RbioRXN (version 1.5.1)

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

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

parse.metacyc.compound(datPath)

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

References

MetaCyc: http://metacyc.org/

Examples

## 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)