Pubchem API Guide

# No API key needed
curl "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/aspirin/JSON"

GET https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/{name}/JSON

curl -s "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/caffeine/JSON" \
  | python3 -m json.tool

GET https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/{cid}/property/{properties}/JSON

curl -s "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/ibuprofen/property/MolecularFormula,MolecularWeight,CanonicalSMILES,IUPACName,XLogP/JSON" \
  | python3 -m json.tool

curl -s "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/fastformula/C8H10N4O2/property/IUPACName,MolecularWeight,CanonicalSMILES/JSON" \
  | python3 -m json.tool

curl -s "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/fastsimilarity_2d/cid/2244/property/IUPACName,MolecularWeight,CanonicalSMILES/JSON?Threshold=90" \
  | python3 -m json.tool

curl -s "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/2244/assaysummary/JSON" \
  | python3 -m json.tool

import requests
import time

PUG_REST = "https://pubchem.ncbi.nlm.nih.gov/rest/pug"

def get_compound_properties(name):
    """Fetch key drug-likeness properties for a named compound."""
    props = "MolecularWeight,XLogP,HBondDonorCount,HBondAcceptorCount,TPSA,RotatableBondCount,IUPACName"
    url = f"{PUG_REST}/compound/name/{name}/property/{props}/JSON"
    resp = requests.get(url)
    resp.raise_for_status()
    data = resp.json()
    return data.get("PropertyTable", {}).get("Properties", [{}])[0]

def check_lipinski(props):
    """Check Lipinski's Rule of Five for oral drug-likeness."""
    violations = 0
    mw = props.get("MolecularWeight", 0)
    logp = props.get("XLogP", 0)
    hbd = props.get("HBondDonorCount", 0)
    hba = props.get("HBondAcceptorCount", 0)

    if mw > 500: violations += 1
    if logp > 5: violations += 1
    if hbd > 5: violations += 1
    if hba > 10: violations += 1
    return violations

drug_candidates = ["metformin", "atorvastatin", "lisinopril", "omeprazole"]
print(f"{'Compound':<20} {'MW':>8} {'LogP':>6} {'HBD':>4} {'HBA':>4} {'Violations':>10}")
print("-" * 60)

for drug in drug_candidates:
    props = get_compound_properties(drug)
    violations = check_lipinski(props)
    print(f"{drug:<20} {props.get('MolecularWeight', 0):>8.1f} "
          f"{props.get('XLogP', 0):>6.1f} "
          f"{props.get('HBondDonorCount', 0):>4} "
          f"{props.get('HBondAcceptorCount', 0):>4} "
          f"{violations:>10}")
    time.sleep(0.3)

import requests

def compare_compounds(cid_list):
    """Compare properties of multiple compounds by CID."""
    cids = ",".join(str(c) for c in cid_list)
    props = "IUPACName,MolecularFormula,MolecularWeight,CanonicalSMILES,XLogP"
    url = f"{PUG_REST}/compound/cid/{cids}/property/{props}/JSON"
    resp = requests.get(url)
    resp.raise_for_status()
    return resp.json().get("PropertyTable", {}).get("Properties", [])

# Compare aspirin (2244), ibuprofen (3672), acetaminophen (1983)
results = compare_compounds([2244, 3672, 1983])
for compound in results:
    print(f"\n{compound.get('IUPACName', 'Unknown')}")
    print(f"  Formula: {compound.get('MolecularFormula')}")
    print(f"  MW: {compound.get('MolecularWeight')}")
    print(f"  SMILES: {compound.get('CanonicalSMILES')}")
    print(f"  LogP: {compound.get('XLogP')}")