Initial import of NousResearch/hermes-agent

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()