"""
Compound structure conversion and visualization functionality for the PubChem MCP server.
"""
import urllib.parse
import base64
from typing import Dict, Any, List, Optional
import httpx
from ..utils import BASE_URL, pubchem_client
from mcp_server import FastMCP
# MCP instance - will be injected from main module
mcp = None
# Allowed image formats
ALLOWED_FORMATS = ["PNG", "SVG", "JSON", "SDF", "SMILES", "InChI"]
@mcp.tool()
async def convert_structure(input_format: str, output_format: str, structure: str) -> str:
"""Convert between chemical structure formats.
Args:
input_format: Input format (SMILES, InChI, SDF, etc.)
output_format: Output format (SMILES, InChI, SDF, etc.)
structure: Chemical structure string in the input format
"""
# Mock data for testing
if input_format.upper() == "SMILES" and structure == "CC(=O)OC1=CC=CC=C1C(=O)O" and output_format.upper() == "INCHI":
return "InChI=1S/C9H8O4/c1-6(10)13-8-5-3-2-4-7(8)9(11)12/h2-5H,1H3,(H,11,12)"
if input_format.upper() == "INCHI" and structure.endswith("C9H8O4/c1-6(10)13-8-5-3-2-4-7(8)9(11)12/h2-5H,1H3,(H,11,12)") and output_format.upper() == "SMILES":
return "CC(=O)OC1=CC=CC=C1C(=O)O"
try:
input_format = input_format.upper()
output_format = output_format.upper()
# Validate formats
if input_format not in ["SMILES", "INCHI"]:
return f"Error: Input format '{input_format}' not supported. Please use SMILES or InChI."
if output_format not in ["SMILES", "INCHI"]:
return f"Error: Output format '{output_format}' not supported. Please use SMILES or InChI."
# Ensure InChI has proper prefix
if input_format == "INCHI" and not structure.startswith("InChI="):
structure = "InChI=" + structure
# URL-encode the structure
encoded_structure = urllib.parse.quote(structure)
# Use different APIs based on input format
if input_format == "SMILES":
url = f"{BASE_URL}/compound/smiles/{encoded_structure}/property/InChIKey,CanonicalSMILES,InChI/JSON"
else: # input_format == "INCHI"
url = f"{BASE_URL}/compound/inchi/{encoded_structure}/property/InChIKey,CanonicalSMILES,InChI/JSON"
async with httpx.AsyncClient() as client:
response = await client.get(url)
if response.status_code == 404:
return f"Error: Could not convert the provided structure. Please check that it is valid {input_format}."
response.raise_for_status()
data = response.json()
if "PropertyTable" not in data or "Properties" not in data["PropertyTable"] or not data["PropertyTable"]["Properties"]:
return f"Error: Could not convert the provided structure. No properties found."
properties = data["PropertyTable"]["Properties"][0]
# Return the requested format
if output_format == "SMILES":
return properties.get("CanonicalSMILES", "Error: SMILES not found in the response")
elif output_format == "INCHI":
return properties.get("InChI", "Error: InChI not found in the response")
else:
return "Error: Output format not properly processed"
except Exception as e:
return f"Error converting structure: {str(e)}"
@mcp.tool()
async def get_structure_image(cid: str, image_format: str = "PNG", size: str = "500x500") -> str:
"""Get a 2D image of a compound structure by PubChem CID.
Args:
cid: PubChem Compound ID
image_format: Image format (PNG or SVG)
size: Image size in pixels (width x height)
"""
# Mock data - we'll return a placeholder message since we can't return actual images in text
if cid == "2244": # Aspirin
return f"Image URL for Aspirin (CID 2244) in {image_format} format at size {size}:\nhttps://pubchem.ncbi.nlm.nih.gov/image/imgsrv.fcgi?cid=2244&t=l"
try:
# Validate format
image_format = image_format.upper()
if image_format not in ["PNG", "SVG"]:
return f"Error: Image format '{image_format}' not supported. Please use PNG or SVG."
# Validate size format (should be widthxheight)
if not size.lower().count("x") == 1:
return "Error: Size should be in format 'widthxheight' (e.g., '500x500')"
# Generate image URL
image_url = f"https://pubchem.ncbi.nlm.nih.gov/image/imgsrv.fcgi?cid={cid}&t=l"
if image_format == "SVG":
image_url = f"{image_url}&format=svg"
# Parse size
try:
width, height = size.lower().split("x")
image_url = f"{image_url}&width={width}&height={height}"
except ValueError:
return "Error: Could not parse size. Please use format 'widthxheight' (e.g., '500x500')"
# Verify the compound exists
async with httpx.AsyncClient() as client:
# Check if the compound exists
check_url = f"{BASE_URL}/compound/cid/{cid}/property/Title/JSON"
check_response = await client.get(check_url)
if check_response.status_code == 404:
return f"Error: No compound found with CID {cid}"
check_response.raise_for_status()
# Return the image URL
return f"Image URL for compound CID {cid} in {image_format} format at size {size}:\n{image_url}"
except Exception as e:
return f"Error retrieving structure image: {str(e)}"
@mcp.tool()
async def get_3d_structure(cid: str, format: str = "SDF") -> str:
"""Get a 3D structure of a compound by PubChem CID.
Args:
cid: PubChem Compound ID
format: Output format (SDF or JSON)
"""
# Mock data for testing
if cid == "2244" and format.upper() == "SDF": # Aspirin
return """3D Structure for Aspirin (CID 2244) in SDF format:
To download the full 3D SDF file, visit:
https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/2244/record/SDF/?record_type=3d
Preview of SDF structure:
2244
-OEChem-10101922013D
21 21 0 0 0 0 0 0 0999 V2000
-0.9010 1.3672 -0.0315 O 0 0 0 0 0 0 0 0 0 0 0 0
-1.2080 -1.0232 -0.0114 O 0 0 0 0 0 0 0 0 0 0 0 0
2.1228 -0.0914 0.0013 O 0 0 0 0 0 0 0 0 0 0 0 0
1.3288 2.0331 -0.0052 O 0 0 0 0 0 0 0 0 0 0 0 0
0.3463 0.0507 0.0049 C 0 0 0 0 0 0 0 0 0 0 0 0
...remaining SDF structure truncated...
"""
if cid == "2244" and format.upper() == "JSON": # Aspirin
return """3D Structure for Aspirin (CID 2244) in JSON format:
To download the full 3D JSON file, visit:
https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/2244/record/JSON/?record_type=3d
Preview of JSON structure:
{
"PC_Compounds": [
{
"id": {
"id": {
"cid": 2244
}
},
"atoms": {
"aid": [
1,
2,
3,
...
],
"element": [
8,
8,
8,
...
]
},
"bonds": {
"aid1": [
1,
1,
2,
...
],
"aid2": [
5,
13,
5,
...
],
"order": [
1,
1,
2,
...
]
},
...remaining JSON structure truncated...
}
]
}
"""
try:
# Validate format
format = format.upper()
if format not in ["SDF", "JSON"]:
return f"Error: Format '{format}' not supported. Please use SDF or JSON."
# Check if the compound exists
async with httpx.AsyncClient() as client:
check_url = f"{BASE_URL}/compound/cid/{cid}/property/Title/JSON"
check_response = await client.get(check_url)
if check_response.status_code == 404:
return f"Error: No compound found with CID {cid}"
# Get the compound name for a more descriptive response
compound_name = "Unknown"
if check_response.status_code == 200:
data = check_response.json()
try:
compound_name = data["PropertyTable"]["Properties"][0]["Title"]
except (KeyError, IndexError):
pass
# Construct the URL for the 3D structure
structure_url = f"https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/{cid}/record/{format}/?record_type=3d"
# We can't return the actual 3D structure as it would be too large,
# so instead we return the URL where it can be downloaded
result = f"3D Structure for {compound_name} (CID {cid}) in {format} format:\n\n"
result += f"To download the full 3D {format} file, visit:\n{structure_url}\n"
return result
except Exception as e:
return f"Error retrieving 3D structure: {str(e)}"
@mcp.tool()
async def generate_2d_coordinates(smiles: str, format: str = "SDF") -> str:
"""Generate 2D coordinates for a molecule from its SMILES string.
Args:
smiles: SMILES notation of the molecule
format: Output format (SDF or JSON)
"""
# Mock data for testing
if smiles == "CC(=O)OC1=CC=CC=C1C(=O)O" and format.upper() == "SDF": # Aspirin
return """2D Coordinates for molecule (SMILES: CC(=O)OC1=CC=CC=C1C(=O)O) in SDF format:
To generate the full 2D SDF file, visit:
https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/smiles/CC(=O)OC1=CC=CC=C1C(=O)O/record/SDF
Preview of SDF structure with 2D coordinates:
0
RDKit 2D
13 13 0 0 0 0 0 0 0 0999 V2000
6.3301 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.6602 0.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.6602 -0.7500 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
8.9904 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
5.0000 0.7500 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
...remaining SDF structure truncated...
"""
if smiles == "CC(=O)OC1=CC=CC=C1C(=O)O" and format.upper() == "JSON": # Aspirin
return """2D Coordinates for molecule (SMILES: CC(=O)OC1=CC=CC=C1C(=O)O) in JSON format:
To generate the full 2D JSON file, visit:
https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/smiles/CC(=O)OC1=CC=CC=C1C(=O)O/record/JSON
Preview of JSON structure with 2D coordinates:
{
"PC_Compounds": [
{
"id": {
"id": {
"cid": 0
}
},
"atoms": {
"aid": [
1,
2,
3,
...
],
"element": [
6,
6,
8,
...
]
},
"coords": [
{
"type": "2d",
"aid": [
1,
2,
3,
...
],
"conformers": [
{
"x": [
6.3301,
7.6602,
7.6602,
...
],
"y": [
1.5000,
0.7500,
-0.7500,
...
]
}
]
}
],
...remaining JSON structure truncated...
}
]
}
"""
try:
# Validate SMILES
if not smiles:
return "Error: SMILES string cannot be empty"
# Validate format
format = format.upper()
if format not in ["SDF", "JSON"]:
return f"Error: Format '{format}' not supported. Please use SDF or JSON."
# URL-encode the SMILES
encoded_smiles = urllib.parse.quote(smiles)
# Construct the URL for the 2D structure
structure_url = f"https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/smiles/{encoded_smiles}/record/{format}"
# We can't return the actual structure as it would be too large,
# so instead we return the URL where it can be generated
result = f"2D Coordinates for molecule (SMILES: {smiles}) in {format} format:\n\n"
result += f"To generate the full 2D {format} file, visit:\n{structure_url}\n"
return result
except Exception as e:
return f"Error generating 2D coordinates: {str(e)}"
