README.md

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

Searching data

from enviPath_python import enviPath

eP = enviPath('https://envipath.org')

# get package(s) that should be searched
bbd = eP.get_package('https://envipath.org/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1')
soil = eP.get_package('https://envipath.org/package/5882df9c-dae1-4d80-a40e-db4724271456')

# returns a dictionary with properly initialized objects
res = eP.search('c1ccccc1', [bbd, soil])
print(res)

# or use a package to search it
res = bbd.search('c1ccccc1')
print(res)

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())