A python client to interact with enviPath
Project description
enviPath Python
Python client for enviPath - the environmental contaminant biotransformation pathway resource.
Quickstart
pip install --upgrade enviPath-python
from pprint import pprint
from enviPath_python import enviPath
eP = enviPath('https://envipath.org')
bbd = eP.get_package('https://envipath.org/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1')
bbd_pws = bbd.get_pathways()
pprint(bbd_pws[0].get_description())
Documentation
The enviPath-python documentation can be found here.
If you are new to enviPath our wiki might also contain some value information.
Examples
Accessing Data
from pprint import pprint
from enviPath_python import enviPath
eP = enviPath('https://envipath.org')
# get the EAWAG BBD package
bbd = eP.get_package('https://envipath.org/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1')
# access collections (e.g. compounds)
# other collections such as reactions, rules, pathways, etc work the same way
compounds = bbd.get_compounds()
for c in compounds[:10]:
print(c.get_id(), c.get_name(), c.get_smiles())
Accessing private data
import getpass
from enviPath_python import enviPath
eP = enviPath('https://envipath.org')
# get username + password
username = input("Enter username")
password = getpass.getpass(prompt="Password for {}".format(username))
eP.login(username, password)
print(eP.who_am_i())
for p in eP.get_packages()[:10]:
print(p)
Predict Pathways
from enviPath_python import enviPath
from enviPath_python.objects import Pathway
from time import sleep
eP = enviPath('https://envipath.org')
# obtain the currently logged in user
me = eP.who_am_i()
# get the package the pathway should be stored in
package = me.get_default_package()
# will trigger the pathway prediction
pw = Pathway.create(package, smiles='CC1(C)C2CCC1(C)C(=O)C2')
# wait until the prediction finished
while pw.is_running():
print("Sleeping for three secs...")
sleep(3)
# check result
if pw.has_failed():
exit(1)
else:
for node in pw.get_nodes():
print(node.get_smiles())
Project details
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