Inchi

compareInchis(model, inchis, met)[source]

Compare inchi strings. Each inchi string is given a score based on its similarity to the chemical formula and charge of the metabolite in the model. Factors such as stereochemistry, if it is a standard inchi, and its similarity to the other inchis are also considered.

USAGE

comparisonTable = compareInchis (model, inchis, met)

INPUT

  • model – COBRA model *.mets - 1xm list of metabolite IDs *.metFormulas - 1xm list of metabolite Formulas *.metCharges - 1xm list of metabolite charges

  • inchis – List of InChIs to compare

  • met – Metabolite ID in the model

OUTPUTS

comparisonTable – Table containing the information used for each InChI

getChargeFromInChI(InChI)[source]

Returns the charge from a given InChI string

USAGE

[charge, chargeWithoutProtons] = getChargeFromInChI (InChI)

INPUT

InChI – The Inchi Identifier - string

OUTPUTS

  • charge – The charge encoded in the InChi string (including protonation)

  • chargeWithoutProtons – The charge encoded in the InChi ignoring the protonation state

Note

InChI Charge is defined in the charge layer and can be modified in the proton layer. If nothing is defined, the compound is uncharged. First: Discard any “Reconnected” parts, as those don’t influence the charge

getFormulaFromInChI(InChI)[source]

Extracts the chemical formula of a given compound from the InChI string provided

USAGE

[formula, protons] = getFormulaFromInChI (InChI)

INPUT

InChI – The Inchi String of the chemical formula (e.g. InChI= extract formula from InChI = 1S/C3H4O3/c1-2(4)3(5)6/h1H3, (H,5,6)/p-1 for pyruvate

OUTPUTS

  • formula – The chemical formula (including the protonation state

  • protons – The total number of protons

getInchiData(inchi)[source]

Classify the inchi according to its various layers of information. All layers and sub-layers (except for the chemical formula sub-layer of the Main layer) start with /? where ? is a lower-case letter to indicate the type of information held in that layer.

USAGE

inchiLayersDetail = getInchiData (inchi)

INPUTS

inchi – String with the InChI to classify

OUTPUTS

detailLevelInchi – Struct file with the following fields:

  • .layers - Number of layers in the InChI.

  • .mainLayer - Number of layers in the InChI.

  • .standart - Logical, indicates whether the inchi is

    standard or not.

  • .metFormula - The molecula formula.

  • .netCharge - Summ of the charges.

  • .stereochemicalLayer - Logical, indicates whether the inchi

    represent stereochemical information or not.

  • .isotopicLayer - Logical, indicates whether the inchi represent

    isotopic information or not.