instantiate.metacyc: Instantiate MetaCyc 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.metacyc(equation, chemical_table, id_col = "UNIQUE.ID", 
  parent_col = "TYPES", formula_col = "CHEMICAL.FORMULA", smiles_col
  = "SMILES", inchi_col = "INCHI", direction_type = c(" => ", " <=> "))

`equation`	MetaCyc generic reaction equation with MetaCyc ID (not compound name)
`chemical_table`	Chemical table containing UNIQUE.ID, TYPES, CEHEMICAL.FORMULA, SMILES and InChI columns. This table can be generated by parse.metacyc.compound() 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

Bioinformatics (Oxford, England) 2012, 28(3):388-396. Construction and completion of flux balance models from pathway databases
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.

parse.metacyc.compound

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

data(example) # Load example rdata

Mc = example$metacyc.c
Mg = example$metacyc_generic$equation

names(Mc)       # Check chemical table columns

# Instantiate: Not run
#instanceM = instantiate.metacyc(Mg, Mc, id_col = "UNIQUE.ID", 
#  parent_col = "TYPES", formula_col = "CHEMICAL.FORMULA", smiles_col
#  = "SMILES", inchi_col = "INCHI", direction_type = c(" => ", " <=> "))

#print(instanceM)