Skip to content

Thecubedaryl patch 1 #14

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
thecubedaryl wants to merge 2 commits into
base: main
Choose a base branch
from
Open

Thecubedaryl patch 1 #14

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
076eb24
Update data_processing.py
thecubedaryl Mar 8, 2026
1e1a0e6
Update chembl_downloading.py
thecubedaryl Mar 8, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
8 changes: 4 additions & 4 deletions chembl_downloading.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -71,10 +71,10 @@ async def fetch_activities_async(self, session: aiohttp.ClientSession, target_id

base_url = "https://www.ebi.ac.uk/chembl/api/data/activity.json"
params = {
'target_id__in': ','.join(target_ids),
'target_chembl_id__in': ','.join(target_ids),
'assay_type__in': ','.join(assay_types),
'pchembl_value__isnull': 'false',
'only': 'molecule_chembl_id,pchembl_value,target_id,bao_label'
'only': 'molecule_chembl_id,pchembl_value,target_chembl_id,bao_label'
}

# First request to get total count and setup pagination
Expand Down Expand Up @@ -208,7 +208,7 @@ async def fetch_all_protein_targets_async(self) -> List[str]:
base_url = "https://www.ebi.ac.uk/chembl/api/data/target.json"
params = {
'target_type': 'SINGLE PROTEIN',
'only': 'target_id'
'only': 'target_chembl_id'
}

async with await self.create_session() as session:
Expand Down Expand Up @@ -377,4 +377,4 @@ def download_target(args):

args = parser.parse_args()

download_target(args)
download_target(args)
4 changes: 2 additions & 2 deletions data_processing.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -451,15 +451,15 @@ def get_chembl_from_uniprot(uniprot_id: str) -> list:
r = requests.get(url)
r.raise_for_status()
data = r.json().get('targets', [])
return [t['target_id'] for t in data]
return [t['target_chembl_id'] for t in data]

# 6) Fetch inactive compounds for a ChEMBL target

def fetch_inactive_compounds(chembl_target_id, pchembl_threshold) -> list:
print("fetch_inactive_compounds started")
url = "https://www.ebi.ac.uk/chembl/api/data/activity.json"
params = {
'target_id': chembl_target_id,
'target_chembl_id': chembl_target_id,
'pchembl_value__lt': pchembl_threshold,
'limit': 10000
}
Expand Down