genesis/molecule_viewer.py

# genesis/molecule_viewer.py
"""
Molecule Viewer for GENESIS-AI
Fetches 3D molecular structure data and metadata from public chemical databases.
"""

import requests

PDBE_API = "https://www.ebi.ac.uk/pdbe/api/pdb/entry/summary/"
PUBCHEM_API = "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name"
CHEMBL_API = "https://www.ebi.ac.uk/chembl/api/data/molecule"

def get_pdbe_structure(pdb_id):
    """Fetch structure summary from PDBe."""
    try:
        r = requests.get(f"{PDBE_API}{pdb_id}")
        r.raise_for_status()
        return r.json()
    except Exception as e:
        return {"error": str(e)}

def get_pubchem_structure(compound_name):
    """Fetch compound data from PubChem."""
    try:
        url = f"{PUBCHEM_API}/{compound_name}/JSON"
        r = requests.get(url)
        r.raise_for_status()
        return r.json()
    except Exception as e:
        return {"error": str(e)}

def get_chembl_structure(query):
    """Search ChEMBL for molecule info."""
    try:
        r = requests.get(f"{CHEMBL_API}?molecule_synonyms__icontains={query}")
        r.raise_for_status()
        return r.json()
    except Exception as e:
        return {"error": str(e)}

def fetch_structure(query):
    """Try PDBe (if PDB ID), else PubChem, else ChEMBL."""
    if len(query) == 4 and query.isalnum():
        return get_pdbe_structure(query)
    pubchem_result = get_pubchem_structure(query)
    if "error" not in pubchem_result:
        return pubchem_result
    return get_chembl_structure(query)