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test1.py
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import sys
sys.path.insert(0,'C:\envipath_code')
from enviPath_python.enviPath import *
from enviPath_python.objects import *
import rdkit
from rdkit import Chem
from rdkit.Chem.MolStandardize import rdMolStandardize
from rdkit.Chem import Descriptors
from rdkit.Chem.rdMolDescriptors import CalcMolFormula
INSTANCE_HOST = 'https://envipath.org'
eP = enviPath(INSTANCE_HOST)
ep.login('leetseng', 'Joan1388')
def main():
package_id = 'https://envipath.org/package/4a3cd0f4-4d2b-4f00-b3e6-a29e721f7038'
sludge = Package(eP.requester, id=package_id)
compounds = sludge.get_compounds() # get the list of compounds
analyze_compounds(compounds, "ouputfile.txt")
def canonicalize_smiles(smiles):
mol = Chem.MolFromSmiles(smiles) # creates mol object from SMILES
uncharger = rdMolStandardize.Uncharger() # easier to access
uncharged = uncharger.uncharge(mol) # protonates or deprotonates the mol object
new_smiles = rdkit.Chem.rdmolfiles.MolToSmiles(uncharged) # converts mol object to canonical SMILES
can_smiles = Chem.CanonSmiles(new_smiles)
return can_smiles
def analyze_compounds(all_compounds, output_filename):
header = '{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\n'.format('Index', 'Name', 'ID','Full_SMILES', 'Cropped_SMILES', 'Is_compoiste', 'Canonical_SMILES', 'Cropped_canonical_SMILES', 'Number_halflives')
outfile = open(output_filename, 'w')
outfile.write(header) #
sludge = Package(eP.requester, id=package_id)
scenarios = sludge.get_scenarios()
i = 0
for scen in scenarios:
# is_composite = False
i += 1
print("Hello, I am compound #", i)
# compound = Compound(eP.requester, id=cpd.get_id())
# cpd_structure = CompoundStructure(eP.requester, id=cpd.get_id())
# cpd_structure.get_scenarios()
name = compound.get_name()
id = compound.get_id()
print(id)
try:
# halflifes = cpd_structure.get_halflifes()
scen = cpd_structure.get_scenarios()
except:
continue
full_smiles = compound.get_smiles()
canonical_smiles = canonicalize_smiles(full_smiles)
cropped_smiles = full_smiles
if '.' in full_smiles:
is_compoiste = True
cropped_smiles = full_smiles.split('.')[0]
cropped_canonical_smiles = canonicalize_smiles(cropped_smiles)
data_list = '{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\n'.format(i, name, id, full_smiles, cropped_smiles, is_composite, canonical_smiles,
cropped_canonical_smiles, len(halflifes))
outfile.write(data_list)
outfile.close()
main()
# #How many cpd/reaction/scenario?
#
# print('Number of compounds:', len(compounds))
# print(compounds[0])
# compound1 = compounds[0]
# print(compound1.get_id())
# scenario1 = full_compound1.get_scenarios()
# print(scenario1)
full_compound1 = CompoundStructure(eP.requester, id='https://envipath.org/package/4a3cd0f4-4d2b-4f00-b3e6-a29e721f7038/scenario/42f1c95b-2d26-42a8-9bab-691ea20968e8') #load the object of compound or reaction or scenarios
# hf1 = full_compound1.get_halflifes()
reaction1 = full_compound1.get_reactions()[0]
# print(hf1)
print(reaction1.get_name())
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