Update genesis/api_clients/chembl_api.py

genesis/api_clients/chembl_api.py

@@ -1,65 +1,91 @@
 # genesis/api_clients/chembl_api.py
+import os
 import requests
 
-CHEMBL_BASE = "https://www.ebi.ac.uk/chembl/api/data"
+CHEMBL_BASE_URL = "https://www.ebi.ac.uk/chembl/api/data"
 
-def search_molecule(query: str, limit: int = 10):
+def _chembl_get(endpoint: str, params: dict = None):
     """
-    Search ChEMBL for a molecule by name, ChEMBL ID, or synonyms.
+    Generic ChEMBL GET request helper.
     """
-    url = f"{CHEMBL_BASE}/molecule"
-    params = {
-        "molecule_structures__standard_inchi_key__flexmatch": query,
-        "limit": limit,
-        "format": "json"
-    }
+    url = f"{CHEMBL_BASE_URL}/{endpoint}"
     res = requests.get(url, params=params)
     res.raise_for_status()
-    return res.json().get("molecules", [])
+    return res.json()
+
 
-def get_molecule_details(chembl_id: str):
+# -----------------------
+# Drug & Compound Search
+# -----------------------
+def search_drug_by_name(drug_name: str, limit: int = 5):
     """
-    Get detailed information for a given ChEMBL molecule ID.
+    Search for a drug/compound by name in ChEMBL.
     """
-    url = f"{CHEMBL_BASE}/molecule/{chembl_id}.json"
-    res = requests.get(url)
-    res.raise_for_status()
-    return res.json()
+    params = {"pref_name__icontains": drug_name, "limit": limit}
+    return _chembl_get("molecule", params)
 
-def get_bioactivity(chembl_id: str, limit: int = 20):
+
+def get_drug_details(chembl_id: str):
     """
-    Get bioactivity data for a given molecule ID.
-    Includes IC50, EC50, Ki, etc.
+    Retrieve detailed information for a specific ChEMBL compound.
     """
-    url = f"{CHEMBL_BASE}/activity"
-    params = {
-        "molecule_chembl_id": chembl_id,
-        "limit": limit,
-        "format": "json"
-    }
-    res = requests.get(url, params=params)
-    res.raise_for_status()
-    return res.json().get("activities", [])
+    return _chembl_get(f"molecule/{chembl_id}")
+
 
-def search_target(target_name: str, limit: int = 10):
+# -----------------------
+# Target & Mechanism
+# -----------------------
+def search_target_by_name(target_name: str, limit: int = 5):
     """
-    Search for a biological target (protein, enzyme, receptor, etc.).
+    Search for a biological target (e.g., protein) by name.
     """
-    url = f"{CHEMBL_BASE}/target"
-    params = {
-        "target_synonym__icontains": target_name,
-        "limit": limit,
-        "format": "json"
-    }
-    res = requests.get(url, params=params)
-    res.raise_for_status()
-    return res.json().get("targets", [])
+    params = {"pref_name__icontains": target_name, "limit": limit}
+    return _chembl_get("target", params)
+
 
 def get_target_details(chembl_target_id: str):
     """
-    Get detailed target info from ChEMBL.
+    Retrieve target details from ChEMBL.
     """
-    url = f"{CHEMBL_BASE}/target/{chembl_target_id}.json"
-    res = requests.get(url)
-    res.raise_for_status()
-    return res.json()
+    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