Reactions¶
- findBondsBrokenAndFormed(model, rxnList, rxnDir, printLevel)[source]¶
Calculate the the bonds broken and formed for the mass balanced reactions in a metabolic network based on atom mapping data.
- USAGE
[bondsBrokenAndFormed, substrateMass] = findBondsBrokenAndFormed (model, rxnDir, printLevel)
- INPUTS
model – COBRA model with following fields:
- .rxns - An n x 1 array of reaction identifiers.
Should match metabolite identifiers in
rxnList List of reactions from which the enthalpy change – will be computed.
rxnDir Directory of with the RXN files.
printLevel Print figure with the relation of mass vs bondsBF bondsE
- OUTPUTS
bondsBF An n x 1 vector with the number of bonds broken and – formed. External or pasive transpor reactions are equal to 0; missing and unbalanced reactions are NaN.
substrateMass Total mass of the substrates
- findEnthalpyChange(model, rxnList, rxnDir, printLevel)[source]¶
Calculate the enthalphy change for mass balanced reactions in a metabolic network based on atom mapping data.
The enthalpy change are based on: Huheey, pps. A-21 to A-34; T.L. Cottrell, “The Strengths of Chemical Bonds,” 2nd ed., Butterworths, London, 1958; B. deB. Darwent, “National Standard Reference Data Series,” National Bureau of Standards, No. 31,Washington, DC, 1970; S.W. Benson, J. Chem. Educ., 42, 502 (1965)
- USAGE
[enthalpyChange, substrateMass] = findEnthalpyChange (model, rxnList, rxnDir, printLevel)
- INPUTS
model – COBRA model with following fields:
- .rxns - An n x 1 array of reaction identifiers.
Should match metabolite identifiers in
rxnList List of reactions from which the number of broken and – formed bonds will be computed.
rxnDir Directory of with the RXN files.
printLevel Print figure with the relation of mass vs bondsBF bondsE
- OUTPUTS
enthalpyChange An n x 1 vector with the bond enthalpies in kJ/mol. – External or pasive transpor reactions are equal to 0; missing and unbalanced reactions are NaN.
substrateMass Total mass of the substrates
- obtainAtomMappingsRDT(model, molFileDir, rxnResultsDir, rxnsToAM, hMapping, writeRXNonly, replaceExistingAtomMappings)[source]¶
Using the reaction decoder tool, compute atom mappings for reactions in a COBRA model. Atom mapping data is presented in a variety of formats, including MDL RXN, SMILES, and images. If this option is selected, the function can remove all protons from the model and represent the reactions as a hydrogen suppressed chemical graph.
- USAGE
standardisedRxns = obtainAtomMappingsRDT (model, molFileDir, rxnResultsDir, rxnsToAM, hMapping, maxTime, standariseRxn)
- INPUTS
model – COBRA model with following fields:
- .S - The m x n stoichiometric matrix for the
metabolic network.
- .mets - An m x 1 array of metabolite identifiers.
Should match metabolite identifiers in RXN.
- .metFormulas - An m x 1 array of metabolite
identifiers. Should match metabolite identifiers in RXN.
- .rxns - An n x 1 array of reaction identifiers.
Should match rxnfile names in rxnResultsDir_atomMapped.
molFileDir – Path to the directory containing MOL files for metabolites in S. File names should correspond to reaction identifiers in input mets.
- OPTIONAL INPUTS
rxnResultsDir – Path to directory that will contain the RXN files with atom mappings (default: current directory).
rxnsToAM – List of reactions to atom map (default: all in the model).
hMapping – Logic value to select if hydrogen atoms will be atom mapped (default: TRUE).
writeRXNonly – True to write out standardised RXN files and not atom map them (default: FALSE).
replaceExistingAtomMappings – True to recompute atom mappings, replacing existing RXN files (default: TRUE).
- OUTPUTS
atomMappingReport – A report with the atom mapping data * .rxnFilesWritten the MDL RXN written * .balanced the balanced reactions * .unbalancedBool the unbalanced reactions * .inconsistentBool the inconsistent reactions * .notMapped the that couldn’t be mapped * .rxnResultsDir_unMapped A directory with standardised RXN files. * .rxnResultsDir_atomMapped A directory with atom mapped RXN files. * .rxnResultsDir_images A directory images for atom mapped reactions. * .rxnResultsDir_txtData A directory with txt files with data of the atom mappings (SMILES, REACTANT INPUT ATOM INDEX, PRODUCT INPUT ATOM INDEX).
Example
example 1: molFileDir = [‘data’ filesep] standariseRxn = true; unmappedRxns = obtainAtomMappingsRDT(model, molFileDir, pwd, 1800, standariseRxn) example 2: molFileDir = [‘data’ filesep] standariseRxn = false; standardisedRxns = obtainAtomMappingsRDT(model, molFileDir, pwd, 1800, standariseRxn)