gnnepcsaft-mcp-server 0.3.1__tar.gz

gnnepcsaft_mcp_server-0.3.1/PKG-INFO

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+Metadata-Version: 2.4
+Name: gnnepcsaft-mcp-server
+Version: 0.3.1
+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
+Classifier: Programming Language :: Python :: 3.14
+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
+
+GNNEPCSAFT MCP Server is an implementation of the [Model Context Protocol (MCP)](https://modelcontextprotocol.io/introduction) for [GNNePCSAFT](https://github.com/wildsonbbl/gnnepcsaft) tools. GNNePCSAFT leverages Graph Neural Networks (GNNs) to estimate [PC-SAFT](https://en.wikipedia.org/wiki/PC-SAFT) pure-component parameters, allowing property predictions such as density and vapor pressure for any molecule or mixture. [FeOs](https://github.com/feos-org/feos) is used for PC-SAFT calculations.
+
+## 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"]
+    }
+  }
+}
+```
+
+---
+
+## License
+
+GNU General Public License v3.0
+

gnnepcsaft_mcp_server-0.3.1/README.md

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+# 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. GNNePCSAFT leverages Graph Neural Networks (GNNs) to estimate [PC-SAFT](https://en.wikipedia.org/wiki/PC-SAFT) pure-component parameters, allowing property predictions such as density and vapor pressure for any molecule or mixture. [FeOs](https://github.com/feos-org/feos) is used for PC-SAFT calculations.
+
+## 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"]
+    }
+  }
+}
+```
+
+---
+
+## License
+
+GNU General Public License v3.0

gnnepcsaft_mcp_server-0.3.1/gnnepcsaft_mcp_server/__init__.py

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+"GNNePCSAFT MCP Server"

gnnepcsaft_mcp_server-0.3.1/gnnepcsaft_mcp_server/mcp_server.py

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+"GNNePCSAFT MCP Server"
+
+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,
+    batch_inchi_to_smiles,
+    batch_molecular_weights,
+    batch_pa_to_bar,
+    batch_predict_epcsaft_parameters,
+    batch_pure_density,
+    batch_pure_h_lv,
+    batch_pure_vapor_pressure,
+    batch_smiles_to_inchi,
+    mixture_density,
+    mixture_phase,
+    mixture_vapor_pressure,
+    pubchem_description,
+    pure_phase,
+)
+
+mcp = FastMCP("gnnepcsaft")
+fn_list: List[Callable[..., Any]] = [
+    batch_convert_pure_density_to_kg_per_m3,
+    batch_critical_points,
+    batch_inchi_to_smiles,
+    batch_molecular_weights,
+    batch_pa_to_bar,
+    batch_predict_epcsaft_parameters,
+    batch_pure_density,
+    batch_pure_h_lv,
+    batch_pure_vapor_pressure,
+    batch_smiles_to_inchi,
+    mixture_density,
+    mixture_phase,
+    mixture_vapor_pressure,
+    pubchem_description,
+    pure_phase,
+    v3000_mol_block,
+]
+for fn in fn_list:
+    mcp.add_tool(fn)
+
+
+def run():
+    "run stdio"
+    mcp.run("stdio")

gnnepcsaft_mcp_server-0.3.1/gnnepcsaft_mcp_server/plot_utils.py

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+"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-0.3.1/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, Tuple
+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, inchitosmiles, mw, smilestoinchi
+from gnnepcsaft.epcsaft.epcsaft_feos import (
+    critical_points_feos,
+    mix_den_feos,
+    mix_vp_feos,
+    pure_den_feos,
+    pure_h_lv_feos,
+    pure_vp_feos,
+)
+
+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 predict_epcsaft_parameters(
+    smiles: str,
+) -> List[float]:
+    """Predict PC-SAFT parameters
+    `[m, sigma, epsilon/kB, kappa_ab, epsilon_ab/kB, dipole moment, na, nb, MW]` with
+    the GNNePCSAFT model.
+
+    Args:
+      smiles (str): SMILES of the molecule.
+    """
+    lower_bounds = np.asarray([1.0, 1.9, 50.0, 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, 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]
+    munanbmw = np.asarray([0.0, na, nb, mw(inchi)])
+    pred = np.hstack([msigmae, assoc, munanbmw], 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(smiles: str) -> str:
+    """
+    Look for information on PubChem for the SMILES.
+
+    Args:
+        smiles (str): The SMILES of the molecule.
+    """
+
+    try:
+        inchi = smilestoinchi(smiles)
+        url = (
+            "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchi/description/json?inchi="
+            + quote(inchi, safe="")
+        )
+        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
+
+
+def mixture_density(
+    parameters: List[List[float]],
+    state: List[float],
+    kij_matrix: List[List[float]],
+) -> float:
+    """Calculates mixture liquid density (mol/m³) with PC-SAFT.
+
+    Args:
+        parameters: A list of
+         `[m, sigma, epsilon/kB, kappa_ab, epsilon_ab/kB, dipole moment, na, nb, MW]`
+         for each component of the mixture
+        state: A list with the state of the mixture
+         `[Temperature (K), Pressure (Pa), mole_fractions_1, mole_fractions_2, ...]`
+        kij_matrix: A matrix of binary interaction parameters
+    """
+
+    return mix_den_feos(parameters, state, kij_matrix)
+
+
+def mixture_vapor_pressure(
+    parameters: List[List[float]],
+    state: List[float],
+    kij_matrix: List[List[float]],
+) -> Tuple[float, float]:
+    """Calculates mixture `(Bubble point (Pa), Dew point (Pa))` with PC-SAFT.
+
+    Args:
+        parameters: A list of
+         `[m, sigma, epsilon/kB, kappa_ab, epsilon_ab/kB, dipole moment, na, nb, MW]`
+         for each component of the mixture
+        state: A list with the state of the mixture
+         `[Temperature (K), Pressure (Pa), mole_fractions_1, molefractions_2, ...]`.
+         The pressure should be any `float` value since it's not used in the calculation.
+        kij_matrix: A matrix of binary interaction parameters.
+    """
+
+    return mix_vp_feos(parameters, state, kij_matrix)
+
+
+def batch_predict_epcsaft_parameters(
+    smiles: List[str],
+) -> List[List[float]]:
+    """Predict PC-SAFT parameters
+    `[m, sigma, epsilon/kB, kappa_ab, epsilon_ab/kB, dipole moment, na, nb, MW]`
+    for a list of SMILES with the GNNePCSAFT model.
+
+    Args:
+      smiles (List[str]): SMILES of the molecules.
+    """
+    return [predict_epcsaft_parameters(smi) for smi in smiles]
+
+
+def batch_molecular_weights(
+    smiles: List[str],
+) -> List[float]:
+    """Calcultes molecular weight in `g/mol` for a list of SMILES
+
+    Args:
+      smiles (List[str]): SMILES of the molecules.
+    """
+    inchi_list = [smilestoinchi(smi) for smi in smiles]
+    return [mw(inchi) for inchi in inchi_list]
+
+
+def batch_inchi_to_smiles(
+    inchi_list: List[str],
+) -> List[str]:
+    """Transform a list of InChI to SMILES.
+
+    Args:
+        inchi_list (List[str]): List of InChI
+    """
+    return [inchitosmiles(inchi) for inchi in inchi_list]
+
+
+def batch_smiles_to_inchi(
+    smiles_list: List[str],
+) -> List[str]:
+    """Transform a list of SMILES to InChI.
+
+    Args:
+        smiles_list (List[str]): List of SMILES
+    """
+    return [smilestoinchi(smi) for smi in smiles_list]
+
+
+def batch_pure_density(
+    smiles_list: List[str],
+    state: List[float],
+) -> List[float]:
+    """Calculates pure liquid density in `mol/m³` with PC-SAFT for a list of SMILES.
+    The state is the same for all molecules. The GNNePCSAFT model is used to predict
+    PCSAFT parameters.
+
+    Args:
+        smiles_list (List[str]): List of SMILES
+        state: A list with
+         `[Temperature (K), Pressure (Pa)]`
+    """
+    return [
+        pure_den_feos(predict_epcsaft_parameters(smi), state) for smi in smiles_list
+    ]
+
+
+def batch_pure_vapor_pressure(
+    smiles_list: List[str],
+    temperature: float,
+) -> List[float]:
+    """Calculates pure vapor pressure in `Pa` with PC-SAFT for a list of SMILES.
+    The temperature is the same for all molecules. The GNNePCSAFT model is used to predict
+    PCSAFT parameters.
+
+    Args:
+        smiles_list (List[str]): List of SMILES
+        temperature: `Temperature (K)`
+    """
+    return [
+        pure_vp_feos(predict_epcsaft_parameters(smi), [temperature])
+        for smi in smiles_list
+    ]
+
+
+def batch_pure_h_lv(
+    smiles_list: List[str],
+    temperature: float,
+) -> List[float]:
+    """Calculates pure liquid enthalpy of vaporization in `kJ/mol`
+    with PC-SAFT for a list of SMILES.
+    The temperature is the same for all molecules.
+    The GNNePCSAFT model is used to predict
+    PCSAFT parameters.
+
+    Args:
+        smiles_list (List[str]): List of SMILES
+        temperature: `Temperature (K)`
+    """
+    return [
+        pure_h_lv_feos(predict_epcsaft_parameters(smi), [temperature])
+        for smi in smiles_list
+    ]
+
+
+def batch_critical_points(
+    smiles_list: List[str],
+) -> List[List[float]]:
+    """
+    Calculates critical points `[Temperature (K), Pressure (Pa), Density (mol/m³)]` with PC-SAFT
+    for a list of SMILES. The GNNePCSAFT model is used to predict PCSAFT parameters.
+
+    Args:
+        smiles_list (List[str]): List of SMILES
+    """
+    return [
+        critical_points_feos(predict_epcsaft_parameters(smi)) for smi in smiles_list
+    ]
+
+
+def batch_pa_to_bar(
+    pressure_in_pa_list: List[float],
+) -> List[float]:
+    """Convert a list of pressure from `Pa` to `bar`.
+
+    Args:
+        pressure_in_pa_list (List[float]): List of pressure in `Pa`
+    """
+    return [pa / 100_000.0 for pa in pressure_in_pa_list]
+
+
+def batch_convert_pure_density_to_kg_per_m3(
+    density_list: List[float],
+    molecular_weight_list: List[float],
+) -> List[float]:
+    """Convert a list of density from `mol/m³` to `kg/m³`
+
+    Args:
+        density_list (List[float]): List of density in `mol/m³`
+        molecular_weight_list (List[float]): List of molecular weight in `g/mol`
+    """
+    return [den * molw / 1000 for den, molw in zip(density_list, molecular_weight_list)]

gnnepcsaft_mcp_server-0.3.1/pyproject.toml

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+[project]
+name = "gnnepcsaft-mcp-server"
+version = "0.3.1"
+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 (>=0.2.4)",
+    "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/msigmae_7.onnx"]
+
+
+
+[tool.poetry.group.dev.dependencies]
+pytest = "^8.3.5"
+
+[build-system]
+requires = ["poetry-core>=2.0.0,<3.0.0"]
+build-backend = "poetry.core.masonry.api"