def __init__(self, name = '', cas = '', inchi = '', inchikey = '', csid = ''):
#first define the SOAP service for searching
searchurl = 'http://www.chemspider.com/Search.asmx?WSDL'
try:
self.searchclient = Client(searchurl)
except Exception as e:
print(e)
#define the soap service for inchi-conversion
inchiurl = 'http://www.chemspider.com/InChI.asmx?WSDL'
try:
self.inchiclient = Client(inchiurl)
except Exception as e:
print(e)
#set all properties to the ones from initiating call
self.cas = cas
self.inchi = inchi
self.inchikey = inchikey
self.name = name
self.csid = csid
#no transaction id for now
self.transaction_id = ''
#how quickly should we ask for results? in seconds
self.timetick = 0.2
self.maxtime = 15
#read chemspider token from config file 'chemspider_token'
try:
f = hl.openfile('chemspider_token.txt')
except IOError:
raise IOError
self.token = f.readline()
# the chemspider_token.txt should only contain the token (available online for free)
# using the argparse module to make use of command line options
parser = argparse.ArgumentParser(
description="Read a list of chemicals and output the same list completed with InChI and Chemspider IDs (tab separated)"
)
parser.add_argument("--version", action="version", version="r1")
parser.add_argument("filename", help="Specify a filename to read.")
# parse it
args = parser.parse_args()
try:
liste = hl.openfile(args.filename)
except IOError:
sys.exit("Could not read file")
try:
outputliste = open(args.filename + "_output.txt", "w")
except:
sys.exit("Could not open output file")
for line in liste:
line = line.rstrip("\r\n")
print("Searching for: " + line)
try:
compound = ChemicalObject(name=line)
except IOError:
sys.exit("No chemspider token given. Aborting.")
elif args.folder is not None:
#adjust file path in case we're running on f*****g windows
args.folder = os.path.normcase(args.folder)
#lets go through that folder and add every filename to the filelist
caldirlist = os.listdir(args.folder)
for file in caldirlist:
filelist.append([os.path.join(args.folder, file), file])
elif args.filelist is not None:
#in this we have to read the list of filenames in a file
f = hl.openfile(args.filelist)
for line in f:
#we split the array by whitespaces or tabs (split tries both)
line = line.strip('\r\n').split()
#first argument should be the filename + path, therefore appending it to a temp array together with the filename
filelist.append(line[0], os.path.basename(line[0]))
#let's walk our filelist
for file in filelist:
#this variable is set to false if we encounter a non-readable file
usefulfile = True
try:
data = hl.readfile(file[0])
except IOError:
