atomTransition

buildAtomTransitionNetwork(model, rxnfileDir)

Builds an atom transition network corresponding to a metabolic network from reaction stoichiometry and atom mappings.

Usage

ATN = buildAtomTransitionNetwork(model, rxnfileDir)

Inputs

• model – Structure 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 rxnfiles.
  • .rxns - An n x 1 array of reaction identifiers. Should match rxnfile names in rxnFileDir.
  • .lb - An n x 1 vector of lower bounds on fluxes.
  • .ub - An n x 1 vector of upper bounds on fluxes.
• rxnfileDir – Path to directory containing rxnfiles with atom mappings for internal reactions in S. File names should correspond to reaction identifiers in input rxns.

Output

• ATN – Structure with following fields:
  • .A - A p x q sparse incidence matrix for the atom transition network, where p is the number of atoms and q is the number of atom transitions.
  • .mets - A p x 1 cell array of metabolite identifiers to link atoms to their metabolites. The order of atoms is the same in A as in the molfile for each metabolite.
  • .rxns - A q x 1 cell array of reaction identifiers to link atom transitions to their reactions. The order of atom transitions is the same in A as in the rxnfile (with atom mappings) for each reaction.
  • .elements - A p x 1 cell array of element symbols for atoms in A.

extractElementalTransitionNetwork(ATN, elements)

Extracts specific chemical elements from an atom transition network.

Usage

ETN = extractElementalTransitionNetwork(ATN, elements)

Inputs

• ATN – An atom transition network
• elements – A cell array of element symbols, e.g., ‘C’ for carbon or {‘C’ ‘O’} for carbon and oxygen

Output

• ETN – An elemental transition network for the specified elements

renameDREAMOutputFiles(zipfile, indir, outdir)

Replaces DREAM file names with original file names.

Usage

renameDREAMOutputFiles(zipfile, indir, outdir)

Inputs

• zipfile – name of zipfile submitted to the DREAM server
• indir – name of directory containing the DREAM output files
• outdir – name of directory where renamed files should be placed