gnnepcsaft-mcp-server 0.1.0__tar.gz

gnnepcsaft_mcp_server-0.1.0/PKG-INFO

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+Metadata-Version: 2.3
+Name: gnnepcsaft-mcp-server
+Version: 0.1.0
+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 (>=0.2.2,<0.3.0)
+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 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 [pipx](https://pipx.pypa.io/latest/installation/) for this.
+
+```bash
+pipx install gnnepcsaft-mcp-server
+```
+
+## Usage
+
+stdio command to start the MCP server:
+
+```json
+{
+  "mcpServers": {
+    "gnnepcsaft": {
+      "command": "gnnepcsaftmcp",
+      "args": []
+    }
+  }
+}
+```
+
+## License
+
+GNU General Public License v3.0
+

gnnepcsaft_mcp_server-0.1.0/README.md

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+# 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 [pipx](https://pipx.pypa.io/latest/installation/) for this.
+
+```bash
+pipx install gnnepcsaft-mcp-server
+```
+
+## Usage
+
+stdio command to start the MCP server:
+
+```json
+{
+  "mcpServers": {
+    "gnnepcsaft": {
+      "command": "gnnepcsaftmcp",
+      "args": []
+    }
+  }
+}
+```
+
+## License
+
+GNU General Public License v3.0

gnnepcsaft_mcp_server-0.1.0/gnnepcsaft_mcp_server/__init__.py

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+"GNNePCSAFT MCP Server"

gnnepcsaft_mcp_server-0.1.0/gnnepcsaft_mcp_server/mcp_server.py

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+"GNNePCSAFT MCP Server"
+
+from typing import Any, Callable, List
+
+from gnnepcsaft.data.rdkit_util import inchitosmiles, mw, smilestoinchi
+from gnnepcsaft.epcsaft.epcsaft_feos import (
+    mix_den_feos,
+    mix_vp_feos,
+    pure_den_feos,
+    pure_h_lv_feos,
+    pure_vp_feos,
+)
+from mcp.server.fastmcp import FastMCP
+
+from .utils import mixture_phase, prediction, pubchem_description, pure_phase
+
+mcp = FastMCP("gnnepcsaft")
+fn_list: List[Callable[..., Any]] = [
+    pure_vp_feos,
+    pure_den_feos,
+    mix_den_feos,
+    mix_vp_feos,
+    pure_phase,
+    mixture_phase,
+    pubchem_description,
+    mw,
+    smilestoinchi,
+    prediction,
+    inchitosmiles,
+    pure_h_lv_feos,
+]
+for fn in fn_list:
+    mcp.add_tool(fn)
+
+
+def run():
+    "run stdio"
+    mcp.run("stdio")

gnnepcsaft_mcp_server-0.1.0/gnnepcsaft_mcp_server/utils.py

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+"Utils for MCP Server"
+
+from json import loads
+from pathlib import Path
+from typing import List, Literal
+from urllib.parse import quote
+from urllib.request import HTTPError, urlopen
+
+import numpy as np
+import onnxruntime as ort
+from gnnepcsaft.data.ogb_utils import smiles2graph
+from gnnepcsaft.data.rdkit_util import assoc_number, smilestoinchi
+
+file_dir = Path(__file__).parent
+model_dir = file_dir / "models"
+ort.set_default_logger_severity(3)
+
+msigmae_onnx = ort.InferenceSession(model_dir / "msigmae_7.onnx")
+assoc_onnx = ort.InferenceSession(model_dir / "assoc_8.onnx")
+
+
+def prediction(
+    smiles: str,
+) -> List[float]:
+    """Predict ePC-SAFT parameters
+    `[m, sigma, epsilon/kB, kappa_ab, epsilon_ab/kB, dipole moment, na, nb]`
+
+    Args:
+      smiles (str): SMILES of the molecule.
+    """
+    lower_bounds = np.asarray([1.0, 1.9, 50.0, 0.0, 0.0, 0, 0, 0])
+    upper_bounds = np.asarray([25.0, 4.5, 550.0, 0.9, 5000.0, np.inf, np.inf, np.inf])
+
+    inchi = smilestoinchi(smiles)
+
+    graph = smiles2graph(smiles)
+    na, nb = assoc_number(inchi)
+    x, edge_index, edge_attr = (
+        graph["node_feat"],
+        graph["edge_index"],
+        graph["edge_feat"],
+    )
+
+    assoc = 10 ** (
+        assoc_onnx.run(
+            None,
+            {
+                "x": x,
+                "edge_index": edge_index,
+                "edge_attr": edge_attr,
+            },
+        )[0][0]
+        * np.asarray([-1.0, 1.0])
+    )
+    if na == 0 and nb == 0:
+        assoc *= 0
+    msigmae = msigmae_onnx.run(
+        None,
+        {
+            "x": x,
+            "edge_index": edge_index,
+            "edge_attr": edge_attr,
+        },
+    )[0][0]
+    munanb = np.asarray([0.0, na, nb])
+    pred = np.hstack([msigmae, assoc, munanb], dtype=np.float64)
+    np.clip(pred, lower_bounds, upper_bounds, out=pred)
+
+    return pred.tolist()  # type: ignore
+
+
+def pure_phase(
+    vapor_pressure: float, system_pressure: float
+) -> Literal["liquid", "vapor"]:
+    """
+    Given the vapor pressure and system pressure, return the phase of the molecule.
+    Both pressures must be in the same unit.
+
+    Args:
+        vapor_pressure (float): The calculated vapor pressure of the pure component.
+        system_pressure (float): The actual system pressure.
+
+    """
+    assert isinstance(vapor_pressure, (int, float)), "vapor_pressure must be a number"
+    assert isinstance(system_pressure, (int, float)), "system_pressure must be a number"
+    assert vapor_pressure > 0, "vapor_pressure must be positive"
+    assert system_pressure > 0, "system_pressure must be positive"
+
+    return "liquid" if vapor_pressure < system_pressure else "vapor"
+
+
+def mixture_phase(
+    bubble_point: float,
+    dew_point: float,
+    system_pressure: float,
+) -> Literal["liquid", "vapor", "two-phase"]:
+    """
+    Given the bubble/dew point of the mixture and the system pressure,
+    return the phase of the mixture.
+    All pressures must be in the same unit.
+
+    Args:
+        bubble_point (float): The calculated bubble point of the mixture.
+        dew_point (float): The calculated dew point of the mixture.
+        system_pressure (float): The actual system pressure.
+    """
+    assert isinstance(bubble_point, (int, float)), "bubble_point must be a number"
+    assert isinstance(dew_point, (int, float)), "dew_point must be a number"
+    assert isinstance(system_pressure, (int, float)), "system_pressure must be a number"
+    assert bubble_point > 0, "bubble_point must be positive"
+    assert dew_point > 0, "dew_point must be positive"
+    assert system_pressure > 0, "system_pressure must be positive"
+    return (
+        "liquid"
+        if bubble_point < system_pressure
+        else ("two-phase" if dew_point <= system_pressure else "vapor")
+    )
+
+
+def pubchem_description(inchi: str) -> str:
+    """
+    Look for information on PubChem for the InChI.
+
+    Args:
+        inchi (str): The InChI of the molecule.
+    """
+    url = (
+        "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchi/description/json?inchi="
+        + quote(inchi, safe="")
+    )
+    try:
+        with urlopen(url) as ans:
+            ans = loads(ans.read().decode("utf8").strip())
+    except (TypeError, HTTPError, ValueError):
+        ans = "no data available on this molecule in PubChem."
+    return ans

gnnepcsaft_mcp_server-0.1.0/pyproject.toml

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+[project]
+name = "gnnepcsaft-mcp-server"
+version = "0.1.0"
+description = "Model Context Protocol server for GNNePCSAFT tools"
+authors = [
+    {name = "wildsonbbl",email = "wil_bbl@hotmail.com"}
+]
+license = {text = "GNU General Public License v3.0"}
+readme = "README.md"
+requires-python = ">=3.10"
+dependencies = [
+    "numpy (>=2.2.4,<3.0.0)",
+    "onnxruntime (>=1.21.0,<2.0.0)",
+    "gnnepcsaft (>=0.2.2,<0.3.0)",
+    "mcp (>=1.6.0,<2.0.0)",
+    "rdkit (>=2024.9.6,<2025.0.0)",
+    "feos (>=0.8.0,<0.9.0)",
+    "si-units (>=0.11.0,<0.12.0)"
+]
+
+[project.scripts]
+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"]
+
+
+
+[build-system]
+requires = ["poetry-core>=2.0.0,<3.0.0"]
+build-backend = "poetry.core.masonry.api"