API Reference.md

Cheat Sheet for ScrumPy

Listed here are methods (functions) associated with the model. Some methods can be used with a variable like m = ScrumPy.Model('toy_model.spy') and use m.method() to call the method.

Model
AddDynMonitor
AddStatMonitor
ConsMoieties	returns a list of conserved moieties.
Core
DeadReactions	returns a list of reactions that cannot carry steady state flux.
DelIsoforms
DelReactions
DeQuote	Removes quotation marks from identifiers.
Destroy
DisconnectsK
ElModes .mo .sto .Modes() .Stos()	ElModes can be called with a model and assigned to a variable. Using mo returns a matrix, similar to null space, from the model of the elementary modes of the network. sto returns a matrix of the relationship between modes and metabolites. Methods Modes() and Stos() return a string of their respective function.
ElType	Changes the value within a stoichiometry matrix (options: rat, float, int, str, bool). Default=rat, arbitrary precision rational which has the advantage of eliminating rounding errors.
EnzSubsets	Returns a dictionary of nested dictionaries of all the enzymatic subsets in the model. The reaction names are keys and the flux ratio is the value. The key DeadReacs is a list of dead reactions
Eval	Forces a re-evaluation of the rates with current parameters and concentration values. Must be called upon when changes are made in order to take effect.
Externals	returns a list of external metabolites
External	Specify external metaboltes. Takes a comma delimited list.
FindIsoforms	identifies reactions that are redundant (set of reactions with identical stoichiometry).
FindSS
GetAllNames
GetConsMets
GetDepSols
GetEigValsJ
GetEquilDeps
GetFluxDesc
GetFluxDic
GetInitState
GetJac
GetLP	Generates a linear programme associated with a model
GetVals
GetVec
Hide	Closes the model GUI (not the IDLE GUI)
Include	Allows modularisation of the model by splitting into seperate files. Example: a genome scale model where one set of reactions originate from a database and the other file contains reactions added by the user.
Init
InitKin
IsIrrev
IsOK	Checks if the model is OK.
MaxCycles
NetSto
OrphanMets	An orphan metabolite is a metabolite that cannot be balanced at steady state as it is involved in only one reaction. It can only be consumed or produced. This function returns a list of those metabolites from the model.
PingConc
ReacTree
Reload	Reloads the model and reverses the unsaved changes.
RemMon
ScaledSensits
SetInitState
SetVals
SetVec
Show	Shows the model GUI.
ShowDepInfo
SimTo
Simulate
Structural	Specifies the model will only be subjected to structural analysis. Saving time and memory and should always be used for genome-scale models.
Transporters
Update
UpdateDynMons
UpdateStatMons
keys
md
sm
smx

Internal Stoichiometry Matrix
AddAndRemoveRows
AddCol
AddRow
AdjMtx
AsEqn
AsEqns
AugCol
AugRow
ChangeType
Clear
ColDict
ColNZIdxs
ColNamesFromIdxs
ColReorder
ConnectedNet
ConnectedNets
Connectedness
Conv
Copy
DelCol
DelDupRows
DelReac
DelRow
Delete
Dims
DivCol
DivRow
DupRows
El2Str
ElTypeAsScrumPy
ElimCol
Externs	Returns a list of externals (which is none because this is intracellular)
Filter
FindIsoforms
FromDicDic
FromDynMatrix
FromNumPyMtx
FromSciMtx
FunAllRows
FunCol
FunRow
GetCol
GetIrrevs	Returns a list of irreversable reactions.
GetRevs
GetRow
InitRows
InsertRow
IntegiseC
IntegiseR
IntegiseReacs
InvolvedWith
IsIrrev
LNullSpace
LOrthNullSpace
LoTriNames
MakeExtern
MakeFirstCol
MakeFirstRow
MakeIdent
MakeIrrev	Make a reaction irreversable
MakeLastCol
MakeLastRow
MakeRevers
MakeSeqSelfType
MakeZero
MaxCountRow
MaxInCol
MaxInRow
MinInCol
MinInRow
Mul
MulCol
MulRow
NZeroesInCol
NamesNonZeroesInCols
Neighbours
NewCol
NewEl
NewReaction
NewRow
NiceOrder
NonZeroR
NonZeroesInCols
NullSpace
OrphanMets
OrthNullSpace
OrthSubSysts
Orthogonalise
PosOfValsInCol
PosOfValsInRow
Products	Takes a string reaction as argument and returns list of products in reaction
PseudoInverse
RandColOrder
RandOrder
RandRowOrder
Range
RateVector
ReacToStr
Reactants	Takes a string reaction as argument and returns list of reactants in reaction
ReactionNJTree
ReadFile
RedRowEch
ReplaceNames
ResetRowNames
RevProps
RowDict
RowDiffMtx
RowDiffMtx2
RowDiffMtxFull
RowNZIdxs
RowNamesFromIdxs
RowReorder
RowsMatching
RowsWithSingCols
SetCol
SetEl
SetElStrRep
SetPivot
SetRow
SetSto
Sort
SortBy
SubCol
SubMtx
SubRow
SubSys
Substrates
SwapCol
SwapRow
ToCMtx
ToColDict
ToColList
ToDicDic
ToDict
ToFile
ToList
ToNJTree
ToNJTreeOld
ToOctaveMtx
ToSciMtx
ToScrumPy
ToStr
ToTexTab
Transporters
Transpose
Unbals
UpTri
UpTriNames
WriteFile
ZapZeroes
cnames
index
rnames	Not a callable method (i.e. is an object). Returns list of metabolites.
rows

External Stoichiometry Matrix
AddAndRemoveRows
AddCol
AddRow
AdjMtx
AsEqn
AsEqns
AugCol
AugRow
ChangeType
Clear
ColDict
ColNZIdxs
ColNamesFromIdxs
ColReorder
ConnectedNet
ConnectedNets
Connectedness
Conv
Copy
DelCol
DelDupRows
DelReac
DelRow
Delete
Dims
DivCol
DivRow
DupRows
El2Str
ElTypeAsScrumPy
ElimCol
Externs
Filter
FindIsoforms
FromDicDic
FromDynMatrix
FromNumPyMtx
FromSciMtx
FunAllRows
FunCol
FunRow
GetCol
GetIrrevs	Returns a list of irreversible reactions from the stoichiometry matrix (i.e. reactions without <>)
GetRevs
GetRow
InitRows
InsertRow
IntegiseC
IntegiseR
IntegiseReacs
InvolvedWith	Returns the neighbouring elements, either neighbouring reactions or substrates depending on the input. If a reaction is given, the adjacent substrates will be returned. Vice versa if a substrate is given.
IsIrrev
LNullSpace
LOrthNullSpace
LoTriNames
MakeExtern
MakeFirstCol
MakeFirstRow
MakeIdent
MakeIrrev
MakeLastCol
MakeLastRow
MakeRevers	Converts an irriversible reaction to a reversible one from the stoichiometry matrix.
MakeSeqSelfType
MakeZero
MaxCountRow
MaxInCol
MaxInRow
MinInCol
MinInRow
Mul
MulCol
MulRow
NZeroesInCol
NamesNonZeroesInCols
Neighbours
NewCol
NewEl
NewReaction
NewRow
NiceOrder
NonZeroR
NonZeroesInCols
NullSpace	To access the null-space from the matrix
OrphanMets
OrthNullSpace
OrthSubSysts
Orthogonalise
PosOfValsInCol
PosOfValsInRow
Products
PseudoInverse
RandColOrder
RandOrder
RandRowOrder
Range
RateVector
ReacToStr	Is a method of the matrix (sm.ReacToStr(reac)) which returns the reaction as it was inputted into the model.
Reactants
ReactionNJTree
ReadFile
RedRowEch
ReplaceNames
ResetRowNames
RevProps
RowDict
RowDiffMtx
RowDiffMtx2
RowDiffMtxFull
RowNZIdxs
RowNamesFromIdxs
RowReorder
RowsMatching
RowsWithSingCols
SetCol
SetEl
SetElStrRep
SetPivot
SetRow
SetSto
Sort
SortBy
SubCol
SubMtx
SubRow
SubSys
Substrates
SwapCol
SwapRow
ToCMtx
ToColDict
ToColList
ToDicDic
ToDict
ToFile
ToList
ToNJTree
ToNJTreeOld
ToOctaveMtx
ToSciMtx
ToScrumPy
ToStr
ToTexTab
Transporters
Transpose
Unbals
UpTri
UpTriNames
WriteFile
ZapZeroes
_getrc
cnames	Returns the column names of the stoichiometry matrix.
index
rnames	Returns the row names of the stoichiometry matrix
rows

Linear Programming
AddCols
AddRows
AddSumConstraint
CheckReac
CleanReacDic
CleanReacList
ClearFluxConstraint	Clears the flux bounds applied to a reaction. Takes the reaction's name as an argument.
ClearFluxConstraints
DelCols
DelRows
FiniteBoundFlux
GetClass
GetCol
GetColDual
GetColIdxs
GetColKind
GetColNames
GetColPrimal
GetDims
GetName
GetNumCols
GetNumRows
GetObjDir
GetObjName
GetObjVal
GetPrimSol	In linear programming, this function returns an optimal solution set after .Solve() has been called
GetReacNames
GetRow
GetRowDual
GetRowIdxs
GetRowName
GetRowNames
GetRowPrimal
GetRowsAsLists
GetSimplexAsMtx
GetStatus
GetStatusMsg
GetStatusSym
HasCol
HasRow
IsStatusOptimal
Klass
LoadMtxFromDic
LoadMtxFromLists
MatchFlux
ObjVal
PrintMtx
Read
SetColBounds
SetColName
SetFixedFlux	In linear programming, the fluxes of reaction can be fixed to a single value using a dictionary whereby keys = reaction name, values = flux.
SetFluxBounds	Sets the flux bounds of a linear programme. Takes a Python dictionary as an argument whereby keys = reaction name, values = a tuple of upper and lower flux bounds.
SetName
SetObjCoef
SetObjCoefsFromDic
SetObjCoefsFromLists
SetObjDir
SetObjDirec	Takes arguments "Min" and "Max", defaults to min if left blank. Assigns the direction of flux for reactions in a linear programme.
SetObjName
SetObjective	Takes a list of reactions as an argument. The object directive is then applied to the list of reactions once set.
SetRowBounds
SetRowName
SetRowVals
SetSumFluxConstraint
SolRateVector
SolStoDic
Solve	Solves the linear programme
UnboundFlux
Write
cidxs
cnames
lpx
model
ridxs
rnames
sm