getCpdNames.py

import requests
from sets import Set
import more_itertools

pathways = requests.get('http://rest.kegg.jp/list/pathway')
compounds = []

for line in pathways.content.split('\n'):
    mapid = line.split('\t')[0].replace('path:', '')
    cpds = requests.get('http://rest.kegg.jp/link/cpd/' + mapid)
    for cpd in cpds.content.split('\n'):
        if len(cpd.split('cpd:')) > 1:
            compounds.append(cpd.split('cpd:')[1])

cpdids = list(Set(compounds))
cpdids.sort()

output = open('compoundNames.txt', 'w')
for ids in more_itertools.chunked(cpdids, 100):
    names = requests.get('http://rest.kegg.jp/list/' + '+'.join(ids))
    output.write(names.content)
output.close