Hermes-agent

optional-skills/research/drug-discovery/scripts/chembl_target.py

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+#!/usr/bin/env python3
+"""
+chembl_target.py — Search ChEMBL for a target and retrieve top active compounds.
+Usage: python3 chembl_target.py "EGFR" --min-pchembl 7 --limit 20
+No external dependencies.
+"""
+import sys, json, time, argparse
+import urllib.request, urllib.parse
+
+BASE = "https://www.ebi.ac.uk/chembl/api/data"
+
+def get(endpoint):
+    try:
+        req = urllib.request.Request(f"{BASE}{endpoint}", headers={"Accept":"application/json"})
+        with urllib.request.urlopen(req, timeout=15) as r:
+            return json.loads(r.read())
+    except Exception as e:
+        print(f"API error: {e}", file=sys.stderr); return None
+
+def main():
+    parser = argparse.ArgumentParser(description="ChEMBL target → active compounds")
+    parser.add_argument("target")
+    parser.add_argument("--min-pchembl", type=float, default=6.0)
+    parser.add_argument("--limit", type=int, default=10)
+    args = parser.parse_args()
+
+    enc = urllib.parse.quote(args.target)
+    data = get(f"/target/search?q={enc}&limit=5&format=json")
+    if not data or not data.get("targets"):
+        print("No targets found."); sys.exit(1)
+
+    t = data["targets"][0]
+    tid = t.get("target_chembl_id","")
+    print(f"\nTarget: {t.get('pref_name')} ({tid})")
+    print(f"Type: {t.get('target_type')} | Organism: {t.get('organism','N/A')}")
+    print(f"\nFetching compounds with pChEMBL ≥ {args.min_pchembl}...\n")
+
+    acts = get(f"/activity?target_chembl_id={tid}&pchembl_value__gte={args.min_pchembl}&assay_type=B&limit={args.limit}&order_by=-pchembl_value&format=json")
+    if not acts or not acts.get("activities"):
+        print("No activities found."); sys.exit(0)
+
+    print(f"{'Molecule':<18} {'pChEMBL':>8} {'Type':<12} {'Value':<10} {'Units'}")
+    print("-"*65)
+    seen = set()
+    for a in acts["activities"]:
+        mid = a.get("molecule_chembl_id","N/A")
+        if mid in seen: continue
+        seen.add(mid)
+        print(f"{mid:<18} {str(a.get('pchembl_value','N/A')):>8} {str(a.get('standard_type','N/A')):<12} {str(a.get('standard_value','N/A')):<10} {a.get('standard_units','N/A')}")
+        time.sleep(0.1)
+    print(f"\nTotal: {len(seen)} unique molecules")
+
+if __name__ == "__main__": main()

optional-skills/research/drug-discovery/scripts/ro5_screen.py

@@ -0,0 +1,44 @@
+#!/usr/bin/env python3
+"""
+ro5_screen.py — Batch Lipinski Ro5 + Veber screening via PubChem API.
+Usage: python3 ro5_screen.py aspirin ibuprofen paracetamol
+No external dependencies beyond stdlib.
+"""
+import sys, json, time
+import urllib.request, urllib.parse
+
+BASE = "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name"
+PROPS = "MolecularWeight,XLogP,HBondDonorCount,HBondAcceptorCount,RotatableBondCount,TPSA"
+
+def fetch(name):
+    url = f"{BASE}/{urllib.parse.quote(name)}/property/{PROPS}/JSON"
+    try:
+        with urllib.request.urlopen(url, timeout=10) as r:
+            return json.loads(r.read())["PropertyTable"]["Properties"][0]
+    except Exception:
+        return None
+
+def check(p):
+    mw,logp,hbd,hba,rot,tpsa = float(p.get("MolecularWeight",0)),float(p.get("XLogP",0)),int(p.get("HBondDonorCount",0)),int(p.get("HBondAcceptorCount",0)),int(p.get("RotatableBondCount",0)),float(p.get("TPSA",0))
+    v = sum([mw>500,logp>5,hbd>5,hba>10])
+    return dict(mw=mw,logp=logp,hbd=hbd,hba=hba,rot=rot,tpsa=tpsa,violations=v,ro5=v<=1,veber=tpsa<=140 and rot<=10,ok=v<=1 and tpsa<=140 and rot<=10)
+
+def report(name, r):
+    if not r: print(f"✗ {name:30s} — not found"); return
+    s = "✓ PASS" if r["ok"] else "✗ FAIL"
+    flags = (f" [Ro5 violations:{r['violations']}]" if not r["ro5"] else "") + (" [Veber fail]" if not r["veber"] else "")
+    print(f"{s}  {name:28s} MW={r['mw']:.0f} LogP={r['logp']:.2f} HBD={r['hbd']} HBA={r['hba']} TPSA={r['tpsa']:.0f} RotB={r['rot']}{flags}")
+
+def main():
+    compounds = sys.stdin.read().splitlines() if len(sys.argv)<2 or sys.argv[1]=="-" else sys.argv[1:]
+    print(f"\n{'Status':<8} {'Compound':<30} Properties\n" + "-"*85)
+    passed = 0
+    for name in compounds:
+        props = fetch(name.strip())
+        result = check(props) if props else None
+        report(name.strip(), result)
+        if result and result["ok"]: passed += 1
+        time.sleep(0.3)
+    print(f"\nSummary: {passed}/{len(compounds)} passed Ro5 + Veber.\n")
+
+if __name__ == "__main__": main()