genesis/api_clients/chembl_api.py

# genesis/api_clients/chembl_api.py
import os
import requests

CHEMBL_BASE_URL = "https://www.ebi.ac.uk/chembl/api/data"

def _chembl_get(endpoint: str, params: dict = None):
    """
    Generic ChEMBL GET request helper.
    """
    url = f"{CHEMBL_BASE_URL}/{endpoint}"
    res = requests.get(url, params=params)
    res.raise_for_status()
    return res.json()


# -----------------------
# Drug & Compound Search
# -----------------------
def search_drug_by_name(drug_name: str, limit: int = 5):
    """
    Search for a drug/compound by name in ChEMBL.
    """
    params = {"pref_name__icontains": drug_name, "limit": limit}
    return _chembl_get("molecule", params)


def get_drug_details(chembl_id: str):
    """
    Retrieve detailed information for a specific ChEMBL compound.
    """
    return _chembl_get(f"molecule/{chembl_id}")


# -----------------------
# Target & Mechanism
# -----------------------
def search_target_by_name(target_name: str, limit: int = 5):
    """
    Search for a biological target (e.g., protein) by name.
    """
    params = {"pref_name__icontains": target_name, "limit": limit}
    return _chembl_get("target", params)


def get_target_details(chembl_target_id: str):
    """
    Retrieve target details from ChEMBL.
    """
    return _chembl_get(f"target/{chembl_target_id}")


def get_mechanism_of_action(chembl_id: str):
    """
    Retrieve the mechanism of action for a given compound.
    """
    params = {"molecule_chembl_id": chembl_id}
    return _chembl_get("mechanism", params)


# -----------------------
# Bioactivity Data
# -----------------------
def get_bioactivity_for_target(chembl_target_id: str, limit: int = 10):
    """
    Get bioactivity data (IC50, Ki, etc.) for a target.
    """
    params = {"target_chembl_id": chembl_target_id, "limit": limit}
    return _chembl_get("activity", params)


def get_bioactivity_for_drug(chembl_id: str, limit: int = 10):
    """
    Get bioactivity data for a compound.
    """
    params = {"molecule_chembl_id": chembl_id, "limit": limit}
    return _chembl_get("activity", params)


# -----------------------
# Clinical Candidates
# -----------------------
def get_clinical_candidates(drug_name: str):
    """
    Find drugs in clinical trials from ChEMBL.
    """
    compounds = search_drug_by_name(drug_name, limit=1)
    if compounds["page_meta"]["total_count"] > 0:
        chembl_id = compounds["molecules"][0]["molecule_chembl_id"]
        return get_mechanism_of_action(chembl_id)
    return None