gnnepcsaft-mcp-server 0.1.1__py3-none-any.whl → 0.1.2__py3-none-any.whl

gnnepcsaft_mcp_server/mcp_server.py

@@ -2,34 +2,43 @@
 
 from typing import Any, Callable, List
 
-from gnnepcsaft.data.rdkit_util import 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,
-)
 from mcp.server.fastmcp import FastMCP
 
-from .utils import mixture_phase, prediction, pubchem_description, pure_phase
+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]] = [
-    pure_vp_feos,
-    pure_den_feos,
-    mix_den_feos,
-    mix_vp_feos,
-    pure_phase,
+    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,
-    mw,
-    smilestoinchi,
-    prediction,
-    inchitosmiles,
-    pure_h_lv_feos,
-    critical_points_feos,
+    pure_phase,
 ]
 for fn in fn_list:
     mcp.add_tool(fn)

gnnepcsaft_mcp_server/utils.py

@@ -2,14 +2,22 @@
 
 from json import loads
 from pathlib import Path
-from typing import List, Literal
+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, smilestoinchi
+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"
@@ -19,11 +27,12 @@ msigmae_onnx = ort.InferenceSession(model_dir / "msigmae_7.onnx")
 assoc_onnx = ort.InferenceSession(model_dir / "assoc_8.onnx")
 
 
-def prediction(
+def predict_epcsaft_parameters(
     smiles: str,
 ) -> List[float]:
     """Predict ePC-SAFT parameters
-    `[m, sigma, epsilon/kB, kappa_ab, epsilon_ab/kB, dipole moment, na, nb]`
+    `[m, sigma, epsilon/kB, kappa_ab, epsilon_ab/kB, dipole moment, na, nb]` with
+    the GNNePCSAFT model.
 
     Args:
       smiles (str): SMILES of the molecule.
@@ -117,20 +126,203 @@ def mixture_phase(
     )
 
 
-def pubchem_description(inchi: str) -> str:
+def pubchem_description(smiles: str) -> str:
     """
-    Look for information on PubChem for the InChI.
+    Look for information on PubChem for the SMILES.
 
     Args:
-        inchi (str): The InChI of the molecule.
+        smiles (str): The SMILES of the molecule.
     """
-    url = (
-        "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchi/description/json?inchi="
-        + quote(inchi, safe="")
-    )
+
     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 ePC-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 ePC-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 ePC-SAFT parameters
+    `[m, sigma, epsilon/kB, kappa_ab, epsilon_ab/kB, dipole moment, na, nb]`
+    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 `kg/m³` with ePC-SAFT for a list of SMILES.
+    The state is the same for all molecules. The GNNePCSAFT model is used to predict
+    ePCSAFT 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 ePC-SAFT for a list of SMILES.
+    The temperature is the same for all molecules. The GNNePCSAFT model is used to predict
+    ePCSAFT 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 ePC-SAFT for a list of SMILES.
+    The temperature is the same for all molecules.
+    The GNNePCSAFT model is used to predict
+    ePCSAFT 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 ePC-SAFT
+    for a list of SMILES. The GNNePCSAFT model is used to predict ePCSAFT 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-0.1.1.dist-info → gnnepcsaft_mcp_server-0.1.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: gnnepcsaft-mcp-server
-Version: 0.1.1
+Version: 0.1.2
 Summary: Model Context Protocol server for GNNePCSAFT tools
 License: GNU General Public License v3.0
 Author: wildsonbbl

{gnnepcsaft_mcp_server-0.1.1.dist-info → gnnepcsaft_mcp_server-0.1.2.dist-info}/RECORD

@@ -1,12 +1,12 @@
 gnnepcsaft_mcp_server/__init__.py,sha256=Npbt9RPLtKrFDK-oeyrAbz0b7lg9Y1Le1mxAQVtD_PY,24
-gnnepcsaft_mcp_server/mcp_server.py,sha256=W-W-C8f2Na7Z6UKFipnrqZlsOkiUkjUve_I4OIra33Q,820
+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=Be62JR9tfJiCP3BOaRExGcetu1Q3xoFAps6r_JXw0nM,4288
-gnnepcsaft_mcp_server-0.1.1.dist-info/METADATA,sha256=sHhC1mq3oNsZDGR4Au0RAWmjOT4wmBk9THiOVlfo3wg,1653
-gnnepcsaft_mcp_server-0.1.1.dist-info/WHEEL,sha256=fGIA9gx4Qxk2KDKeNJCbOEwSrmLtjWCwzBz351GyrPQ,88
-gnnepcsaft_mcp_server-0.1.1.dist-info/entry_points.txt,sha256=5tsnxZG8Vtdrr3CT-8Pv35RjpcDiR0L28cYxxHeCsPI,70
-gnnepcsaft_mcp_server-0.1.1.dist-info/RECORD,,
+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,,