gnnepcsaft-mcp-server 0.1.2__tar.gz → 0.2.3__tar.gz

{gnnepcsaft_mcp_server-0.1.2 → gnnepcsaft_mcp_server-0.2.3}/PKG-INFO

@@ -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/README.md

@@ -0,0 +1,42 @@
+# GNNEPCSAFT MCP Server
+
+## 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 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
+
+- 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
+
+You're gonna need [uvx](https://docs.astral.sh/uv/).
+
+## Usage
+
+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
+{
+  "mcpServers": {
+    "gnnepcsaft": {
+      "command": "uvx",
+      "args": ["--from", "gnnepcsaft-mcp-server", "gnnepcsaftmcp"]
+    }
+  }
+}
+```
+
+## License
+
+GNU General Public License v3.0

{gnnepcsaft_mcp_server-0.1.2 → gnnepcsaft_mcp_server-0.2.3}/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-0.2.3/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 → gnnepcsaft_mcp_server-0.2.3}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "gnnepcsaft-mcp-server"
-version = "0.1.2"
+version = "0.2.3"
 description = "Model Context Protocol server for GNNePCSAFT tools"
 authors = [
     {name = "wildsonbbl",email = "wil_bbl@hotmail.com"}
@@ -22,7 +22,7 @@ dependencies = [
 gnnepcsaftmcp = 'gnnepcsaft_mcp_server.mcp_server:run'
 
 [tool.poetry]
-include = ["gnnepcsaft_mcp_server/models/assoc_8.onnx", "gnnepcsaft_mcp_server/models/assoc_8.onnx.data", "gnnepcsaft_mcp_server/models/msigmae_7.onnx", "gnnepcsaft_mcp_server/models/msigmae_7.onnx.data"]
+include = ["gnnepcsaft_mcp_server/models/assoc_8.onnx", "gnnepcsaft_mcp_server/models/msigmae_7.onnx"]
 
 
 

gnnepcsaft_mcp_server-0.1.2/README.md

@@ -1,35 +0,0 @@
-# GNNEPCSAFT MCP Server
-
-## 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.
-
-## Features
-
-- Model context management
-- Protocol handling for model communication
-- Client request processing
-- Context state synchronization
-
-## Installation
-
-You're gonna need [uvx](https://docs.astral.sh/uv/).
-
-## Usage
-
-stdio config to start the MCP server:
-
-```json
-{
-  "mcpServers": {
-    "gnnepcsaft": {
-      "command": "uvx",
-      "args": ["--from", "gnnepcsaft-mcp-server", "gnnepcsaftmcp"]
-    }
-  }
-}
-```
-
-## License
-
-GNU General Public License v3.0