parse.metacyc.compound: Parse MetaCyc compound data (compounds.dat in attribute-value...
In RbioRXN: Process Rhea, KEGG, MetaCyc, Unipathway Biochemical Reaction Data

Description Usage Arguments Value Note Author(s) References Examples

Parse MetaCyc compounds.dat file in attribute-value format. The output includes compound name, synonyms, ChEBI ID, PubChem ID, KEGG ID, CAS ID, types, molecular formula, SMILES code and InChI

1	parse.metacyc.compound(datPath)

datPath

Path to compounds.dat file from MetaCyc (BioCyc and EcoCyc also applicable)

data.frame() object where data fields include

`UNIQUE.ID`
`TYPES`
`COMMON.NAME`
`CHEMICAL.FORMULA`
`INCHI`
`MOLECULAR.WEIGHT`
`MONOISOTOPIC.MW`
`NON.STANDARD.INCHI`
`SMILES`
`ATOM.CHARGES`
`SYNONYMS`
`CREDITS`
`SUPERATOMS`
`REGULATES`
`CITATIONS`
`COMMENT.INTERNAL`
`COMMENT`
`SYSTEMATIC.NAME`
`HAS.NO.STRUCTURE.`
`COMPONENT.OF`
`ABBREV.NAME`
`TAUTOMERS`
`PKA1`
`COFACTORS.OF`
`PKA2`
`PKA3`
`N.1.NAME.1`
`N.NAME`
`N.1.NAME`
`SPECIES`
`IN.MIXTURE`
`INTERNALS.OF.GROUP`
`COMPONENTS`
`GROUP.COORDS.2D`
`STRUCTURE.GROUPS`
`STRUCTURE.LINKS`
`RADICAL.ATOMS`
`CFG.ICON.COLOR`
`GROUP.INTERNALS`
`COFACTORS.OR.PROSTHETIC.GROUPS.OFCHEMSPIDER`
`PUBCHEM`
`CHEBI`
`LIGAND.CPD`
`NCI`
`CAS`
`X.Wikipedia.`
`UM.BBD.CPD`
`KNAPSACK`
`BRENDA.COMPOUND`
`LIPID_MAPS`
`LIGAND`

BioCyc and EcoCyc also applicable

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

MetaCyc: http://metacyc.org/

## parse.metacyc.compound: Not run
#url = 'http://bioinformatics.ai.sri.com/ptools/flatfile-samples/compounds.dat'
#tmpdest = tempfile(pattern = "compounds")
#download.file(url, destfile=tmpdest)

#sample.compounds = parse.metacyc.compound(datPath=tmpdest)

RbioRXN documentation built on May 29, 2017, 10:56 a.m.