pyphyschemtools 0.3.5__py3-none-any.whl → 0.3.7__py3-none-any.whl

pyphyschemtools/.ipynb_checkpoints/ML-checkpoint.py

@@ -0,0 +1,44 @@
+############################################################
+#          Machine Learning
+############################################################
+from .visualID_Eng import fg, bg, hl
+from .core import centerTitle, centertxt
+
+def y2c(mc2i,y):
+    import tensorflow as tf
+    from tensorflow import keras
+    #from keras.utils import np_utils
+    from keras.utils import to_categorical
+    y_array = y.copy()
+    y_array = y_array.to_numpy() # transformation au format numpy
+    # transformation des valeurs de y1 & y2 en entiers
+    for x in range(len(y_array)):
+        #print(x, y_array[x], mapc2i[y_array[x]])
+        y_array[x] = mc2i[y_array[x]]
+    yohe = to_categorical(y_array)
+    del y_array
+    return yohe
+
+def categorizeY_2ohe(Ctot, y1, y2):
+    """
+    one-hot-encodes a pandas column of categorical data
+
+    input:
+    - Ctot is the reference pandas column, necessary to find all unique categories in this column
+    - y1 and y2 are the actual pandas column that will be categorized. y1 and y2 are supposed to be the ytest and ytrain subsets of Ctot  
+    output:
+    - y1ohe and y2ohe are the numpy arrays returned by this routine
+
+    """
+    
+    uv = Ctot.unique()
+    print(f"Catégories uniques : {uv}") 
+    mapc2i = {}
+    for x in range(len(uv)):
+        mapc2i[uv[x]] = x
+    print(f"Correspondance entre chaque catégorie unique et un entier : {mapc2i}")
+    y1ohe = y2c(mapc2i,y1)
+    y2ohe = y2c(mapc2i,y2)
+    print(f"Structure (shape) des tableaux renvoyés par categorize1C_2ohe. y1 : {y1ohe.shape}, y2 : {y2ohe.shape}")
+    del mapc2i, uv
+    return y1ohe, y2ohe

pyphyschemtools/.ipynb_checkpoints/PeriodicTable-checkpoint.py

@@ -7,6 +7,16 @@ from .core import centerTitle, centertxt
 import mendeleev
 
 class TableauPeriodique:
+    """
+    Classe permettant de manipuler et d'afficher les données du tableau périodique.
+    
+    Cette classe utilise la bibliothèque 'mendeleev' pour récupérer les données chimiques
+    et 'bokeh' pour la visualisation interactive. Elle francise les noms et corrige
+    certaines classifications de familles chimiques.
+
+    Initialise l'objet TableauPeriodique en chargeant les données de la bibliothèque mendeleev.
+    """
+    
     nomsFr=['Hydrogène','Hélium','Lithium','Béryllium','Bore','Carbone','Azote','Oxygène',
             'Fluor','Néon','Sodium','Magnésium','Aluminium','Silicium','Phosphore','Soufre',
             'Chlore','Argon','Potassium','Calcium','Scandium','Titane','Vanadium','Chrome',
@@ -63,10 +73,12 @@ class TableauPeriodique:
             return s
 
         def name_eng2fr():
+            """Remplace les noms anglais des éléments par leurs équivalents français."""
             self.elements["nom"] = TableauPeriodique.nomsFr
             return
 
         def ajouter_donnees():
+            """Récupère et fusionne des données supplémentaires comme l'énergie de première ionisation."""
             import numpy as np
             from mendeleev.fetch import fetch_table, fetch_ionization_energies
             import pandas as pd
@@ -99,6 +111,12 @@ class TableauPeriodique:
         return
 
     def prop(self,elt_id):
+        """
+        Affiche les propriétés détaillées d'un élément chimique.
+
+        Args:
+            elt_id (str ou int): Symbole de l'élément (ex: 'O') ou numéro atomique (ex: 8).
+        """
         from mendeleev import element
 
         elt = element(elt_id)
@@ -137,6 +155,11 @@ class TableauPeriodique:
         print()
 
     def afficher(self):
+        """
+        Génère et affiche le tableau périodique interactif dans un notebook Jupyter.
+        
+        Le tableau permet de visualiser les propriétés au survol de la souris.
+        """
         from bokeh.plotting import show, output_notebook
         from mendeleev.vis import periodic_table_bokeh
         

pyphyschemtools/.ipynb_checkpoints/aithermo-checkpoint.py

@@ -13,16 +13,14 @@ class aiThermo:
     """
     A class to handle thermodynamic surface stability analysis and visualization
     within the tools4pyPhysChem framework.
+    Initialize the aiThermo object.
+    
+    Args:
+        folder_path (str or Path): Path to the working directory.
+        color_scales (list, optional): List of plotly-compatible color scales.
     """
 
     def __init__(self, folder_path=None, color_scales=None):
-        """
-        Initialize the aiThermo object.
-
-        Args:
-            folder_path (str or Path): Path to the working directory.
-            color_scales (list, optional): List of plotly-compatible color scales.
-        """
         self.folder_path = Path(folder_path) if folder_path else None
         self.color_scales = color_scales or [
             [[0, "#dadada"], [1, "#dadada"]], [[0, "#99daaf"], [1, "#99daaf"]],

pyphyschemtools/.ipynb_checkpoints/cheminformatics-checkpoint.py

@@ -16,17 +16,15 @@ class easy_rdkit():
     """
     A helper class to analyze and visualize molecules using RDKit.
     Provides tools for Lewis structure analysis and advanced 2D drawing.
+    Initialize the molecule object from a SMILES string.
+    
+    Args:
+        smiles (str): The SMILES representation of the molecule.
+        canonical (bool): If True, converts the SMILES to its canonical form 
+                          to ensure consistent atom numbering and uniqueness.
     """
 
     def __init__(self,smiles, canonical=True):
-        """
-        Initialize the molecule object from a SMILES string.
-        
-        Args:
-            smiles (str): The SMILES representation of the molecule.
-            canonical (bool): If True, converts the SMILES to its canonical form 
-                              to ensure consistent atom numbering and uniqueness.
-        """
         from rdkit import Chem
         
         mol = Chem.MolFromSmiles(smiles)

pyphyschemtools/.ipynb_checkpoints/kinetics-checkpoint.py

@@ -62,12 +62,14 @@ class KORD:
         Static method to extract data from an Excel file.
         Selects the pair of columns (t, G) corresponding to the experiment number.
         Also loads parameters (A0, alpha, beta)
+        
         Format:
-        - Row 1: Headers for t and G
-        - Row 2: [A]0 value (in the G column)
-        - Row 3: alpha value (in the G column)
-        - Row 4: beta value (in the G column)
-        - Row 5+: [t, G] data points
+            - Row 1: Headers for t and G
+            - Row 2: [A]0 value (in the G column)
+            - Row 3: alpha value (in the G column)
+            - Row 4: beta value (in the G column)
+            - Row 5+: [t, G] data points
+        
         """
         # 1. Check if file exists
         if not os.path.exists(file_path):

pyphyschemtools/.ipynb_checkpoints/spectra-checkpoint.py

@@ -10,27 +10,29 @@ import scipy.constants as sc
 
 class SpectrumSimulator:
 
+    """
+    Initializes the spectrum simulator
+
+    Args:
+        - sigma_ev (float): Gaussian half-width at half-maximum in electron-volts (eV).
+                            Default is 0.3 eV (GaussView default is 0.4 eV).
+        - plotWH (tuple(int,int)): Width and Height of the matplotlib figures in inches. Default is (12,8).
+        - colorS: color of the simulated spectrum (default ='#3e89be')
+        - colorVT: color of the vertical transition line (default = '#469cd6')
+
+    Returns:
+        None: This method initializes the instance attributes.
+    Calculates:
+        sigmanm = half-width of the Gaussian band, in nm
+        
+    """
+    
     def __init__(self, sigma_ev=0.3, plotWH=(12,8), \
                  fontSize_axisText=14, fontSize_axisLabels=14, fontSize_legends=12,
                  fontsize_peaks=12,
                  colorS='#3e89be',colorVT='#469cd6'
                 ):
-        """
-        Initializes the spectrum simulator
 
-        Args:
-            - sigma_ev (float): Gaussian half-width at half-maximum in electron-volts (eV).
-                                Default is 0.3 eV (GaussView default is 0.4 eV).
-            - plotWH (tuple(int,int)): Width and Height of the matplotlib figures in inches. Default is (12,8).
-            - colorS: color of the simulated spectrum (default ='#3e89be')
-            - colorVT: color of the vertical transition line (default = '#469cd6')
-
-        Returns:
-            None: This method initializes the instance attributes.
-        Calculates:
-            sigmanm = half-width of the Gaussian band, in nm
-            
-        """
         self.sigma_ev = sigma_ev
         # Conversion constante eV -> nm sigma
         self.ev2nm_const = (sc.h * sc.c) * 1e9 / sc.e

pyphyschemtools/PeriodicTable.py

@@ -7,6 +7,16 @@ from .core import centerTitle, centertxt
 import mendeleev
 
 class TableauPeriodique:
+    """
+    Classe permettant de manipuler et d'afficher les données du tableau périodique.
+    
+    Cette classe utilise la bibliothèque 'mendeleev' pour récupérer les données chimiques
+    et 'bokeh' pour la visualisation interactive. Elle francise les noms et corrige
+    certaines classifications de familles chimiques.
+
+    Initialise l'objet TableauPeriodique en chargeant les données de la bibliothèque mendeleev.
+    """
+    
     nomsFr=['Hydrogène','Hélium','Lithium','Béryllium','Bore','Carbone','Azote','Oxygène',
             'Fluor','Néon','Sodium','Magnésium','Aluminium','Silicium','Phosphore','Soufre',
             'Chlore','Argon','Potassium','Calcium','Scandium','Titane','Vanadium','Chrome',
@@ -63,10 +73,12 @@ class TableauPeriodique:
             return s
 
         def name_eng2fr():
+            """Remplace les noms anglais des éléments par leurs équivalents français."""
             self.elements["nom"] = TableauPeriodique.nomsFr
             return
 
         def ajouter_donnees():
+            """Récupère et fusionne des données supplémentaires comme l'énergie de première ionisation."""
             import numpy as np
             from mendeleev.fetch import fetch_table, fetch_ionization_energies
             import pandas as pd
@@ -99,6 +111,12 @@ class TableauPeriodique:
         return
 
     def prop(self,elt_id):
+        """
+        Affiche les propriétés détaillées d'un élément chimique.
+
+        Args:
+            elt_id (str ou int): Symbole de l'élément (ex: 'O') ou numéro atomique (ex: 8).
+        """
         from mendeleev import element
 
         elt = element(elt_id)
@@ -137,6 +155,11 @@ class TableauPeriodique:
         print()
 
     def afficher(self):
+        """
+        Génère et affiche le tableau périodique interactif dans un notebook Jupyter.
+        
+        Le tableau permet de visualiser les propriétés au survol de la souris.
+        """
         from bokeh.plotting import show, output_notebook
         from mendeleev.vis import periodic_table_bokeh
         

pyphyschemtools/__init__.py

@@ -1,5 +1,5 @@
 # tools4pyPhysChem/__init__.py
-__version__ = "0.3.5"
+__version__ = "0.3.7"
 __last_update__ = "2026-02-03"
 
 import importlib

pyphyschemtools/aithermo.py

@@ -13,16 +13,14 @@ class aiThermo:
     """
     A class to handle thermodynamic surface stability analysis and visualization
     within the tools4pyPhysChem framework.
+    Initialize the aiThermo object.
+    
+    Args:
+        folder_path (str or Path): Path to the working directory.
+        color_scales (list, optional): List of plotly-compatible color scales.
     """
 
     def __init__(self, folder_path=None, color_scales=None):
-        """
-        Initialize the aiThermo object.
-
-        Args:
-            folder_path (str or Path): Path to the working directory.
-            color_scales (list, optional): List of plotly-compatible color scales.
-        """
         self.folder_path = Path(folder_path) if folder_path else None
         self.color_scales = color_scales or [
             [[0, "#dadada"], [1, "#dadada"]], [[0, "#99daaf"], [1, "#99daaf"]],

pyphyschemtools/cheminformatics.py

@@ -16,17 +16,15 @@ class easy_rdkit():
     """
     A helper class to analyze and visualize molecules using RDKit.
     Provides tools for Lewis structure analysis and advanced 2D drawing.
+    Initialize the molecule object from a SMILES string.
+    
+    Args:
+        smiles (str): The SMILES representation of the molecule.
+        canonical (bool): If True, converts the SMILES to its canonical form 
+                          to ensure consistent atom numbering and uniqueness.
     """
 
     def __init__(self,smiles, canonical=True):
-        """
-        Initialize the molecule object from a SMILES string.
-        
-        Args:
-            smiles (str): The SMILES representation of the molecule.
-            canonical (bool): If True, converts the SMILES to its canonical form 
-                              to ensure consistent atom numbering and uniqueness.
-        """
         from rdkit import Chem
         
         mol = Chem.MolFromSmiles(smiles)

pyphyschemtools/kinetics.py

@@ -62,12 +62,14 @@ class KORD:
         Static method to extract data from an Excel file.
         Selects the pair of columns (t, G) corresponding to the experiment number.
         Also loads parameters (A0, alpha, beta)
+        
         Format:
-        - Row 1: Headers for t and G
-        - Row 2: [A]0 value (in the G column)
-        - Row 3: alpha value (in the G column)
-        - Row 4: beta value (in the G column)
-        - Row 5+: [t, G] data points
+            - Row 1: Headers for t and G
+            - Row 2: [A]0 value (in the G column)
+            - Row 3: alpha value (in the G column)
+            - Row 4: beta value (in the G column)
+            - Row 5+: [t, G] data points
+        
         """
         # 1. Check if file exists
         if not os.path.exists(file_path):

pyphyschemtools/spectra.py

@@ -10,27 +10,29 @@ import scipy.constants as sc
 
 class SpectrumSimulator:
 
+    """
+    Initializes the spectrum simulator
+
+    Args:
+        - sigma_ev (float): Gaussian half-width at half-maximum in electron-volts (eV).
+                            Default is 0.3 eV (GaussView default is 0.4 eV).
+        - plotWH (tuple(int,int)): Width and Height of the matplotlib figures in inches. Default is (12,8).
+        - colorS: color of the simulated spectrum (default ='#3e89be')
+        - colorVT: color of the vertical transition line (default = '#469cd6')
+
+    Returns:
+        None: This method initializes the instance attributes.
+    Calculates:
+        sigmanm = half-width of the Gaussian band, in nm
+        
+    """
+    
     def __init__(self, sigma_ev=0.3, plotWH=(12,8), \
                  fontSize_axisText=14, fontSize_axisLabels=14, fontSize_legends=12,
                  fontsize_peaks=12,
                  colorS='#3e89be',colorVT='#469cd6'
                 ):
-        """
-        Initializes the spectrum simulator
 
-        Args:
-            - sigma_ev (float): Gaussian half-width at half-maximum in electron-volts (eV).
-                                Default is 0.3 eV (GaussView default is 0.4 eV).
-            - plotWH (tuple(int,int)): Width and Height of the matplotlib figures in inches. Default is (12,8).
-            - colorS: color of the simulated spectrum (default ='#3e89be')
-            - colorVT: color of the vertical transition line (default = '#469cd6')
-
-        Returns:
-            None: This method initializes the instance attributes.
-        Calculates:
-            sigmanm = half-width of the Gaussian band, in nm
-            
-        """
         self.sigma_ev = sigma_ev
         # Conversion constante eV -> nm sigma
         self.ev2nm_const = (sc.h * sc.c) * 1e9 / sc.e

{pyphyschemtools-0.3.5.dist-info → pyphyschemtools-0.3.7.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pyphyschemtools
-Version: 0.3.5
+Version: 0.3.7
 Summary: A comprehensive Python toolbox for physical chemistry and cheminformatics
 Author-email: "Romuald POTEAU, LPCNO" <romuald.poteau@utoulouse.fr>
 Project-URL: Repository, https://github.com/rpoteau/pyphyschemtools
@@ -10,10 +10,12 @@ Project-URL: Issues, https://github.com/rpoteau/pyphyschemtools/issues
 Requires-Python: >=3.8
 Description-Content-Type: text/markdown
 License-File: LICENSE
+Requires-Dist: bokeh
 Requires-Dist: CageCavityCalc
 Requires-Dist: ipywidgets
 Requires-Dist: jupyter
 Requires-Dist: matplotlib
+Requires-Dist: mendeleev
 Requires-Dist: numpy
 Requires-Dist: openpyxl
 Requires-Dist: pandas

{pyphyschemtools-0.3.5.dist-info → pyphyschemtools-0.3.7.dist-info}/RECORD

@@ -1,25 +1,26 @@
 pyphyschemtools/.readthedocs.yaml,sha256=ZTw2bOyF9p3JpeF8Ux0fwhYWO6KHCsroNEOvnXxbYGM,469
 pyphyschemtools/Chem3D.py,sha256=NuhoLvWpeATO88UklXg-3XqPpIiHqvP__b2tLHrypL8,34718
 pyphyschemtools/ML.py,sha256=kR_5vm5TOOjVef8uXCW57y7685ts6K6OkRMBYKP_cYw,1599
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-pyphyschemtools/cheminformatics.py,sha256=Qps_JSYWOzZQcXwKElI1iWGjWAPDgwmtDKuJwONsKmI,8977
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 pyphyschemtools/core.py,sha256=5fRu83b125w2p_m2H521fLjktyswZHJXNKww1wfBwbU,4847
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-pyphyschemtools/spectra.py,sha256=eCN9X6pK5k4KMcfWUskedWYwtxbrmJH_BvFXU1GZfVo,21702
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 pyphyschemtools/survey.py,sha256=YjZhhb8GFVNXoXSCxgGdZFqmCtNCx7O_uiFVCcGBYYo,24268
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 pyphyschemtools/visualID_Eng.py,sha256=W-rYHg4g090JUpTJxtbBZVZ2lXShq8f0ALeiNjFqWD0,5356
 pyphyschemtools/.ipynb_checkpoints/Chem3D-checkpoint.py,sha256=NuhoLvWpeATO88UklXg-3XqPpIiHqvP__b2tLHrypL8,34718
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-pyphyschemtools/.ipynb_checkpoints/aithermo-checkpoint.py,sha256=kF8wtuYIJzkUKM2AGubmn9haAJKz-XaBskZ7HjivJeY,14984
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+pyphyschemtools/.ipynb_checkpoints/ML-checkpoint.py,sha256=kR_5vm5TOOjVef8uXCW57y7685ts6K6OkRMBYKP_cYw,1599
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+pyphyschemtools/.ipynb_checkpoints/cheminformatics-checkpoint.py,sha256=EVmgZOHatxFt5DwTgZiyZbWkwVb5mKH8odetcLJHZFc,8929
 pyphyschemtools/.ipynb_checkpoints/core-checkpoint.py,sha256=5fRu83b125w2p_m2H521fLjktyswZHJXNKww1wfBwbU,4847
-pyphyschemtools/.ipynb_checkpoints/kinetics-checkpoint.py,sha256=WlBnpwVIeaSTF1fZ4j4PRL6hp_C-8zKFa2bN21bU1VQ,11727
-pyphyschemtools/.ipynb_checkpoints/spectra-checkpoint.py,sha256=eCN9X6pK5k4KMcfWUskedWYwtxbrmJH_BvFXU1GZfVo,21702
+pyphyschemtools/.ipynb_checkpoints/kinetics-checkpoint.py,sha256=QAYwX7UTQel40iSZr8TIgBQuViLw7LsGiNPpLyOOsho,11765
+pyphyschemtools/.ipynb_checkpoints/spectra-checkpoint.py,sha256=e_pbs4ojxlQvZuGzaoEyzDALcnA82f8kc4eW0JyINzQ,21652
 pyphyschemtools/.ipynb_checkpoints/survey-checkpoint.py,sha256=Rcw0xb0_nwsxETleB1C2xjKmZfrUw4PXDm48CMSptHU,45816
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@@ -87,8 +88,8 @@ pyphyschemtools/resources/svg/qrcode-pyPhysChem.png,sha256=rP7X-9eHL7HYj4ffmwBML
 pyphyschemtools/resources/svg/repository-open-graph-template.png,sha256=UlnW5BMkLGOv6IAnEi7teDYS_5qeSLmpxRMT9r9m-5Q,51470
 pyphyschemtools/resources/svg/tools4pyPC_banner.png,sha256=z7o_kBK0sIBsXHEJrT2GyLHu-0T0T3S8YkWcpxR2joA,89058
 pyphyschemtools/resources/svg/tools4pyPC_banner.svg,sha256=BXxXHra9vwahaiet1IJW4q8QLA03crSeCIQYo30VpN8,651579
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-pyphyschemtools-0.3.5.dist-info/top_level.txt,sha256=N92w2qk4LQ42OSdzK1R2h_x1CyUFaFBOrOML2RnmFgE,16
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