instantiate.rhea: Instantiate Rhea generic reaction
In RbioRXN: Process Rhea, KEGG, MetaCyc, Unipathway Biochemical Reaction Data

Description Usage Arguments Value Author(s) References See Also Examples

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

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

`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(' <\\?> ', ' <=> ', ' => ')

List object containing instance reactions

Byoungnam Min <mbnmbn00@gmail.com>, Byeonghyuk Park, Kyoung Heon Kim and In-Geol Choi

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.

get.chebi.all

# 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)