gnnepcsaft-mcp-server 0.1.3__tar.gz → 0.3.0__tar.gz

gnnepcsaft_mcp_server-0.3.0/PKG-INFO

@@ -0,0 +1,100 @@
+Metadata-Version: 2.3
+Name: gnnepcsaft-mcp-server
+Version: 0.3.0
+Summary: Model Context Protocol server for GNNePCSAFT tools
+License: GNU General Public License v3.0
+Author: wildsonbbl
+Author-email: wil_bbl@hotmail.com
+Requires-Python: >=3.10
+Classifier: License :: Other/Proprietary License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Requires-Dist: feos (>=0.8.0,<0.9.0)
+Requires-Dist: gnnepcsaft (>=0.2.4)
+Requires-Dist: mcp (>=1.6.0,<2.0.0)
+Requires-Dist: numpy (>=2.2.4,<3.0.0)
+Requires-Dist: onnxruntime (>=1.21.0,<2.0.0)
+Requires-Dist: rdkit (>=2024.9.6,<2025.0.0)
+Requires-Dist: si-units (>=0.11.0,<0.12.0)
+Description-Content-Type: text/markdown
+
+# GNNEPCSAFT MCP Server
+
+## What is GNNEPCSAFT MCP Server?
+
+GNNEPCSAFT MCP Server is an implementation of the [Model Context Protocol (MCP)](https://modelcontextprotocol.io/introduction) for [GNNePCSAFT](https://github.com/wildsonbbl/gnnepcsaft) tools. It enables seamless communication and context management between large language models (LLMs) and clients for advanced thermodynamic calculations. GNNePCSAFT leverages Graph Neural Networks (GNNs) to estimate [ePC-SAFT](https://en.wikipedia.org/wiki/PC-SAFT) parameters, allowing property predictions such as density and vapor pressure for any molecule, even without experimental data. [FeOS](https://github.com/feos-org/feos) is used for PC-SAFT calculations.
+
+---
+
+## Key Features
+
+- **Estimate ePC-SAFT parameters** using GNNs
+- **Calculate density, vapor pressure, enthalpy of vaporization, critical points, and others**
+- **Support for pure components and mixtures**
+- **Automatic data collection from PubChem** for any molecule
+- **Designed for thermodynamics-aware LLMs**
+
+---
+
+## How to Use
+
+### Installation
+
+You need [uvx](https://docs.astral.sh/uv/) installed.
+
+### Starting the Server
+
+```bash
+uvx --from gnnepcsaft-mcp-server gnnepcsaftmcp
+```
+
+### Example: Claude Desktop Configuration
+
+```json
+{
+  "mcpServers": {
+    "gnnepcsaft": {
+      "command": "uvx",
+      "args": ["--from", "gnnepcsaft-mcp-server", "gnnepcsaftmcp"]
+    }
+  }
+}
+```
+
+---
+
+## Use Cases
+
+- Predicting thermodynamic properties for new or existing molecules
+- Running property calculations for mixtures in research or industry
+- Integrating with LLMs for chemistry and materials science applications
+- Automating data collection and property estimation in pipelines
+
+---
+
+## FAQ
+
+**Q: What do I need to run the server?**  
+A: You need Python, [uvx](https://docs.astral.sh/uv/), and the GNNEPCSAFT MCP Server package.
+
+**Q: Can I use this for mixtures as well as pure components?**  
+A: Yes, the server supports both pure components and mixtures.
+
+**Q: Where does the molecular data come from?**  
+A: The server can automatically fetch molecular information from PubChem.
+
+**Q: What calculations are supported?**  
+A: Density, vapor pressure, enthalpy of vaporization, critical points, and ePC-SAFT parameter estimation.
+
+**Q: Is this open source?**  
+A: Yes, it is licensed under the GNU General Public License v3.0.
+
+---
+
+## License
+
+GNU General Public License v3.0
+

gnnepcsaft_mcp_server-0.3.0/README.md

@@ -0,0 +1,76 @@
+# GNNEPCSAFT MCP Server
+
+## What is GNNEPCSAFT MCP Server?
+
+GNNEPCSAFT MCP Server is an implementation of the [Model Context Protocol (MCP)](https://modelcontextprotocol.io/introduction) for [GNNePCSAFT](https://github.com/wildsonbbl/gnnepcsaft) tools. It enables seamless communication and context management between large language models (LLMs) and clients for advanced thermodynamic calculations. GNNePCSAFT leverages Graph Neural Networks (GNNs) to estimate [ePC-SAFT](https://en.wikipedia.org/wiki/PC-SAFT) parameters, allowing property predictions such as density and vapor pressure for any molecule, even without experimental data. [FeOS](https://github.com/feos-org/feos) is used for PC-SAFT calculations.
+
+---
+
+## Key Features
+
+- **Estimate ePC-SAFT parameters** using GNNs
+- **Calculate density, vapor pressure, enthalpy of vaporization, critical points, and others**
+- **Support for pure components and mixtures**
+- **Automatic data collection from PubChem** for any molecule
+- **Designed for thermodynamics-aware LLMs**
+
+---
+
+## How to Use
+
+### Installation
+
+You need [uvx](https://docs.astral.sh/uv/) installed.
+
+### Starting the Server
+
+```bash
+uvx --from gnnepcsaft-mcp-server gnnepcsaftmcp
+```
+
+### Example: Claude Desktop Configuration
+
+```json
+{
+  "mcpServers": {
+    "gnnepcsaft": {
+      "command": "uvx",
+      "args": ["--from", "gnnepcsaft-mcp-server", "gnnepcsaftmcp"]
+    }
+  }
+}
+```
+
+---
+
+## Use Cases
+
+- Predicting thermodynamic properties for new or existing molecules
+- Running property calculations for mixtures in research or industry
+- Integrating with LLMs for chemistry and materials science applications
+- Automating data collection and property estimation in pipelines
+
+---
+
+## FAQ
+
+**Q: What do I need to run the server?**  
+A: You need Python, [uvx](https://docs.astral.sh/uv/), and the GNNEPCSAFT MCP Server package.
+
+**Q: Can I use this for mixtures as well as pure components?**  
+A: Yes, the server supports both pure components and mixtures.
+
+**Q: Where does the molecular data come from?**  
+A: The server can automatically fetch molecular information from PubChem.
+
+**Q: What calculations are supported?**  
+A: Density, vapor pressure, enthalpy of vaporization, critical points, and ePC-SAFT parameter estimation.
+
+**Q: Is this open source?**  
+A: Yes, it is licensed under the GNU General Public License v3.0.
+
+---
+
+## License
+
+GNU General Public License v3.0

{gnnepcsaft_mcp_server-0.1.3 → gnnepcsaft_mcp_server-0.3.0}/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-0.3.0/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-0.1.3 → gnnepcsaft_mcp_server-0.3.0}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "gnnepcsaft-mcp-server"
-version = "0.1.3"
+version = "0.3.0"
 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-0.1.3/PKG-INFO

@@ -1,66 +0,0 @@
-Metadata-Version: 2.3
-Name: gnnepcsaft-mcp-server
-Version: 0.1.3
-Summary: Model Context Protocol server for GNNePCSAFT tools
-License: GNU General Public License v3.0
-Author: wildsonbbl
-Author-email: wil_bbl@hotmail.com
-Requires-Python: >=3.10
-Classifier: License :: Other/Proprietary License
-Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.10
-Classifier: Programming Language :: Python :: 3.11
-Classifier: Programming Language :: Python :: 3.12
-Classifier: Programming Language :: Python :: 3.13
-Requires-Dist: feos (>=0.8.0,<0.9.0)
-Requires-Dist: gnnepcsaft (>=0.2.4)
-Requires-Dist: mcp (>=1.6.0,<2.0.0)
-Requires-Dist: numpy (>=2.2.4,<3.0.0)
-Requires-Dist: onnxruntime (>=1.21.0,<2.0.0)
-Requires-Dist: rdkit (>=2024.9.6,<2025.0.0)
-Requires-Dist: si-units (>=0.11.0,<0.12.0)
-Description-Content-Type: text/markdown
-
-# 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-0.1.3/README.md

@@ -1,42 +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 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