RbioRXN (version 1.3.1)

instantiate.rhea: Instantiate Rhea generic reaction

Description

Generic reaction is a reaction with at least one compound class. This function gains instance reactions from given generic reaction

Usage

instantiate.rhea(equation, chemical_table, id_col='chebi',
  parent_col='parent', formula_col='formula', smiles_col='smiles', 
  inchi_col='inchi', direction_type=c(' <\\?> ', ' <=> ', ' => '))

Arguments

equation
Rhea generic reaction equation with ChEBI ID (not compound name)
chemical_table
Chemical table containing chebi, parent, formula, smiles and inchi columns. This table can be generated by get.chebi.all() function
id_col
In chemical table, choose the column name which contains chemical id (usually first column)
parent_col
In chemical table, choose the column name which contains parent compound ("TYPES" in MetaCyc)
formula_col
In chemical table, choose the column name which contains molecular formula
smiles_col
In chemical table, choose the column name which contains SMILES code
inchi_col
In chemical table, choose the column name which contains InChI code
direction_type
In reaction equation, provide reaction direction charaters. Default is c(' <\\?> ', ' <=> ', ' => ')

Value

  • List object containing instance reactions

References

Rhea: http://www.ebi.ac.uk/rhea ChEBI: http://www.ebi.ac.uk/chebi Open babel: O'Boyle NM, Banck M, James CA, Morley C, Vandermeersch T, Hutchison GR. Open Babel: An open chemical toolbox. J Cheminform. 2011 Oct 7;3:33. doi: 10.1186/1758-2946-3-33. PubMed PMID: 21982300; PubMed Central PMCID: PMC3198950.

See Also

get.chebi.all

Examples

Run this code
# You need to load 'ChemmineOB' package before running this function.

data(example) # Load example data

chebi = example$chebi # Sample ChEBI
Rg = example$rhea_generic$equationWithChebi # Sample Rhea generic reaction

## Instantiate: Not run
#instanceR = instantiate.rhea(Rg, chebi, id_col = "chebi", parent_col="parent",
#  formula_col="formula", smiles_col="smiles", inchi_col="inchi", 
#  direction_type=c(" <\\\\?> ", " <=> ", " => "))

#print(instanceR)

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