parse.metacyc.compound: Parse MetaCyc compound data (compounds.dat in attribute-value...

Description Usage Arguments Value Note Author(s) References Examples

View source: R/parse.metacyc.compound.R

Description

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

Usage

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Arguments

datPath

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

Value

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

Note

BioCyc and EcoCyc also applicable

Author(s)

Byoungnam Min <[email protected]>, Byeonghyuk Park, Kyoung Heon Kim and In-Geol Choi

References

MetaCyc: http://metacyc.org/

Examples

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## 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.