Description Usage Arguments Value Author(s) References See Also Examples
View source: R/instantiate.metacyc.R
Generic reaction is a reaction with at least one compound class. This function gains instance reactions from given generic reaction
1 2 3 | 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.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 | # 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)
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