RbioRXN (version 1.3.1)

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)