gnnepcsaft-mcp-server 0.1.2__py3-none-any.whl → 0.2.3__py3-none-any.whl

gnnepcsaft_mcp_server/mcp_server.py

@@ -4,6 +4,7 @@ from typing import Any, Callable, List
 
 from mcp.server.fastmcp import FastMCP
 
+from .plot_utils import v3000_mol_block
 from .utils import (
     batch_convert_pure_density_to_kg_per_m3,
     batch_critical_points,
@@ -39,6 +40,7 @@ fn_list: List[Callable[..., Any]] = [
     mixture_vapor_pressure,
     pubchem_description,
     pure_phase,
+    v3000_mol_block,
 ]
 for fn in fn_list:
     mcp.add_tool(fn)

gnnepcsaft_mcp_server/plot_utils.py

@@ -0,0 +1,28 @@
+"plot utils"
+
+from rdkit.Chem import AllChem as Chem
+
+from .utils import smilestoinchi
+
+
+def v3000_mol_block(smiles: str) -> str:
+    """Returns a V3000 Mol block for a molecule.
+
+    Args:
+        smiles (str): SMILES of the molecule.
+
+    """
+    inchi = smilestoinchi(smiles)
+
+    mol = Chem.MolFromInchi(inchi)
+    mol = Chem.AddHs(mol)  # type: ignore
+    params = Chem.ETKDGv3()  # type: ignore
+    params.randomSeed = 0xF00D
+    result = Chem.EmbedMolecule(mol, params)  # type: ignore
+    if result == 0:
+        Chem.MMFFOptimizeMolecule(  # type: ignore
+            mol, maxIters=1000, nonBondedThresh=100, ignoreInterfragInteractions=False
+        )
+    # mol = Chem.RemoveHs(mol, implicitOnly=False)
+    imgmol = Chem.MolToV3KMolBlock(mol)  # type: ignore
+    return imgmol

{gnnepcsaft_mcp_server-0.1.2.dist-info → gnnepcsaft_mcp_server-0.2.3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: gnnepcsaft-mcp-server
-Version: 0.1.2
+Version: 0.2.3
 Summary: Model Context Protocol server for GNNePCSAFT tools
 License: GNU General Public License v3.0
 Author: wildsonbbl
@@ -25,14 +25,15 @@ Description-Content-Type: text/markdown
 
 ## Overview
 
-This is the Model Context Protocol ([MCP](https://modelcontextprotocol.io/introduction)) server implementation for [GNNePCSAFT](https://github.com/wildsonbbl/gnnepcsaft) tools. The server handles communication and context management between models and clients using the MCP protocol.
+This is the Model Context Protocol ([MCP](https://modelcontextprotocol.io/introduction)) server implementation for [GNNePCSAFT](https://github.com/wildsonbbl/gnnepcsaft) tools. The server handles communication and context management between LLM models and clients using the MCP protocol. GNNePCSAFT is a Graph Neural Network ([GNN](https://en.wikipedia.org/wiki/Graph_neural_network)) that can estimate [ePC-SAFT](https://en.wikipedia.org/wiki/PC-SAFT) parameters. This allows thermodynamic calculations like density and vapor pressure without experimental data for any molecule. [FeOS](https://github.com/feos-org/feos) is used for the PC-SAFT calculations.
 
 ## Features
 
-- Model context management
-- Protocol handling for model communication
-- Client request processing
-- Context state synchronization
+- Calculates density, vapor pressure, enthalpy of vaporization and critical points
+- Estimates ePC-SAFT parameters
+- Thermodynamic calculations for pure components and mixtures
+- Collects information from PubChem, if any, for any molecule
+- Allows thermodynamics-aware LLMs
 
 ## Installation
 
@@ -40,7 +41,13 @@ You're gonna need [uvx](https://docs.astral.sh/uv/).
 
 ## Usage
 
-stdio config to start the MCP server:
+The command to start the server would be:
+
+```bash
+uvx --from gnnepcsaft-mcp-server gnnepcsaftmcp
+```
+
+[Claude Desktop](https://claude.ai/download) config to start the MCP server:
 
 ```json
 {

gnnepcsaft_mcp_server-0.2.3.dist-info/RECORD

@@ -0,0 +1,11 @@
+gnnepcsaft_mcp_server/__init__.py,sha256=Npbt9RPLtKrFDK-oeyrAbz0b7lg9Y1Le1mxAQVtD_PY,24
+gnnepcsaft_mcp_server/mcp_server.py,sha256=bjxUDiRu5mZFWuqwRuPsy1l-LHQNt_kW_wxjNEnp444,1146
+gnnepcsaft_mcp_server/models/.gitignore,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+gnnepcsaft_mcp_server/models/assoc_8.onnx,sha256=dYSYGfCq-8TNmM2qamhFfGAhtCTPVCbYHBbapwBOTMA,7510456
+gnnepcsaft_mcp_server/models/msigmae_7.onnx,sha256=cP42XuaH_auXsVl4iUuv5J4nMdGXf6V3KkIr8wY5epw,11255526
+gnnepcsaft_mcp_server/plot_utils.py,sha256=-iUZy-54bF1Sv-5Nuug4DjOACI7KA97YxiizJKK_E0E,786
+gnnepcsaft_mcp_server/utils.py,sha256=6NJ5lB4q-EjC1KXBKXXBPQ4qtVCZcjvR82I2lD06hIk,9916
+gnnepcsaft_mcp_server-0.2.3.dist-info/METADATA,sha256=VqXDWRsQ8WAWcnQ0jLYvpDuW9qy8q1xlXgILu43QMoE,2313
+gnnepcsaft_mcp_server-0.2.3.dist-info/WHEEL,sha256=fGIA9gx4Qxk2KDKeNJCbOEwSrmLtjWCwzBz351GyrPQ,88
+gnnepcsaft_mcp_server-0.2.3.dist-info/entry_points.txt,sha256=5tsnxZG8Vtdrr3CT-8Pv35RjpcDiR0L28cYxxHeCsPI,70
+gnnepcsaft_mcp_server-0.2.3.dist-info/RECORD,,

gnnepcsaft_mcp_server-0.1.2.dist-info/RECORD

@@ -1,12 +0,0 @@
-gnnepcsaft_mcp_server/__init__.py,sha256=Npbt9RPLtKrFDK-oeyrAbz0b7lg9Y1Le1mxAQVtD_PY,24
-gnnepcsaft_mcp_server/mcp_server.py,sha256=XUM9ir7RvJA8npgIlo7n8J1ZhnQzDslGnsxwOnItbEo,1085
-gnnepcsaft_mcp_server/models/.gitignore,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-gnnepcsaft_mcp_server/models/assoc_8.onnx,sha256=FBSU3cP1NyelkwCtLaWVhaeX8QuzQGp6Mf3lSV97mzE,2287889
-gnnepcsaft_mcp_server/models/assoc_8.onnx.data,sha256=AMg5VrBZi1F-kZ_YAQay_BDaQQtbs8ihfn4BgWbYzeM,11468800
-gnnepcsaft_mcp_server/models/msigmae_7.onnx,sha256=TiKHrwBbNPyoOeeRQ_W_xnEqEtopmI_FIBtZJyN4afk,2288073
-gnnepcsaft_mcp_server/models/msigmae_7.onnx.data,sha256=kExPbT75jMLRAYRQQZ8WPeY0rYvAfDZx-Bnji_dLJ1s,11469056
-gnnepcsaft_mcp_server/utils.py,sha256=6NJ5lB4q-EjC1KXBKXXBPQ4qtVCZcjvR82I2lD06hIk,9916
-gnnepcsaft_mcp_server-0.1.2.dist-info/METADATA,sha256=juIntwbiIW1lwI5vTYLl7QcGUXCkCBlcf8ffKVDSCAU,1653
-gnnepcsaft_mcp_server-0.1.2.dist-info/WHEEL,sha256=fGIA9gx4Qxk2KDKeNJCbOEwSrmLtjWCwzBz351GyrPQ,88
-gnnepcsaft_mcp_server-0.1.2.dist-info/entry_points.txt,sha256=5tsnxZG8Vtdrr3CT-8Pv35RjpcDiR0L28cYxxHeCsPI,70
-gnnepcsaft_mcp_server-0.1.2.dist-info/RECORD,,