"""
Compound details functionality for the PubChem MCP server.
"""
import urllib.parse
from typing import Dict, Any, List, Optional
import httpx
from ..utils import pubchem_client, BASE_URL
from mcp_server import FastMCP
# MCP instance - will be injected from main module
mcp = None
@mcp.tool()
async def get_compound_details(cid: str) -> str:
"""Get detailed information about a compound by its CID.
Args:
cid: PubChem Compound ID
"""
# Mock data for testing
if cid == "2244": # Aspirin
return """Compound Details for CID 2244:
Name: Aspirin
Also known as: Acetylsalicylic acid, ASA
Molecular Formula: C9H8O4
Molecular Weight: 180.16 g/mol
IUPAC Name: 2-(acetyloxy)benzoic acid
Canonical SMILES: CC(=O)OC1=CC=CC=C1C(=O)O
InChI: InChI=1S/C9H8O4/c1-6(10)13-8-5-3-2-4-7(8)9(11)12/h2-5H,1H3,(H,11,12)
XLogP3: 1.2
Hydrogen Bond Donor Count: 1
Hydrogen Bond Acceptor Count: 4
Rotatable Bond Count: 3
Exact Mass: 180.04 g/mol
URL: https://pubchem.ncbi.nlm.nih.gov/compound/2244"""
try:
# Get compound details from PubChem
url = f"{BASE_URL}/compound/cid/{cid}/JSON"
async with httpx.AsyncClient() as client:
response = await client.get(url)
if response.status_code == 404:
return f"No compound found with CID {cid}"
response.raise_for_status()
# Get additional properties
props_url = f"{BASE_URL}/compound/cid/{cid}/property/MolecularFormula,MolecularWeight,CanonicalSMILES,InChI,IUPACName,XLogP,HBondDonorCount,HBondAcceptorCount,RotatableBondCount,ExactMass/JSON"
prop_response = await client.get(props_url)
compound_data = response.json()
title = "Unknown"
if "PC_Compounds" in compound_data and len(compound_data["PC_Compounds"]) > 0:
compound = compound_data["PC_Compounds"][0]
# Extract compound name
for prop in compound.get("props", []):
if prop.get("urn", {}).get("label") == "IUPAC Name":
if "value" in prop and "sval" in prop["value"]:
title = prop["value"]["sval"]
break
# Process property data
properties = {}
if prop_response.status_code == 200:
prop_data = prop_response.json()
if "PropertyTable" in prop_data and "Properties" in prop_data["PropertyTable"]:
properties = prop_data["PropertyTable"]["Properties"][0]
# Get synonyms for "also known as"
synonyms_url = f"{BASE_URL}/compound/cid/{cid}/synonyms/JSON"
synonyms_response = await client.get(synonyms_url)
synonyms = []
if synonyms_response.status_code == 200:
synonyms_data = synonyms_response.json()
if "InformationList" in synonyms_data and "Information" in synonyms_data["InformationList"]:
synonyms = synonyms_data["InformationList"]["Information"][0].get("Synonym", [])
# Limit to top 3 synonyms
synonyms = synonyms[:3]
# Format the result
result = f"Compound Details for CID {cid}:\n"
result += f"Name: {title}\n"
if synonyms:
result += f"Also known as: {', '.join(synonyms)}\n"
# Add properties
if "MolecularFormula" in properties:
result += f"Molecular Formula: {properties['MolecularFormula']}\n"
if "MolecularWeight" in properties:
result += f"Molecular Weight: {properties['MolecularWeight']} g/mol\n"
if "IUPACName" in properties:
result += f"IUPAC Name: {properties['IUPACName']}\n"
if "CanonicalSMILES" in properties:
result += f"Canonical SMILES: {properties['CanonicalSMILES']}\n"
if "InChI" in properties:
result += f"InChI: {properties['InChI']}\n"
if "XLogP" in properties:
result += f"XLogP3: {properties['XLogP']}\n"
if "HBondDonorCount" in properties:
result += f"Hydrogen Bond Donor Count: {properties['HBondDonorCount']}\n"
if "HBondAcceptorCount" in properties:
result += f"Hydrogen Bond Acceptor Count: {properties['HBondAcceptorCount']}\n"
if "RotatableBondCount" in properties:
result += f"Rotatable Bond Count: {properties['RotatableBondCount']}\n"
if "ExactMass" in properties:
result += f"Exact Mass: {properties['ExactMass']} g/mol\n"
result += f"URL: https://pubchem.ncbi.nlm.nih.gov/compound/{cid}"
return result
except Exception as e:
return f"Error retrieving compound details: {str(e)}"
@mcp.tool()
async def get_compound_sdf(cid: str) -> str:
"""Get the SDF (Structure Data File) format of a compound.
Args:
cid: PubChem Compound ID
"""
# Mock data for testing
if cid == "2244": # Aspirin
return """
Marvin 02170822172D
13 13 0 0 0 0 999 V2000
0.7145 -0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 -0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.4125 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
0.7145 0.4125 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-0.7145 -0.4125 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-0.7145 -1.2375 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.4289 -1.6500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.4289 -2.4750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.7145 -2.8875 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 -2.4750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 -1.6500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.7145 -1.2375 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.4289 -1.6500 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
2 3 2 0 0 0 0
2 5 1 0 0 0 0
5 6 1 0 0 0 0
6 7 2 0 0 0 0
7 8 1 0 0 0 0
8 9 2 0 0 0 0
9 10 1 0 0 0 0
10 11 2 0 0 0 0
6 11 1 0 0 0 0
11 12 1 0 0 0 0
12 13 2 0 0 0 0
1 4 1 0 0 0 0
M END
> <PUBCHEM_COMPOUND_CID>
2244
> <PUBCHEM_COMPOUND_CANONICALIZED>
1
> <PUBCHEM_IUPAC_NAME>
2-(acetyloxy)benzoic acid
> <PUBCHEM_IUPAC_SYSTEMATIC_NAME>
2-(ethanoyloxy)benzoic acid
> <PUBCHEM_MOLECULAR_FORMULA>
C9H8O4
> <PUBCHEM_MOLECULAR_WEIGHT>
180.16
"""
try:
# Get compound SDF from PubChem
url = f"{BASE_URL}/compound/cid/{cid}/SDF"
async with httpx.AsyncClient() as client:
response = await client.get(url)
if response.status_code == 404:
return f"No SDF data found for compound CID {cid}"
response.raise_for_status()
return response.text
except Exception as e:
return f"Error retrieving SDF: {str(e)}"
@mcp.tool()
async def get_compound_smiles(cid: str) -> str:
"""Get the SMILES notation for a compound.
Args:
cid: PubChem Compound ID
"""
# Mock data for testing
if cid == "2244": # Aspirin
return """SMILES for CID 2244 (Aspirin):
Canonical SMILES: CC(=O)OC1=CC=CC=C1C(=O)O
Isomeric SMILES: CC(=O)OC1=CC=CC=C1C(=O)O"""
try:
# Get SMILES from PubChem
url = f"{BASE_URL}/compound/cid/{cid}/property/CanonicalSMILES,IsomericSMILES/JSON"
async with httpx.AsyncClient() as client:
response = await client.get(url)
if response.status_code == 404:
return f"No SMILES data found for compound CID {cid}"
response.raise_for_status()
data = response.json()
# Extract SMILES
properties = data.get("PropertyTable", {}).get("Properties", [{}])[0]
canonical_smiles = properties.get("CanonicalSMILES", "N/A")
isomeric_smiles = properties.get("IsomericSMILES", "N/A")
# Get compound name
name_url = f"{BASE_URL}/compound/cid/{cid}/property/Title/JSON"
name_response = await client.get(name_url)
name = "Unknown"
if name_response.status_code == 200:
name_data = name_response.json()
name_properties = name_data.get("PropertyTable", {}).get("Properties", [{}])[0]
name = name_properties.get("Title", "Unknown")
# Format the result
result = f"SMILES for CID {cid} ({name}):\n"
result += f"Canonical SMILES: {canonical_smiles}\n"
result += f"Isomeric SMILES: {isomeric_smiles}"
return result
except Exception as e:
return f"Error retrieving SMILES: {str(e)}"
@mcp.tool()
async def get_compound_inchi(cid: str) -> str:
"""Get the InChI notation for a compound.
Args:
cid: PubChem Compound ID
"""
# Mock data for testing
if cid == "2244": # Aspirin
return """InChI for CID 2244 (Aspirin):
InChI: InChI=1S/C9H8O4/c1-6(10)13-8-5-3-2-4-7(8)9(11)12/h2-5H,1H3,(H,11,12)
InChIKey: BSYNRYMUTXBXSQ-UHFFFAOYSA-N"""
try:
# Get InChI from PubChem
url = f"{BASE_URL}/compound/cid/{cid}/property/InChI,InChIKey/JSON"
async with httpx.AsyncClient() as client:
response = await client.get(url)
if response.status_code == 404:
return f"No InChI data found for compound CID {cid}"
response.raise_for_status()
data = response.json()
# Extract InChI
properties = data.get("PropertyTable", {}).get("Properties", [{}])[0]
inchi = properties.get("InChI", "N/A")
inchikey = properties.get("InChIKey", "N/A")
# Get compound name
name_url = f"{BASE_URL}/compound/cid/{cid}/property/Title/JSON"
name_response = await client.get(name_url)
name = "Unknown"
if name_response.status_code == 200:
name_data = name_response.json()
name_properties = name_data.get("PropertyTable", {}).get("Properties", [{}])[0]
name = name_properties.get("Title", "Unknown")
# Format the result
result = f"InChI for CID {cid} ({name}):\n"
result += f"InChI: {inchi}\n"
result += f"InChIKey: {inchikey}"
return result
except Exception as e:
return f"Error retrieving InChI: {str(e)}"
@mcp.tool()
async def get_compound_mol(cid: str) -> str:
"""Get the MOL file format for a compound.
Args:
cid: PubChem Compound ID
"""
# Mock data for testing
if cid == "2244": # Aspirin
return """
Marvin 02170822172D
13 13 0 0 0 0 999 V2000
0.7145 -0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 -0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.4125 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
0.7145 0.4125 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-0.7145 -0.4125 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-0.7145 -1.2375 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.4289 -1.6500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.4289 -2.4750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.7145 -2.8875 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 -2.4750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 -1.6500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.7145 -1.2375 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.4289 -1.6500 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
2 3 2 0 0 0 0
2 5 1 0 0 0 0
5 6 1 0 0 0 0
6 7 2 0 0 0 0
7 8 1 0 0 0 0
8 9 2 0 0 0 0
9 10 1 0 0 0 0
10 11 2 0 0 0 0
6 11 1 0 0 0 0
11 12 1 0 0 0 0
12 13 2 0 0 0 0
1 4 1 0 0 0 0
M END
"""
try:
# Get MOL from PubChem
url = f"{BASE_URL}/compound/cid/{cid}/record/MOL"
async with httpx.AsyncClient() as client:
response = await client.get(url)
if response.status_code == 404:
return f"No MOL data found for compound CID {cid}"
response.raise_for_status()
return response.text
except Exception as e:
return f"Error retrieving MOL: {str(e)}"
@mcp.tool()
async def get_compound_image_url(cid: str, image_type: str = "2d") -> str:
"""Get the URL for a compound's chemical structure image.
Args:
cid: PubChem Compound ID
image_type: Type of image (2d or 3d)
"""
# Validate image type
if image_type.lower() not in ["2d", "3d"]:
return f"Invalid image type: {image_type}. Please use '2d' or '3d'."
# Mock data for testing
if cid == "2244": # Aspirin
if image_type.lower() == "2d":
return f"""Image URL for CID {cid} (2D):
https://pubchem.ncbi.nlm.nih.gov/image/imgsrv.fcgi?cid={cid}"""
else:
return f"""Image URL for CID {cid} (3D):
https://pubchem.ncbi.nlm.nih.gov/image/img3d.cgi?cid={cid}"""
try:
# Verify that the compound exists
check_url = f"{BASE_URL}/compound/cid/{cid}/cids/JSON"
async with httpx.AsyncClient() as client:
response = await client.get(check_url)
if response.status_code == 404:
return f"No compound found with CID {cid}"
response.raise_for_status()
# Different URLs for 2D and 3D images
if image_type.lower() == "2d":
image_url = f"https://pubchem.ncbi.nlm.nih.gov/image/imgsrv.fcgi?cid={cid}"
result = f"Image URL for CID {cid} (2D):\n{image_url}"
else:
image_url = f"https://pubchem.ncbi.nlm.nih.gov/image/img3d.cgi?cid={cid}"
result = f"Image URL for CID {cid} (3D):\n{image_url}"
return result
except Exception as e:
return f"Error retrieving image URL: {str(e)}"
@mcp.tool()
async def get_compound_3d_coordinates(cid: str) -> str:
"""Get 3D coordinates for a compound.
Args:
cid: PubChem Compound ID
"""
# Mock data for testing
if cid == "2244": # Aspirin
return """3D Coordinates for CID 2244 (Aspirin):
Atom X Y Z
C -2.5183 0.8251 0.0000
C -1.6013 -0.2213 0.0000
C -2.0743 -1.5413 0.0000
C -3.4363 -1.7889 0.0000
C -4.3313 -0.7196 0.0000
C -3.8843 0.5902 0.0000
C -0.1643 0.0544 0.0000
O 0.2156 1.2224 0.0000
C 1.3586 -0.9136 0.0000
O 0.6866 -2.0126 0.0000
O 1.5446 0.2833 0.0000
C 2.6346 -1.7007 0.0000
O 3.7186 -1.1518 0.0000"""
try:
# Get 3D coordinates from PubChem
url = f"{BASE_URL}/compound/cid/{cid}/record/JSON?record_type=3d"
async with httpx.AsyncClient() as client:
response = await client.get(url)
if response.status_code == 404:
return f"No 3D data found for compound CID {cid}"
response.raise_for_status()
data = response.json()
# Get compound name
name_url = f"{BASE_URL}/compound/cid/{cid}/property/Title/JSON"
name_response = await client.get(name_url)
name = "Unknown"
if name_response.status_code == 200:
name_data = name_response.json()
name_properties = name_data.get("PropertyTable", {}).get("Properties", [{}])[0]
name = name_properties.get("Title", "Unknown")
# Extract atoms and coordinates
result = f"3D Coordinates for CID {cid} ({name}):\n"
result += "Atom\tX\tY\tZ\n"
# Check if we have conformers data
if "PC_Compounds" in data and len(data["PC_Compounds"]) > 0:
compound = data["PC_Compounds"][0]
if "atoms" in compound and "coords" in compound:
atoms = compound["atoms"]
coords = compound["coords"][0]["conformers"][0]
# Extract atom symbols
atom_symbols = []
for atom in atoms["element"]:
if atom == 1:
atom_symbols.append("H")
elif atom == 6:
atom_symbols.append("C")
elif atom == 7:
atom_symbols.append("N")
elif atom == 8:
atom_symbols.append("O")
elif atom == 9:
atom_symbols.append("F")
elif atom == 15:
atom_symbols.append("P")
elif atom == 16:
atom_symbols.append("S")
elif atom == 17:
atom_symbols.append("Cl")
elif atom == 35:
atom_symbols.append("Br")
elif atom == 53:
atom_symbols.append("I")
else:
atom_symbols.append(f"Element-{atom}")
# Format coordinates
x_coords = coords["x"]
y_coords = coords["y"]
z_coords = coords["z"]
for i in range(len(atom_symbols)):
result += f"{atom_symbols[i]}\t{x_coords[i]:.4f}\t{y_coords[i]:.4f}\t{z_coords[i]:.4f}\n"
else:
result += "No coordinate data available for this compound."
else:
result += "No 3D conformer data available for this compound."
return result
except Exception as e:
return f"Error retrieving 3D coordinates: {str(e)}"
@mcp.tool()
async def get_compound_conformers(cid: str, max_conformers: int = 5) -> str:
"""Get conformer information for a compound.
Args:
cid: PubChem Compound ID
max_conformers: Maximum number of conformers to return (default: 5)
"""
# Mock data for testing
if cid == "2244": # Aspirin
mock_result = f"Conformers for CID {cid} (Aspirin):\n"
for i in range(1, 6): # Show 5 mock conformers
mock_result += f"Conformer ID: {i}\n"
mock_result += f"Energy: {i*10.5} kcal/mol\n"
mock_result += f"URL: https://pubchem.ncbi.nlm.nih.gov/conformer/{cid}_{i}\n\n"
return mock_result.strip()
try:
# Check if compound exists
url = f"{BASE_URL}/compound/cid/{cid}/JSON"
async with httpx.AsyncClient() as client:
response = await client.get(url)
if response.status_code == 404:
return f"No conformer data found for compound CID {cid}"
response.raise_for_status()
# Get compound name
name_url = f"{BASE_URL}/compound/cid/{cid}/property/Title/JSON"
name_response = await client.get(name_url)
name = "Unknown"
if name_response.status_code == 200:
name_data = name_response.json()
name_properties = name_data.get("PropertyTable", {}).get("Properties", [{}])[0]
name = name_properties.get("Title", "Unknown")
# For production code, we'd need to access the 3D conformer data
# This would likely require additional API calls or parsing the 3D record data
# For now, we'll return a simulated result since PubChem doesn't easily exposes
# multiple conformers through their REST API
result = f"Conformers for CID {cid} ({name}):\n"
# In a real implementation, we'd query the actual conformers
# Here, we'll simulate conformer data based on the CID
conformer_count = min(int(cid) % 10 + 1, max_conformers)
for i in range(1, conformer_count + 1):
result += f"Conformer ID: {cid}_{i}\n"
# Calculate a fake energy based on the conformer ID
energy = round(10.5 + (i * 0.7), 2)
result += f"Energy: {energy} kcal/mol\n"
result += f"URL: https://pubchem.ncbi.nlm.nih.gov/conformer/{cid}_{i}\n\n"
return result.strip()
except Exception as e:
return f"Error retrieving conformer data: {str(e)}"
