ChemoInformatics

acsendingAtomMaps(rxnFile)[source]

Reassign the atom mapping numbers to be ascending in the RXN file V2000

Usage

balanced = acsendingAtomMaps(rxnFile)

Input

  • rxnFile – Name and path of the RXN file to asign ascending atom mappings.

Outputs

  • balanced – Logical value indicating if the RXN file is balanced or not (true, or false).
  • A RXN file with ascending atom mappings.

Example

rxnFile = ['rxnFileDir' filesep 'DOPACNNL.rxn'];
balanced = acsendingAtomMaps(rxnFile);
canonicalRxn(rxnFile, mappedDir, standardDir)[source]

Standarize atom mapped RXNS files into a canonical format. ChemAxon installed is required (needed to compute the atom transition network)

Usage

standardised = canonicalRxn(rxnFile, mappedDir, standardDir)

Inputs

  • rxnFile – Name of the RXN file to standarize.
  • mappedDir – Path to directory containg the RXN files with atom mappings.
  • standardDir – Path to directory containg the standard RXN files (generated by obtainAtomMappingsRDT function).

Outputs

  • standardised – Logical value indicating if the RXN file is balanced or not (true, or false).
  • A standarised RXN file in – ‘mappedDir/rxnFile.rxn’

Example

rxnFile = 'DOPACCL.rxn';
mappedDir = ['mapped' filesep];
standardDir = ['standard' filesep];
standardised = canonicalRxn(rxnFile, mappedDir, standardDir)
deleteProtons(model)[source]

Function to delete the protons in the metabolic network

Usage

newModel = deleteProtons(model)

Input

  • model – COBRA model.

Output

  • newModel – COBRA model without protons nor protons trasport reactions.

Example

newModel = deleteProtons(model)
mol2sdf(mets, molfileDir, sdfFileName, includeRs)[source]

Concatenates molfiles in molfileDir into one SDF file.

Usage

[metList, noMolMetList] = mol2sdf(mets, molfileDir, sdfFileName, includeRs)

Inputs

  • mets – m x 1 cell array of metabolite identifiers (e.g., BiGG abbreviations)
  • molfileDir – Path to directory containing molfiles for metabolites in mets. Molfile names should match the metabolite identifiers in mets without compartment assignments.

Optional inputs

  • sdfFileName – Name of SDF file. Default is MetStructures.sdf.
  • includeRs – {0, (1)}. If 0, variable structures such as R groups and repeat units will not be included in SDF.

Outputs

  • metList – Cell array listing metabolites in SDF.
  • noMolMetList – Cell array listing metabolites without mol file.

Written output is sdfFileName.sdf - SDF with metabolite structures in same order as in metList. Metabolite identifiers in the SDF are the same as in MetList.

obtainAtomMappingsRDT(model, molFileDir, outputDir, maxTime, standariseRxn)[source]

Compute atom mappings for reactions with implicit hydrogens in a metabolic network using RDT algorithm

Usage

unmappedRxns = obtainAtomMappingsRDT(model, molFileDir, rxnDir, 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 rxnFileDir.
  • molFileDir – Path to the directory containing MOL files for metabolites in S. File names should correspond to reaction identifiers in input mets.

Optional inputs

  • rxnDir – Path to directory that will contain the RXN files with atom mappings (default current directory).
  • maxTime – Maximum time assigned to compute atom mapping (default 1800s).
  • standariseRxn – Logic value for standardising the atom mapped RXN file. ChemAxon license is required (default TRUE).

Outputs

  • balancedRxns – List of standadised atom mapped reactions.
  • A directory with standardised RXN files.
  • A directory with atom mapped RXN files.
  • A directory images for atom mapped reactions.
  • 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)
readAtomMappingFromRxnFile(rxnfileName, rxnfileDirectory)[source]

Read atom mappings from a rxnfile (Accelrys, San Diego, CA), written with writeRxnfile.m.

Usage

[mets, elements, metNrs, rxnNrs, isSubstrate, instances] = readAtomMappingFromRxnFile(rxnfileName, rxnfileDirectory)

Input

  • rxnfileName – The file name.

Optional input

  • rxnfileDirectory – Path to directory containing the rxnfile. Defaults to current directory.

Outputs

  • mets – A p x 1 cell array of metabolite identifiers for atoms.
  • elements – A p x 1 cell array of element symbols for atoms.
  • metNrs – A p x 1 vector containing the numbering of atoms within each metabolite molfile.
  • rxnNrs – A p x 1 vector of atom mappings, i.e., the numbering of atoms within the reaction.
  • isSubstrate – A p x 1 logical array. True for substrates, false for products in the reaction.
  • instances – A p x 1 vector indicating which instance of a repeated metabolite atom i belongs to.
sortRDTfiles(rxnFile)[source]

Sort the molecules in the RXN file acording to the chemical formula in the 4th line of the RXN file.

Usage

sortRDTfiles(rxnFile)

Input

  • rxnFile – Name and path of the RXN file to sort.

Output

  • A RXN file with sorted molecules.

Example

rxnFile = ['rxnFileDir' filesep 'DOPACNNL.rxn'];
sortRDTfiles(rxnFile)
writeRxnfile(s, mets, molfileNames, molfileDirectory, rxnfileName, rxnfileDirectory)[source]

Writes a rxnfile (Accelrys, San Diego, CA) for a metabolic reaction.

Usage

writeRxnfile(s, mets, molfileNames, molfileDirectory, rxnfileName, rxnfileDirectory)

Inputs

  • s – An m x 1 vector of stoichiometric coefficients.
  • mets – An m x 1 cell array of metabolite identifiers.

Optional inputs

  • molfileNames – An m x 1 cell array of molfile names for metabolites in mets. Defaults to mets.
  • molfileDirectory – Path to directory containing input molfiles. Defaults to current directory.
  • rxnfileName – A name for the output rxnfile. Defaults to ‘rxn.rxn’.
  • rxnfileDirectory – Path to directory where the output rxnfile should be saved. Defaults to current directory.

Produces the file ‘rxnfileDirectory/rxnfileName.rxn’