"""Raised when organisms or rules have not been caculated in advance"""

def __init__(self, msg = "Not Ready. Need to run set-up scripts"):

self._msg = msg

def __str__(self):

with open(csv_file) as csv_handle:

dict_reader = csv.DictReader(csv_handle, delimiter = ',')

compound_list = []

for row in dict_reader:

name = row["name"]

inchi = row["inchi"]

if inchi is None or inchi == "None" or inchi =="":

pass

else:

try:

if name.startswith("InChI"):

compound = Compound(InChI = inchi, heavy_standardisation = True, force_add_H = add_Hs)

else:

compound = Compound(InChI = inchi, name = name, heavy_standardisation = True, force_add_H = add_Hs)

if not compound.in_list(compound_list, main_layer = False):

compound_list.append(compound)

except ChemConversionError as e:

logging.error("For compound {} with inchi {}: error ChemConversionError".format(name, inchi))

organism = ChemicalCompoundState(compound_list, main_layer = False)

# organism.set_main_layer(True)