AuxillaryFiles¶
- assignRxnWeights(MatricesSUX, weights, WeightsPerRxn, NoWeight)¶
Assigns reaction weights
USAGE:
MatricesSUX = assignRxnWeights(MatricesSUX, weights, WeightsPerRxn, NoWeight)
- INPUTS:
MatricesSUX: Input model structure weights: Weight structure that permits to add weights to
non-core reactions (it is recommended to use values other than 0 and 1, with lower weight corresponding to higher priority. Format:
weights.MetabolicRxns = 10; % Universal database metabolic reactions
weights.ExchangeRxns = 10; % Exchange reactions
weights.TransportRxns = 10; % Transport reactions
Default: weigth of 10 for all non-core reactions.
- WeightsPerRxn: Structure containing a list of reactions that should be assined with
individual weights (WeightsPerRxn.rxns) AND a list of Reaction weights (WeightsPerRxn.weights) in the same order.
- NoWeight: Weight that should be assigned to those reactions NOT
in core reaction set and NOT in WeightsPerRxn (default:1000)
- OUTPUT:
MatricesSUX: Output model structure
- createUniversalReactionModel2(KEGGFilename, KEGGBlackList)¶
Creates the U matrix using the universal data from the KEGG
USAGE:
KEGG = createUniversalReactionModel2(KEGGFilename, KEGGBlackList)
- INPUTS:
KEGGFilename: File name containing universal database (e.g., KEGG; optional input, default: reaction.lst) KEGGblackList: List of excluded reactions from the universal database
(e.g., KEGG) (optional input, default: no blacklist)
- OUTPUT:
KEGG: Contains universal database (U matrix) in matrix format
Note
This file is KEGG-specific: if non-KEGG-type metabolite IDs are used it will not parse the reactions correctly and will throw an error.
- createXMatrix2(compoundsIn, transport, compartment, model)¶
Creates a matrix full of exchange reactions based on the input list (creates an exchange reaction for each of the metabolites present in the model)
USAGE:
ExchangeRxnMatrix = createXMatrix2(compoundsIn, transport, compartment, model)
- INPUTS:
compoundsIn: List of metabolites transport: if 1, transport reactions will be defined as well for every
compounds (default: 0, which corresponds to only exchange reactions)
- compartment: [c] –> transport from cytoplasm [c] to extracellular space
[e] (default), [p] creates transport from [c] to [p] and from [p] to [c]
- model: model structure - used to check if exchange reaction exists
already before adding it to ExchangeRxnMatrix
- OUTPUT:
- ExchangeRxnMatrix: Model structure containing all exchange and
transport reactions
- findIntracellularRxns(model)¶
This function finds all reactions that do not contain metabolites in [e] comparment.
USAGE:
[intracellRxnList] = findIntracellularRxns(model)
- INPUT:
model: Model structure
- OUTPUT:
intracellRxnList: List of intracellular reactions in model
- generateSUXComp(model, dictionary, KEGGFilename, KEGGBlackList, listCompartments, KEGGMatrixLoad)¶
Creates the matrices for gap filling for compartmentalized metabolic models (S) such that the universal database (U, e.g., KEGG) is placed in each compartment specified and reversible transport reactions (X) are added for each compound present in U and S, between the compartment and the cytosol. Additionally, exchange reactions are added for each metabolite in the extracellular space.
USAGE:
MatricesSUX =generateSUXComp(model, dictionary, KEGGFilename, KEGGBlackList, listCompartments)
- INPUTS:
model: Model structure dictionary: List of universal database IDs and their counterpart in the model (e.g.,
KEGG_dictionary.xls)
KEGGFilename: File name containing the universal database (e.g., KEGG - reaction.lst) KEGGBlackList: List of excluded reactions from the universal database
(e.g., KEGG)
- listCompartments: List of intracellular compartments in the model
(optional input, default compartments to be considered: ‘[c]’ ,’[m]’, ‘[l]’, ‘[g]’, ‘[r]’, ‘[x]’, ‘[n]’)
KEGGMatrixLoad load precomputed KEGG matrix (default: 0)
- OUTPUT:
MatricesSUX: SUX matrix
Based on generateSUX.m but updated and expanded for compartmentalized gap filling efforts.
Ines Thiele, Jan 2021, added the option to preload KEGG matrix and
KeggExchangeRxnMatrix, if multiple reconstructions will be tested this is faster