mirror of
https://github.com/NousResearch/hermes-agent.git
synced 2026-04-25 00:51:20 +00:00
a91b9bb855
Pharmaceutical research skill covering bioactive compound search (ChEMBL), drug-likeness screening (Lipinski Ro5 + Veber via PubChem), drug-drug interaction lookups (OpenFDA), gene-disease associations (OpenTargets GraphQL), and ADMET reasoning guidance. All free public APIs, zero auth, stdlib-only Python. Includes helper scripts for batch Ro5 screening and target-to-compound pipelines. Moved to optional-skills/research/ (niche domain skill, not built-in). Fixed: authors→author frontmatter, removed unused jq prerequisite, bare except→except Exception. Co-authored-by: bennytimz <oluwadareab12@gmail.com> Salvaged from PR #8695.
44 lines
2 KiB
Python
44 lines
2 KiB
Python
#!/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, argparse
|
|
import urllib.request, urllib.parse, urllib.error
|
|
|
|
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()
|