#!/usr/bin/env python3
"""
Compound Cross-Database Search
This script searches for a compound by name and retrieves identifiers
from multiple databases:
- KEGG Compound
- ChEBI
- ChEMBL (via UniChem)
- Basic compound properties
Usage:
python compound_cross_reference.py COMPOUND_NAME [--output FILE]
Examples:
python compound_cross_reference.py Geldanamycin
python compound_cross_reference.py "Adenosine triphosphate"
python compound_cross_reference.py Aspirin --output aspirin_info.txt
"""
import sys
import argparse
from bioservices import KEGG, UniChem, ChEBI, ChEMBL
def search_kegg_compound(compound_name):
"""Search KEGG for compound by name."""
print(f"\n{'='*70}")
print("STEP 1: KEGG Compound Search")
print(f"{'='*70}")
k = KEGG()
print(f"Searching KEGG for: {compound_name}")
try:
results = k.find("compound", compound_name)
if not results or not results.strip():
print(f"✗ No results found in KEGG")
return k, None
# Parse results
lines = results.strip().split("\n")
print(f"✓ Found {len(lines)} result(s):\n")
for i, line in enumerate(lines[:5], 1):
parts = line.split("\t")
kegg_id = parts[0]
description = parts[1] if len(parts) > 1 else "No description"
print(f" {i}. {kegg_id}: {description}")
# Use first result
first_result = lines[0].split("\t")
kegg_id = first_result[0].replace("cpd:", "")
print(f"\nUsing: {kegg_id}")
return k, kegg_id
except Exception as e:
print(f"✗ Error: {e}")
return k, None
def get_kegg_info(kegg, kegg_id):
"""Retrieve detailed KEGG compound information."""
print(f"\n{'='*70}")
print("STEP 2: KEGG Compound Details")
print(f"{'='*70}")
try:
print(f"Retrieving KEGG entry for {kegg_id}...")
entry = kegg.get(f"cpd:{kegg_id}")
if not entry:
print("✗ Failed to retrieve entry")
return None
# Parse entry
compound_info = {
'kegg_id': kegg_id,
'name': None,
'formula': None,
'exact_mass': None,
'mol_weight': None,
'chebi_id': None,
'pathways': []
}
current_section = None
for line in entry.split("\n"):
if line.startswith("NAME"):
compound_info['name'] = line.replace("NAME", "").strip().rstrip(";")
elif line.startswith("FORMULA"):
compound_info['formula'] = line.replace("FORMULA", "").strip()
elif line.startswith("EXACT_MASS"):
compound_info['exact_mass'] = line.replace("EXACT_MASS", "").strip()
elif line.startswith("MOL_WEIGHT"):
compound_info['mol_weight'] = line.replace("MOL_WEIGHT", "").strip()
elif "ChEBI:" in line:
parts = line.split("ChEBI:")
if len(parts) > 1:
compound_info['chebi_id'] = parts[1].strip().split()[0]
elif line.startswith("PATHWAY"):
current_section = "pathway"
pathway = line.replace("PATHWAY", "").strip()
if pathway:
compound_info['pathways'].append(pathway)
elif current_section == "pathway" and line.startswith(" "):
pathway = line.strip()
if pathway:
compound_info['pathways'].append(pathway)
elif line.startswith(" ") and not line.startswith(" "):
current_section = None
# Display information
print(f"\n✓ KEGG Compound Information:")
print(f" ID: {compound_info['kegg_id']}")
print(f" Name: {compound_info['name']}")
print(f" Formula: {compound_info['formula']}")
print(f" Exact Mass: {compound_info['exact_mass']}")
print(f" Molecular Weight: {compound_info['mol_weight']}")
if compound_info['chebi_id']:
print(f" ChEBI ID: {compound_info['chebi_id']}")
if compound_info['pathways']:
print(f" Pathways: {len(compound_info['pathways'])} found")
return compound_info
except Exception as e:
print(f"✗ Error: {e}")
return None
def get_chembl_id(kegg_id):
"""Map KEGG ID to ChEMBL via UniChem."""
print(f"\n{'='*70}")
print("STEP 3: ChEMBL Mapping (via UniChem)")
print(f"{'='*70}")
try:
u = UniChem()
print(f"Mapping KEGG:{kegg_id} to ChEMBL...")
chembl_id = u.get_compound_id_from_kegg(kegg_id)
if chembl_id:
print(f"✓ ChEMBL ID: {chembl_id}")
return chembl_id
else:
print("✗ No ChEMBL mapping found")
return None
except Exception as e:
print(f"✗ Error: {e}")
return None
def get_chebi_info(chebi_id):
"""Retrieve ChEBI compound information."""
print(f"\n{'='*70}")
print("STEP 4: ChEBI Details")
print(f"{'='*70}")
if not chebi_id:
print("⊘ No ChEBI ID available")
return None
try:
c = ChEBI()
print(f"Retrieving ChEBI entry for {chebi_id}...")
# Ensure proper format
if not chebi_id.startswith("CHEBI:"):
chebi_id = f"CHEBI:{chebi_id}"
entity = c.getCompleteEntity(chebi_id)
if entity:
print(f"\n✓ ChEBI Information:")
print(f" ID: {entity.chebiId}")
print(f" Name: {entity.chebiAsciiName}")
if hasattr(entity, 'Formulae') and entity.Formulae:
print(f" Formula: {entity.Formulae}")
if hasattr(entity, 'mass') and entity.mass:
print(f" Mass: {entity.mass}")
if hasattr(entity, 'charge') and entity.charge:
print(f" Charge: {entity.charge}")
return {
'chebi_id': entity.chebiId,
'name': entity.chebiAsciiName,
'formula': entity.Formulae if hasattr(entity, 'Formulae') else None,
'mass': entity.mass if hasattr(entity, 'mass') else None
}
else:
print("✗ Failed to retrieve ChEBI entry")
return None
except Exception as e:
print(f"✗ Error: {e}")
return None
def get_chembl_info(chembl_id):
"""Retrieve ChEMBL compound information."""
print(f"\n{'='*70}")
print("STEP 5: ChEMBL Details")
print(f"{'='*70}")
if not chembl_id:
print("⊘ No ChEMBL ID available")
return None
try:
c = ChEMBL()
print(f"Retrieving ChEMBL entry for {chembl_id}...")
compound = c.get_compound_by_chemblId(chembl_id)
if compound:
print(f"\n✓ ChEMBL Information:")
print(f" ID: {chembl_id}")
if 'pref_name' in compound and compound['pref_name']:
print(f" Preferred Name: {compound['pref_name']}")
if 'molecule_properties' in compound:
props = compound['molecule_properties']
if 'full_mwt' in props:
print(f" Molecular Weight: {props['full_mwt']}")
if 'alogp' in props:
print(f" LogP: {props['alogp']}")
if 'hba' in props:
print(f" H-Bond Acceptors: {props['hba']}")
if 'hbd' in props:
print(f" H-Bond Donors: {props['hbd']}")
if 'molecule_structures' in compound:
structs = compound['molecule_structures']
if 'canonical_smiles' in structs:
smiles = structs['canonical_smiles']
print(f" SMILES: {smiles[:60]}{'...' if len(smiles) > 60 else ''}")
return compound
else:
print("✗ Failed to retrieve ChEMBL entry")
return None
except Exception as e:
print(f"✗ Error: {e}")
return None
def save_results(compound_name, kegg_info, chembl_id, output_file):
"""Save results to file."""
print(f"\n{'='*70}")
print(f"Saving results to {output_file}")
print(f"{'='*70}")
with open(output_file, 'w') as f:
f.write("=" * 70 + "\n")
f.write(f"Compound Cross-Reference Report: {compound_name}\n")
f.write("=" * 70 + "\n\n")
# KEGG information
if kegg_info:
f.write("KEGG Compound\n")
f.write("-" * 70 + "\n")
f.write(f"ID: {kegg_info['kegg_id']}\n")
f.write(f"Name: {kegg_info['name']}\n")
f.write(f"Formula: {kegg_info['formula']}\n")
f.write(f"Exact Mass: {kegg_info['exact_mass']}\n")
f.write(f"Molecular Weight: {kegg_info['mol_weight']}\n")
f.write(f"Pathways: {len(kegg_info['pathways'])} found\n")
f.write("\n")
# Database IDs
f.write("Cross-Database Identifiers\n")
f.write("-" * 70 + "\n")
if kegg_info:
f.write(f"KEGG: {kegg_info['kegg_id']}\n")
if kegg_info['chebi_id']:
f.write(f"ChEBI: {kegg_info['chebi_id']}\n")
if chembl_id:
f.write(f"ChEMBL: {chembl_id}\n")
f.write("\n")
print(f"✓ Results saved")
def main():
"""Main workflow."""
parser = argparse.ArgumentParser(
description="Search compound across multiple databases",
formatter_class=argparse.RawDescriptionHelpFormatter,
epilog="""
Examples:
python compound_cross_reference.py Geldanamycin
python compound_cross_reference.py "Adenosine triphosphate"
python compound_cross_reference.py Aspirin --output aspirin_info.txt
"""
)
parser.add_argument("compound", help="Compound name to search")
parser.add_argument("--output", default=None,
help="Output file for results (optional)")
args = parser.parse_args()
print("=" * 70)
print("BIOSERVICES: Compound Cross-Database Search")
print("=" * 70)
# Step 1: Search KEGG
kegg, kegg_id = search_kegg_compound(args.compound)
if not kegg_id:
print("\n✗ Failed to find compound. Exiting.")
sys.exit(1)
# Step 2: Get KEGG details
kegg_info = get_kegg_info(kegg, kegg_id)
# Step 3: Map to ChEMBL
chembl_id = get_chembl_id(kegg_id)
# Step 4: Get ChEBI details
chebi_info = None
if kegg_info and kegg_info['chebi_id']:
chebi_info = get_chebi_info(kegg_info['chebi_id'])
# Step 5: Get ChEMBL details
chembl_info = None
if chembl_id:
chembl_info = get_chembl_info(chembl_id)
# Summary
print(f"\n{'='*70}")
print("SUMMARY")
print(f"{'='*70}")
print(f" Compound: {args.compound}")
if kegg_info:
print(f" KEGG ID: {kegg_info['kegg_id']}")
if kegg_info['chebi_id']:
print(f" ChEBI ID: {kegg_info['chebi_id']}")
if chembl_id:
print(f" ChEMBL ID: {chembl_id}")
print(f"{'='*70}")
# Save to file if requested
if args.output:
save_results(args.compound, kegg_info, chembl_id, args.output)
if __name__ == "__main__":
main()