSV() (in module cbmpy.CBTools) exportArray2TXT() (in module cbmpy.CBTools) exportFVAdata() (cbmpy.CBModel.Model method) exportLabelledArray() (in module cbmpy.CBTools) exportLabelledArray2CSV() (in module cbmpy.CBTools)

exportLabelledArray2TXT() (in module cbmpy.CBTools) exportLabelledArrayWithHeader() (in module cbmpy.CBTools) exportLabelledArrayWithHeader2CSV() (in module cbmpy.CBTools) exportLabelledArrayWithHeader2TXT() (in module cbmpy.CBTools) exportLabelledLinkedList() (in module cbmpy.CBTools) exportModel() (in module cbmpy.CBWrite) extractGeneIdsFromString() (in module cbmpy.CBCommon)

F

Fbase (class in cbmpy.CBModel) fetchAll() (cbmpy.CBNetDB.DBTools method) fetchSeqfromKeGG() (cbmpy.CBNetDB.KeGGTools method) findDeadEndMetabolites() (in module cbmpy.CBTools) findDeadEndReactions() (in module cbmpy.CBTools)

findFluxesForConnectedSpecies() (cbmpy.CBModel.Model method) fixId() (in module cbmpy.CBCommon) fixReversibility() (in module cbmpy.CBTools) FluxBound (class in cbmpy.CBModel) FluxObjective (class in cbmpy.CBModel)

G

Gene (class in cbmpy.CBModel) GeneProteinAssociation (class in cbmpy.CBModel) generateBGID() (in module cbmpy.CBWrite) Get() (cbmpy.CBNetDB.RESTClient method) getActiveGenes() (cbmpy.CBModel.GeneProteinAssociation method) getActiveObjective() (cbmpy.CBModel.Model method) getActiveObjectiveReactionIds() (cbmpy.CBModel.Model method) getActiveObjectiveStoichiometry() (cbmpy.CBModel.Model method) getAllFluxBounds() (cbmpy.CBModel.Model method) getAllGeneActivities() (cbmpy.CBModel.Model method) getAllGeneProteinAssociations() (cbmpy.CBModel.Model method) getAllMIRIAMUris() (cbmpy.CBDataStruct.MIRIAMannotation method) getAllProteinActivities() (cbmpy.CBModel.Model method) getAllProteinGeneAssociations() (cbmpy.CBModel.Model method) getAndViewUrisForQualifier() (cbmpy.CBDataStruct.MIRIAMannotation method) getAnnotation() (cbmpy.CBModel.Fbase method) getAnnotations() (cbmpy.CBModel.Fbase method) getAssociations() (cbmpy.CBModel.Parameter method) getAssociationStr() (cbmpy.CBModel.GeneProteinAssociation method) getBoundarySpeciesIds() (cbmpy.CBModel.Model method) getBoundsDict() (in module cbmpy.CBTools) getCell() (cbmpy.CBNetDB.DBTools method) getCharge() (cbmpy.CBModel.Species method) getChemFormula() (cbmpy.CBModel.Species method) getCoefficient() (cbmpy.CBModel.Reagent method) getColsByIdx() (cbmpy.CBDataStruct.StructMatrix method) (cbmpy.PyscesStoich.StructMatrix method) getColsByName() (cbmpy.CBDataStruct.StructMatrix method) (cbmpy.PyscesStoich.StructMatrix method) getColumns() (cbmpy.CBNetDB.DBTools method) getCompartment() (cbmpy.CBModel.Model method) getCompartmentId() (cbmpy.CBModel.Fbase method) getCompartmentIds() (cbmpy.CBModel.Model method) getCopy() (cbmpy.CBDataStruct.StructMatrixLP method) getDescription() (cbmpy.CBModel.Model method) getDimensions() (cbmpy.CBModel.Compartment method) getEquation() (cbmpy.CBModel.Reaction method) getExchangeReactionIds() (cbmpy.CBModel.Model method) getExchangeReactions() (cbmpy.CBModel.Model method) getExchBoundsDict() (in module cbmpy.CBTools) getFluxBoundByID() (cbmpy.CBModel.Model method) getFluxBoundByReactionID() (cbmpy.CBModel.Model method) getFluxBoundIds() (cbmpy.CBModel.Model method) getFluxBoundsByReactionID() (cbmpy.CBModel.Model method) getFluxesAssociatedWithSpecies() (cbmpy.CBModel.Model method) getFluxObjective() (cbmpy.CBModel.Objective method) getFluxObjectiveData() (cbmpy.CBModel.Objective method) getFluxObjectiveForReaction() (cbmpy.CBModel.Objective method) getFluxObjectiveIDs() (cbmpy.CBModel.Objective method) getFluxObjectiveReactions() (cbmpy.CBModel.Objective method) getFluxObjectives() (cbmpy.CBModel.Objective method) getFVAdata() (cbmpy.CBModel.Reaction method) getGene() (cbmpy.CBModel.GeneProteinAssociation method) (cbmpy.CBModel.Model method) getGeneByLabel() (cbmpy.CBModel.Model method) getGeneIdFromLabel() (cbmpy.CBModel.Model method) getGeneIds() (cbmpy.CBModel.GeneProteinAssociation method) (cbmpy.CBModel.Model method) getGeneLabels() (cbmpy.CBModel.GeneProteinAssociation method) (cbmpy.CBModel.Model method) getGenes() (cbmpy.CBModel.GeneProteinAssociation method) getGPRassociation() (cbmpy.CBModel.Model method) getGPRforReaction() (cbmpy.CBModel.Model method) getGroup() (cbmpy.CBModel.Model method) getGroupIds() (cbmpy.CBModel.Model method) getId() (cbmpy.CBModel.Fbase method) getIndexes() (cbmpy.CBDataStruct.StructMatrix method) (cbmpy.PyscesStoich.StructMatrix method) getIrreversibleReactionIds() (cbmpy.CBModel.Model method) getKind() (cbmpy.CBModel.Group method) getLabel() (cbmpy.CBModel.Gene method) getLabels() (cbmpy.CBDataStruct.StructMatrix method) (cbmpy.PyscesStoich.StructMatrix method) GetLog() (cbmpy.CBNetDB.RESTClient method) getLowerBound() (cbmpy.CBModel.Reaction method) getMemberIDs() (cbmpy.CBModel.Group method) getMembers() (cbmpy.CBModel.Group method) getMetaId() (cbmpy.CBModel.Fbase method)

getMIRIAMannotations() (cbmpy.CBModel.Fbase method) getMIRIAMUrisForQualifier() (cbmpy.CBDataStruct.MIRIAMannotation method) getModelCreators() (cbmpy.CBModel.Model method) getModelGenesPerReaction() (in module cbmpy.CBTools) getName() (cbmpy.CBModel.Fbase method) getNotes() (cbmpy.CBModel.Fbase method) getObjectiveIds() (cbmpy.CBModel.Model method) getObjFuncValue() (cbmpy.CBModel.Model method) getOperation() (cbmpy.CBModel.Objective method) getParameter() (cbmpy.CBModel.Model method) getPid() (cbmpy.CBModel.Fbase method) getProductIds() (cbmpy.CBModel.Reaction method) getProtein() (cbmpy.CBModel.GeneProteinAssociation method) getReaByMetSuf() (in module cbmpy.CBTools) getReaction() (cbmpy.CBModel.Model method) getReactionActivity() (cbmpy.CBModel.Model method) getReactionBounds() (cbmpy.CBModel.Model method) getReactionIds() (cbmpy.CBModel.Model method) getReactionIdsAssociatedWithSpecies() (cbmpy.CBModel.Model method) getReactionLowerBound() (cbmpy.CBModel.Model method) getReactionNames() (cbmpy.CBModel.Model method) getReactionUpperBound() (cbmpy.CBModel.Model method) getReactionValues() (cbmpy.CBModel.Model method) getReagent() (cbmpy.CBModel.Reaction method) getReagentObjIds() (cbmpy.CBModel.Reaction method) getReagentOf() (cbmpy.CBModel.Species method) getReagentRefs() (cbmpy.CBModel.Reaction method) getReagentWithSpeciesRef() (cbmpy.CBModel.Reaction method) getReducedCosts() (in module cbmpy.CBCPLEX) (in module cbmpy.CBGLPK) getReversibleReactionIds() (cbmpy.CBModel.Model method) getRole() (cbmpy.CBModel.Reagent method) getRow() (cbmpy.CBNetDB.DBTools method) getRowsByIdx() (cbmpy.CBDataStruct.StructMatrix method) (cbmpy.PyscesStoich.StructMatrix method) getRowsByName() (cbmpy.CBDataStruct.StructMatrix method) (cbmpy.PyscesStoich.StructMatrix method) getSBOterm() (cbmpy.CBModel.Fbase method) getSharedAnnotations() (cbmpy.CBModel.Group method) getSharedMIRIAMannotations() (cbmpy.CBModel.Group method) getSharedNotes() (cbmpy.CBModel.Group method) getSharedSBOterm() (cbmpy.CBModel.Group method) getSize() (cbmpy.CBModel.Compartment method) getSolutionVector() (cbmpy.CBModel.Model method) getSpecies() (cbmpy.CBModel.Model method) (cbmpy.CBModel.Reagent method) getSpeciesIds() (cbmpy.CBModel.Model method) (cbmpy.CBModel.Reaction method) getSpeciesObj() (cbmpy.CBModel.Reaction method) getStoichiometry() (cbmpy.CBModel.Reaction method) getSubstrateIds() (cbmpy.CBModel.Reaction method) getTable() (cbmpy.CBNetDB.DBTools method) getType() (cbmpy.CBModel.FluxBound method) getUpperBound() (cbmpy.CBModel.Reaction method) GetUpperMatrix() (cbmpy.PyscesStoich.Stoich method) GetUpperMatrixUsingQR() (cbmpy.PyscesStoich.Stoich method) getValue() (cbmpy.CBModel.FluxBound method) (cbmpy.CBModel.Objective method) (cbmpy.CBModel.Parameter method) (cbmpy.CBModel.Reaction method) (cbmpy.CBModel.Species method) glpk_analyzeModel() (in module cbmpy.CBGLPK) glpk_constructLPfromFBA() (in module cbmpy.CBGLPK) glpk_FluxVariabilityAnalysis() (in module cbmpy.CBGLPK) glpk_func_GetCPXandPresolve() (in module cbmpy.CBGLPK) glpk_func_SetObjectiveFunctionAsConstraint() (in module cbmpy.CBGLPK) glpk_getOptimalSolution() (in module cbmpy.CBGLPK) glpk_getReducedCosts() (in module cbmpy.CBGLPK) glpk_getSolutionStatus() (in module cbmpy.CBGLPK) glpk_MinimizeSumOfAbsFluxes() (in module cbmpy.CBGLPK) glpk_setFBAsolutionToModel() (in module cbmpy.CBGLPK) glpk_setObjective() (in module cbmpy.CBGLPK) glpk_setSingleConstraint() (in module cbmpy.CBGLPK) glpk_setSolutionStatusToModel() (in module cbmpy.CBGLPK) glpk_Solve() (in module cbmpy.CBGLPK) glpk_writeLPtoLPTfile() (in module cbmpy.CBGLPK) Group (class in cbmpy.CBModel) grouper() (in module cbmpy.CBMultiCore) GroupMemberAttributes (class in cbmpy.CBModel)

H

hasAnnotation() (cbmpy.CBModel.Fbase method)

HtmlWindowMod (class in cbmpy.CBWx)

I

insertData() (cbmpy.CBNetDB.DBTools method) isActive() (cbmpy.CBModel.Gene method)

isProteinActive() (cbmpy.CBModel.GeneProteinAssociation method) isReagentOf() (cbmpy.CBModel.Species method)

K

K_split_R() (cbmpy.PyscesStoich.Stoich method) KeGGSequenceTools (class in cbmpy.CBNetDB)

KeGGTools (class in cbmpy.CBNetDB)

L

L_split_R() (cbmpy.PyscesStoich.Stoich method) loadCBGUI() (in module cbmpy.CBGUI)

loadObj() (in module cbmpy.CBTools) Log() (cbmpy.CBNetDB.RESTClient method)

M

MathArrayFunc (class in cbmpy.PyscesStoich) MatrixFloatFix() (cbmpy.PyscesStoich.MathArrayFunc method) MatrixValueCompare() (cbmpy.PyscesStoich.MathArrayFunc method) merge2Models() (in module cbmpy.CBTools)

MIRIAMannotation (class in cbmpy.CBDataStruct) MIRIAMTools (class in cbmpy.CBNetDB) MLStripper (class in cbmpy.CBXML) Model (class in cbmpy.CBModel)

O

Objective (class in cbmpy.CBModel)

P

Parameter (class in cbmpy.CBModel) parseGeneAssociation() (in module cbmpy.CBCommon) parseXMLtoText() (cbmpy.CBNetDB.SemanticSBML method) PivotSort() (cbmpy.PyscesStoich.Stoich method) PivotSort_initial() (cbmpy.PyscesStoich.Stoich method) plotFluxVariability() (in module cbmpy.CBPlot) PLUfactorize() (cbmpy.PyscesStoich.Stoich method)

printFBASolution() (in module cbmpy.CBWrite) processBiGGannotationNote() (in module cbmpy.CBTools) processBiGGchemFormula() (in module cbmpy.CBTools) processExchangeReactions() (in module cbmpy.CBTools) processSBMLAnnotationNotes() (in module cbmpy.CBTools) processSpeciesChargeChemFormulaAnnot() (in module cbmpy.CBCommon)

Q

quickLookup() (cbmpy.CBNetDB.SemanticSBML method)

R

Reaction (class in cbmpy.CBModel) reactivateReaction() (cbmpy.CBModel.Reaction method) readCOBRASBML() (in module cbmpy.CBRead) readCSV() (in module cbmpy.CBReadtxt) readExcel97Model() (in module cbmpy.CBRead) readSBML2FBA() (in module cbmpy.CBRead) readSBML3FBC() (in module cbmpy.CBRead) readSK_FVA() (in module cbmpy.CBRead) readSK_vertex() (in module cbmpy.CBRead) readSK_vertexOld() (in module cbmpy.CBRead)

Reagent (class in cbmpy.CBModel) removeFixedSpeciesReactions() (in module cbmpy.CBTools) rename() (cbmpy.CBModel.Species method) renameObjectIds() (cbmpy.CBModel.Model method) resetActivity() (cbmpy.CBModel.Gene method) resetAllGenes() (cbmpy.CBModel.Model method) resetAllInactiveGPRBounds() (cbmpy.CBModel.Model method) RESTClient (class in cbmpy.CBNetDB) roundOffWithSense() (in module cbmpy.CBTools) runMultiCoreFVA() (in module cbmpy.CBMultiCore)

S

sbml_convertCOBRASBMLtoFBC() (in module cbmpy.CBXML) sbml_convertSBML3FBCToCOBRA() (in module cbmpy.CBXML) sbml_createAssociationFromAST() (in module cbmpy.CBXML) sbml_createModelL2() (in module cbmpy.CBXML) sbml_exportSBML2FBAModel() (in module cbmpy.CBXML) sbml_fileFindVersion() (in module cbmpy.CBXML) sbml_fileValidate() (in module cbmpy.CBXML) sbml_getCVterms() (in module cbmpy.CBXML) sbml_getGeneRefs() (in module cbmpy.CBXML) sbml_getNotes() (in module cbmpy.CBXML) SBML_NS (in module cbmpy.CBXML) sbml_readCOBRANote() (in module cbmpy.CBXML) sbml_readCOBRASBML() (in module cbmpy.CBXML) sbml_readKeyValueDataAnnotation() (in module cbmpy.CBXML) sbml_readSBML2FBA() (in module cbmpy.CBXML) sbml_readSBML3FBC() (in module cbmpy.CBXML) sbml_setAnnotationsL3Fbc() (in module cbmpy.CBXML) sbml_setCompartmentsL3() (in module cbmpy.CBXML) sbml_setCVterms() (in module cbmpy.CBXML) sbml_setDescription() (in module cbmpy.CBXML) sbml_setGroupsL3() (in module cbmpy.CBXML) sbml_setNotes3() (in module cbmpy.CBXML) sbml_setParametersL3Fbc() (in module cbmpy.CBXML) sbml_setReactionsL2() (in module cbmpy.CBXML) sbml_setReactionsL3Fbc() (in module cbmpy.CBXML) sbml_setSpeciesL2() (in module cbmpy.CBXML) sbml_setSpeciesL3() (in module cbmpy.CBXML) sbml_setUnits() (in module cbmpy.CBXML) sbml_setValidationOptions() (in module cbmpy.CBXML) sbml_validateDocument() (in module cbmpy.CBXML) sbml_writeAnnotationsAsCOBRANote() (in module cbmpy.CBXML) sbml_writeCOBRASBML() (in module cbmpy.CBXML) sbml_writeKeyValueDataAnnotation() (in module cbmpy.CBXML) sbml_writeSBML2FBA() (in module cbmpy.CBXML) sbml_writeSBML3FBC() (in module cbmpy.CBXML) ScalePivots() (cbmpy.PyscesStoich.Stoich method) scanForReactionDuplicates() (in module cbmpy.CBTools) scanForUnbalancedReactions() (in module cbmpy.CBTools) SemanticSBML (class in cbmpy.CBNetDB) serialize() (cbmpy.CBModel.Fbase method) (cbmpy.CBModel.Model method) serializeToDisk() (cbmpy.CBModel.Fbase method) (cbmpy.CBModel.Model method) setActive() (cbmpy.CBModel.Gene method) setAllFluxBounds() (cbmpy.CBModel.Model method) setAllGenesActive() (cbmpy.CBModel.GeneProteinAssociation method) setAllGenesInactive() (cbmpy.CBModel.GeneProteinAssociation method) setAllInactiveGPRBounds() (cbmpy.CBModel.Model method) setAllProteinActivities() (cbmpy.CBModel.Model method) setAnnotation() (cbmpy.CBModel.Fbase method) setBoundary() (cbmpy.CBModel.Species method) setBoundValueByName() (cbmpy.CBModel.Model method) setCBSBOterm() (in module cbmpy.CBXML) setCharge() (cbmpy.CBModel.Species method) setChemFormula() (cbmpy.CBModel.Species method) setCoefficient() (cbmpy.CBModel.Reagent method) setCol() (cbmpy.CBDataStruct.StructMatrix method) (cbmpy.PyscesStoich.StructMatrix method) setCompartmentId() (cbmpy.CBModel.Fbase method) setCreatedDate() (cbmpy.CBModel.Model method) setDescription() (cbmpy.CBModel.Model method)

setDimensions() (cbmpy.CBModel.Compartment method) setFluxBoundsFromDict() (cbmpy.CBModel.Model method) setGeneActive() (cbmpy.CBModel.GeneProteinAssociation method) (cbmpy.CBModel.Model method) setGeneInactive() (cbmpy.CBModel.GeneProteinAssociation method) (cbmpy.CBModel.Model method) setId() (cbmpy.CBModel.Fbase method) (cbmpy.CBModel.Reaction method) (cbmpy.CBModel.Species method) setInactive() (cbmpy.CBModel.Gene method) setKind() (cbmpy.CBModel.Group method) setLabel() (cbmpy.CBModel.Gene method) setLowerBound() (cbmpy.CBModel.Reaction method) setMetaId() (cbmpy.CBModel.Fbase method) setModifiedDate() (cbmpy.CBModel.Model method) setName() (cbmpy.CBModel.Fbase method) setNotes() (cbmpy.CBModel.Fbase method) setObjectiveFlux() (cbmpy.CBModel.Model method) setOperation() (cbmpy.CBModel.Objective method) setPid() (cbmpy.CBModel.Fbase method) setPrefix() (cbmpy.CBModel.Model method) setProtein() (cbmpy.CBModel.GeneProteinAssociation method) setReactionBound() (cbmpy.CBModel.Model method) setReactionBounds() (cbmpy.CBModel.Model method) setReactionId() (cbmpy.CBModel.FluxBound method) setReactionLowerBound() (cbmpy.CBModel.Model method) setReactionUpperBound() (cbmpy.CBModel.Model method) setReagentOf() (cbmpy.CBModel.Species method) setReducedCosts() (in module cbmpy.CBCPLEX) (in module cbmpy.CBGLPK) setRow() (cbmpy.CBDataStruct.StructMatrix method) (cbmpy.PyscesStoich.StructMatrix method) setSBOterm() (cbmpy.CBModel.Fbase method) setSharedAnnotation() (cbmpy.CBModel.Group method) setSharedNotes() (cbmpy.CBModel.Group method) setSharedSBOterm() (cbmpy.CBModel.Group method) setSize() (cbmpy.CBModel.Compartment method) setSpecies() (cbmpy.CBModel.Reagent method) setSpeciesPropertiesFromAnnotations() (in module cbmpy.CBTools) setStoichCoefficient() (cbmpy.CBModel.Reaction method) setSuffix() (cbmpy.CBModel.Model method) setUpperBound() (cbmpy.CBModel.Reaction method) setValue() (cbmpy.CBModel.FluxBound method) (cbmpy.CBModel.Objective method) (cbmpy.CBModel.Parameter method) (cbmpy.CBModel.Reaction method) (cbmpy.CBModel.Species method) sortReactionsById() (cbmpy.CBModel.Model method) sortSpeciesById() (cbmpy.CBModel.Model method) Species (class in cbmpy.CBModel) splitEqualityFluxBounds() (cbmpy.CBModel.Model method) SplitLU() (cbmpy.PyscesStoich.Stoich method) splitReversibleReactions() (in module cbmpy.CBTools) splitSingleReversibleReaction() (in module cbmpy.CBTools) Stoich (class in cbmpy.PyscesStoich) storeObj() (in module cbmpy.CBTools) stringReplace() (in module cbmpy.CBTools) StructMatrix (class in cbmpy.CBDataStruct) (class in cbmpy.PyscesStoich) StructMatrixLP (class in cbmpy.CBDataStruct) SVD_Rank_Check() (cbmpy.PyscesStoich.Stoich method) SwapCol() (cbmpy.PyscesStoich.MathArrayFunc method) SwapCold() (cbmpy.PyscesStoich.MathArrayFunc method) SwapColz() (cbmpy.PyscesStoich.MathArrayFunc method) SwapElem() (cbmpy.PyscesStoich.MathArrayFunc method) SwapRow() (cbmpy.PyscesStoich.MathArrayFunc method) SwapRowd() (cbmpy.PyscesStoich.MathArrayFunc method) SwapRowz() (cbmpy.PyscesStoich.MathArrayFunc method)

T

testGeneProteinAssociations() (cbmpy.CBModel.Model method)

U

unsetBoundary() (cbmpy.CBModel.Species method) updateData() (cbmpy.CBNetDB.DBTools method)

updateNetwork() (cbmpy.CBModel.Model method)

V

viewDataInWebrowser() (cbmpy.CBNetDB.SemanticSBML method)

viewURL() (cbmpy.CBDataStruct.MIRIAMannotation method)

W

writeCOBRASBML() (in module cbmpy.CBWrite) WriteFVAdata() (in module cbmpy.CBWrite) writeFVAdata() (in module cbmpy.CBWrite) WriteFVAtoCSV() (in module cbmpy.CBWrite) writeFVAtoCSV() (in module cbmpy.CBWrite) writeMinDistanceLPwithCost() (in module cbmpy.CBWrite) WriteModelHFormatFBA() (in module cbmpy.CBWrite) writeModelHFormatFBA() (in module cbmpy.CBWrite) WriteModelHFormatFBA2() (in module cbmpy.CBWrite) writeModelHFormatFBA2() (in module cbmpy.CBWrite) writeModelInfoToFile() (in module cbmpy.CBWrite) WriteModelLP() (in module cbmpy.CBWrite) writeModelLP() (in module cbmpy.CBWrite) WriteModelLPOld() (in module cbmpy.CBWrite) writeModelLPOld() (in module cbmpy.CBWrite)

WriteModelRaw() (in module cbmpy.CBWrite) writeModelRaw() (in module cbmpy.CBWrite) writeModelToCOMBINEarchive() (in module cbmpy.CBWrite) writeModelToExcel97() (in module cbmpy.CBWrite) writeOptimalSolution() (in module cbmpy.CBWrite) writeProteinCostToCSV() (in module cbmpy.CBWrite) writeReactionInfoToFile() (in module cbmpy.CBWrite) writeSBML2FBA() (in module cbmpy.CBWrite) writeSBML3FBC() (in module cbmpy.CBWrite) writeSBML3FBCV2() (in module cbmpy.CBWrite) writeSensitivitiesToCSV() (in module cbmpy.CBWrite) writeSolutions() (in module cbmpy.CBWrite) writeSpeciesInfoToFile() (in module cbmpy.CBWrite) writeStoichiometricMatrix() (in module cbmpy.CBWrite)

X

xml_addSBML2FBAFluxBound() (in module cbmpy.CBXML) xml_addSBML2FBAObjective() (in module cbmpy.CBXML) xml_createListOfFluxObjectives() (in module cbmpy.CBXML) xml_createSBML2FBADoc() (in module cbmpy.CBXML)

xml_createSBML2FBAObjective() (in module cbmpy.CBXML) xml_getSBML2FBAannotation() (in module cbmpy.CBXML) xml_stripTags() (in module cbmpy.CBXML) xml_viewSBML2FBAXML() (in module cbmpy.CBXML)