"""

used NCBO Annotator from BioPortal to return ChEBI IDS

for substrates and products of reactions from Expasy enzyme

"""

url = 'http://data.bioontology.org/annotator'

params = dict(apikey=sys.argv[1], text=compound, ontologies='CHEBI', longest_only='true',

include='properties', exlude_numbers='false', exclude_synonyms='false', mappins='all')

tm_results = requests.get(url=url, params=params).json()

for i in tm_results:

prefLabel = i['annotatedClass']['properties']['http://data.bioontology.org/metadata/def/prefLabel']

text_input = i['annotations'][0]['text']

if prefLabel[0].lower() == text_input.lower():

final_chebi = i['annotatedClass']['@id'].split("/")[-1]

"""

takes list of compound names and replaces with names formatted for NCBO annotator

"""

names = {'H(2)O': 'water',

'CO(2)': 'carbon dioxide'

}

for k, v in names.items():

if compound == k:

return compound.replace(k,v)

else:

"""

"""

url = "ftp://ftp.expasy.org/databases/enzyme/enzyme.dat"

enzyme = urllib.request.urlretrieve(url)

enzyme_p = bee.parse(open(enzyme[0], 'r'))

enz_records = []

count = 0

for record in enzyme_p:

count += 1

enz_rec = {}

enz_rec['Reaction(s)'] = record['CA']

#create record for each enzyme with EC number as primary key

enz_rec['PreferedName'] = record['DE']

enz_rec['ECNumber'] = record['ID']

enz_rec['Reaction(s)'] = []

enz_rec['Substrates'] = {}

enz_rec['Products'] = {}

enz_rec['UniProt'] = {}

enz_records.append(enz_rec)

# split split to seperate multiple reactions

reaction1 = record['CA'].split('.')

for rxn in reaction1:

if len(reaction1) > 2:

rxn = rxn[3:]

enz_rec['Reaction(s)'].append(rxn)

#split reactions into [substrates, products]

constituents = rxn.split('=')

# split each side of reaction on '+' not '(+)'

r = re.compile(r'(?:[^\+(]|\([^)]*\))+')

for sub in r.findall(constituents[0]):

sub = replace_strings(sub.lstrip().rstrip())

schebi = link_compound2chebi(sub)

enz_rec['Substrates'][sub] = schebi

for prod in r.findall(constituents[-1]):

prod = replace_strings(prod.lstrip().rstrip())

pchebi = link_compound2chebi(prod)

enz_rec['Products'][prod] = pchebi

# populate enz_rec['UniProt'] with dictionary of uniprotid:name key, value pairs for protein

for unpid in record['DR']:

enz_rec['UniProt'][unpid[0]] = unpid[1]

enz_records.append(enz_rec)