drug-discovery

1#!/usr/bin/env python32"""3ro5_screen.py — Batch Lipinski Ro5 + Veber screening via PubChem API.4Usage: python3 ro5_screen.py aspirin ibuprofen paracetamol5No external dependencies beyond stdlib.6"""7import sys, json, time8import urllib.request, urllib.parse9 10BASE = "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name"11PROPS = "MolecularWeight,XLogP,HBondDonorCount,HBondAcceptorCount,RotatableBondCount,TPSA"12 13def fetch(name):14    url = f"{BASE}/{urllib.parse.quote(name)}/property/{PROPS}/JSON"15    try:16        with urllib.request.urlopen(url, timeout=10) as r:17            return json.loads(r.read())["PropertyTable"]["Properties"][0]18    except Exception:19        return None20 21def check(p):22    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))23    v = sum([mw>500,logp>5,hbd>5,hba>10])24    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)25 26def report(name, r):27    if not r: print(f"✗ {name:30s} — not found"); return28    s = "✓ PASS" if r["ok"] else "✗ FAIL"29    flags = (f" [Ro5 violations:{r['violations']}]" if not r["ro5"] else "") + (" [Veber fail]" if not r["veber"] else "")30    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}")31 32def main():33    compounds = sys.stdin.read().splitlines() if len(sys.argv)<2 or sys.argv[1]=="-" else sys.argv[1:]34    print(f"\n{'Status':<8} {'Compound':<30} Properties\n" + "-"*85)35    passed = 036    for name in compounds:37        props = fetch(name.strip())38        result = check(props) if props else None39        report(name.strip(), result)40        if result and result["ok"]: passed += 141        time.sleep(0.3)42    print(f"\nSummary: {passed}/{len(compounds)} passed Ro5 + Veber.\n")43 44if __name__ == "__main__": main()45