pyphyschemtools 0.1.0__py3-none-any.whl → 0.1.2__py3-none-any.whl

pyphyschemtools/.readthedocs.yaml

@@ -0,0 +1,23 @@
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the OS, Python version, and other tools you might need
+build:
+  os: ubuntu-24.04
+  tools:
+    python: "3.11"
+
+# Build documentation in the "docs/" directory with Sphinx
+sphinx:
+   configuration: docs/conf.py
+
+# Optional but recommended
+python:
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - docs

pyphyschemtools/Chem3D.py

@@ -223,14 +223,15 @@ class molView:
     """
     Initializes a molecular/crystal viewer and coordinate extractor.
 
-        This class acts as a bridge between various molecular data sources and 
-        the py3Dmol interactive viewer. It can operate in 'Full' mode (display + 
-        analysis) or 'Headless' mode (analysis only) by toggling the `viewer` parameter.
+    This class acts as a bridge between various molecular data sources and 
+    the py3Dmol interactive viewer. It can operate in 'Full' mode (display + 
+    analysis) or 'Headless' mode (analysis only) by toggling the `viewer` parameter.
 
-        The class automatically extracts geometric data into the `self.data` attribute 
-        (an XYZData object), allowing for volume, dimension, and cavity calculations.
+    The class automatically extracts geometric data into the `self.data` attribute 
+    (an XYZData object), allowing for volume, dimension, and cavity calculations.
         
     Display molecular and crystal structures in py3Dmol from various sources:
+    
     - XYZ/PDB/CIF local files
     - XYZ-format string
     - PubChem CID
@@ -239,9 +240,10 @@ class molView:
     - RSCB PDB ID
 
     Three visualization styles are available:
-      - 'bs'     : ball-and-stick (default)
-      - 'cpk'    : CPK space-filling spheres (with adjustable size)
-      - 'cartoon': protein backbone representation
+    
+    - 'bs'     : ball-and-stick (default)
+    - 'cpk'    : CPK space-filling spheres (with adjustable size)
+    - 'cartoon': protein backbone representation
       
     Upon creation, an interactive 3D viewer is shown directly in a Jupyter notebook cell, unless the headless viewer parameter is set to False.
 
@@ -249,6 +251,7 @@ class molView:
     ----------
         mol : str or ase.Atoms
             The molecular structure to visualize.
+            
             - If `source='file'`, this should be a path to a structure file (XYZ, PDB, etc.)
             - If `source='mol'`, this should be a string containing the structure (XYZ, PDB...)
             - If `source='cif'`, this should be a cif file (string)
@@ -260,6 +263,7 @@ class molView:
             The type of the input `mol` (default: 'file').
         style : {'bs', 'cpk', 'cartoon'}, optional
             Visualization style (default: 'bs').
+            
             - 'bs'  → ball-and-stick
             - 'cpk' → CPK space-filling spheres
             - 'cartoon' → draws a smooth tube or ribbon through the protein backbone

pyphyschemtools/ML.py

@@ -22,11 +22,13 @@ def y2c(mc2i,y):
 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  
+    - 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
+    - y1ohe and y2ohe are the numpy arrays returned by this routine
+
     """
     
     uv = Ctot.unique()
@@ -39,4 +41,4 @@ def categorizeY_2ohe(Ctot, y1, y2):
     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
+    return y1ohe, y2ohe

pyphyschemtools/PeriodicTable.py

@@ -47,10 +47,15 @@ class TableauPeriodique:
         Ce patch, appliqué à self.elements, créé par l'appel à create_vis_dataframe(), va servir à :
         - ajouter des informations en français : les noms des éléments et des séries (familles) auxquelles ils appartiennent
         - retirer les éléments du groupe 12 de la famille des métaux de transition, qui est le choix CONTESTABLE par défaut de la bibliothèque mendeleev
-        input : elements est un dataframe pandas préalablement créé par la fonction create_vis_dataframe() de mendeleev.vis
-        output : elements avec deux nouvelles colonnes name_seriesFr et nom, qui contient dorénavant les noms des éléments en français
-                        + correction des données name_series et series_id pour les éléments Zn, Cd, Hg, Cn
-                        + de nouvelles colonnes qui contiennent l'énergie de première ionisation et les isotopes naturels
+        
+        input :
+        elements est un dataframe pandas préalablement créé par la fonction create_vis_dataframe() de mendeleev.vis
+        
+        output :
+        elements avec deux nouvelles colonnes name_seriesFr et nom, qui contient dorénavant les noms des éléments en français
+        + correction des données name_series et series_id pour les éléments Zn, Cd, Hg, Cn
+        + de nouvelles colonnes qui contiennent l'énergie de première ionisation et les isotopes naturels
+                        
         '''
         def series_eng2fr(s):
             '''Correspondance entre nom des séries (familles) en anglais et en français'''

pyphyschemtools/__init__.py

@@ -1,6 +1,6 @@
 # tools4pyPhysChem/__init__.py
-__version__ = "0.1.0"
-__last_update__ = "2026-02-01"
+__version__ = "0.1.2"
+__last_update__ = "2026-02-02"
 
 import importlib
 import importlib.util
@@ -26,7 +26,7 @@ def __getattr__(name):
 
     modules_to_search = [
         ".ML", ".PeriodicTable", ".Chem3D",  
-        ".aithermo", ".cheminformatics", ".kinetics", # Virgule corrigée ici
+        ".aithermo", ".cheminformatics", ".kinetics", 
         ".spectra", ".survey",  
         ".sympyUtilities", ".tools4AS"
     ]

pyphyschemtools/aithermo.py

@@ -53,20 +53,19 @@ class aiThermo:
         extract surface names and legend labels.
 
         Args:
-            vib (bool): If True, filters for files including vibrational corrections 
-                (prefixed with 'vib_'). If False, looks for standard thermodynamic data.
+            vib (bool): If True, filters for files including vibrational corrections (prefixed with ``vib_``). If False, looks for standard thermodynamic data.
 
         Returns:
             tuple: A triplet containing:
-                - file_paths (list of str): Absolute or relative paths to the .dat files.
-                - names (list of str): Internal identifiers for each surface phase.
-                - legends (list of str): LaTeX-formatted or plain text labels for 
-                  graphical legends.
+            - file_paths (list of str): Absolute or relative paths to the .dat files.
+            - names (list of str): Internal identifiers for each surface phase.
+            - legends (list of str): LaTeX-formatted or plain text labels for graphical legends.
 
         Notes:
             - The lists are returned in reverse order to ensure correct layering 
               during 3D plotting.
             - Relies on 'ListOfStableSurfaces.dat' existing in the folder_path.
+            
         """
         self._check_folder()
         from .core import centertxt

pyphyschemtools/core.py

@@ -15,13 +15,14 @@ def centerTitle(content=None):
 def centertxt(content=None,font='sans', size=12,weight="normal",bgc="#000000",fgc="#ffffff"):
     '''
     centers and renders as HTML a text in the notebook
+    
     input: 
-        - content = the text to render (default: None)
-        - font = font family (default: 'sans', values allowed =  'sans-serif' | 'serif' | 'monospace' | 'cursive' | 'fantasy' | ...)
-        - size = font size (default: 12)
-        - weight = font weight (default: 'normal', values allowed = 'normal' | 'bold' | 'bolder' | 'lighter' | 100 | 200 | 300 | 400 | 500 | 600 | 700 | 800 | 900 )
-        - bgc = background color (name or hex code, default = '#ffffff')
-        - fgc = foreground color (name or hex code, default = '#000000')
+    - content = the text to render (default: None)
+    - font = font family (default: 'sans', values allowed =  'sans-serif' | 'serif' | 'monospace' | 'cursive' | 'fantasy' | ...)
+    - size = font size (default: 12)
+    - weight = font weight (default: 'normal', values allowed = 'normal' | 'bold' | 'bolder' | 'lighter' | 100 | 200 | 300 | 400 | 500 | 600 | 700 | 800 | 900 )
+    - bgc = background color (name or hex code, default = '#ffffff')
+    - fgc = foreground color (name or hex code, default = '#000000')
     '''
     from IPython.display import display, HTML
     display(HTML(f"<div style='text-align:center; font-family: {font}; font-weight: {weight}; font-size:{size}px;background-color: {bgc};color: {fgc}'>{content}</div>"))

pyphyschemtools/spectra.py

@@ -28,7 +28,8 @@ class SpectrumSimulator:
         Returns:
             None: This method initializes the instance attributes.
         Calculates:
-            - sigmanm = half-width of the Gaussian band, in nm
+            sigmanm = half-width of the Gaussian band, in nm
+            
         """
         self.sigma_ev = sigma_ev
         # Conversion constante eV -> nm sigma
@@ -55,15 +56,18 @@ class SpectrumSimulator:
         return fig, graph
     
     def _calc_epsiG(self,lambdaX,lambdai,fi):
-        '''
+        """
         calculates a Gaussian band shape around a vertical transition
+        
         input:
             - lambdaX = wavelength variable, in nm
             - lambdai = vertical excitation wavelength for i_th state, in nm
             - fi = oscillator strength for state i (dimensionless)
+            
         output :
             molar absorption coefficient, in L mol-1 cm-1
-        '''
+            
+        """
         import scipy.constants as sc
         import numpy as np
         c = sc.c*1e2 #cm-1
@@ -78,20 +82,21 @@ class SpectrumSimulator:
         return epsi
     
     def _Absorbance(self,eps,opl,cc):
-        '''
+        """
         Calculates the Absorbance with the Beer-Lambert law
+        
         input:
             - eps = molar absorption coefficient, in L mol-1 cm-1
             - opl = optical path length, in cm
             - cc = concentration of the attenuating species, in mol.L-1
+        
         output :
             Absorbance, A (dimensionless)
-        '''
+            
+        """
         return eps*opl*cc
     
     def _sumStatesWithGf(self,wavel,wavelTAB,feTAB):
-        '''
-        '''
         import numpy as np
         sumInt = np.zeros(len(wavel))
         for l in wavel:
@@ -100,7 +105,7 @@ class SpectrumSimulator:
         return sumInt
     
     def _FindPeaks(self,sumInt,height,prom=1):
-        '''
+        """
         Finds local maxima within the spectrum based on height and prominence.
         
         Prominence is crucial when switching between linear and logarithmic scales:
@@ -117,7 +122,8 @@ class SpectrumSimulator:
         Returns:
             - PeakIndex: Indices of the detected peaks in the wavelength array.
             - PeakHeight: The intensity values at these peak positions.
-        '''
+            
+        """
         from scipy.signal import find_peaks
         peaks = find_peaks(sumInt, height = height, threshold = None, distance = 1, prominence=prom)
         PeakIndex = peaks[0]
@@ -130,8 +136,8 @@ class SpectrumSimulator:
         return PeakIndex,PeakHeight
 
     def _FindShoulders(self, data, tP):
-        '''
-        ###not working
+        """
+        ###not working###
         Detects shoulders using the second derivative.
         A shoulder appears as a peak in the negative second derivative.
         
@@ -145,7 +151,8 @@ class SpectrumSimulator:
             - shoulder_idx (ndarray): Array of indices where shoulders were found.
             - shoulder_heights (ndarray): The intensity values at these positions 
               extracted from the input data.
-        '''
+              
+        """
         import numpy as np
         # Calculate the second derivative (rate of change of the slope)
         d2 = np.gradient(np.gradient(data))
@@ -162,11 +169,13 @@ class SpectrumSimulator:
     
     def _pickPeak(self,wavel,peaksIndex,peaksH,color,\
                   shift=500,height=500,posAnnotation=200, ylog=False):
-        '''
+        """
         Annotates peaks with a small vertical tick and the wavelength value.
         Adjusts offsets based on whether the plot is in log10 scale or linear.
         In log mode, peaksH must already be log10 values.
-        '''
+        
+        """
+        
         s=shift
         h=height
         a=posAnnotation
@@ -202,19 +211,20 @@ class SpectrumSimulator:
     
     def plotTDDFTSpectrum(self,wavel,sumInt,wavelTAB,feTAB,tP,ylog,labelSpectrum,colorS='#0000ff',colorT='#0000cf'):
         
-        '''
+        """
         Called by plotEps_lambda_TDDFT. Plots a single simulated UV-Vis spectrum, i.e. after
         gaussian broadening, together with the TDDFT vertical transitions (i.e. plotted as lines)
         
-        input:
-            - wavel = array of gaussian-broadened wavelengths, in nm
-            - sumInt = corresponding molar absorptiopn coefficients, in L. mol-1 cm-1
-            - wavelTAB = wavelength of TDDFT, e.g. discretized, transitions
-            - ylog = log plot of epsilon
-            - tP: threshold for finding the peaks
-            - feTAB = TDDFT oscillator strength for each transition of wavelTAB
-            - labelSpectrum = title for the spectrum
-        '''
+        Args:
+            wavel: array of gaussian-broadened wavelengths, in nm
+            sumInt: corresponding molar absorptiopn coefficients, in L. mol-1 cm-1
+            wavelTAB: wavelength of TDDFT, e.g. discretized, transitions
+            ylog: log plot of epsilon
+            tP: threshold for finding the peaks
+            feTAB: TDDFT oscillator strength for each transition of wavelTAB
+            labelSpectrum: title for the spectrum
+            
+        """
 
         # # --- DEBUG START ---
         # if ylog:
@@ -261,19 +271,26 @@ class SpectrumSimulator:
                              epsMax=None, titles=None, tP = 10, \
                              ylog=False,\
                              filename=None):
-        '''
+        """
         Plots a TDDFT VUV simulated spectrum (vertical transitions and transitions summed with gaussian functions)
-        between lambdamin and lambdamax (sum of states done in the range [lambdamin-50, lambdamlax+50] nm)
-        input:
-            - datFile: list of pathway/names to "XXX_ExcStab.dat" files generated by 'GParser Gaussian.log -S'
-            - lambdamin, lambdamax: plot range
-            - epsMax: y axis graph limit
-            - titles: list of titles (1 per spectrum plot)
-            - tP: threshold for finding the peaks (default = 10 L. mol-1 cm-1)
-            - ylog: y logarithmic axis (default: False).
-            - save: saves in a png file (300 dpi) if True (default = False)
-            - filename: saves figure in a 300 dpi png file if not None (default), with filename=full pathway
-        '''
+        between lambdamin and lambdamax
+
+        The sum of states is done in the range
+        [lambdamin-50, lambdamax+50] nm.
+        
+        Args:
+            datFile: list of pathway/names to "XXX_ExcStab.dat" files generated by 'GParser Gaussian.log -S'
+            lambdamin, lambdamax: plot range
+            epsMax: y axis graph limit
+            titles: list of titles (1 per spectrum plot)
+            tP: threshold for finding the peaks (default = 10 L. mol-1 cm-1)
+            ylog: y logarithmic axis (default: False).
+            save: saves in a png file (300 dpi) if True (default = False)
+            filename: saves figure in a 300 dpi png file if not None (default), with filename=full pathway
+            
+        """
+        import matplotlib.ticker as ticker
+
         if self.fig is not None:
             graph = self.graph
             fig = self.fig
@@ -296,7 +313,6 @@ class SpectrumSimulator:
 
             graph.set_xlim(lambdamin,lambdamax)
 
-            import matplotlib.ticker as ticker
             graph.xaxis.set_major_locator(ticker.MultipleLocator(50)) # sets a tick for every integer multiple of the base (here 250) within the view interval
         
         istate,state,wavel,fe,SSq = np.genfromtxt(datFile,skip_header=1,dtype="<U20,<U20,float,float,<U20",unpack=True)
@@ -333,25 +349,27 @@ class SpectrumSimulator:
                              titles=None, linestyles=[], annotateP=[], tP = 0.1,\
                              resetColors=False,\
                              filename=None):
-        '''
+        """
         Plots a simulated TDDFT VUV absorbance spectrum (transitions summed with gaussian functions)
         between lambdamin and lambdamax (sum of states done in the range [lambdamin-50, lambdamlax+50] nm)
-        input:
-            - datFiles: list of pathway/name to files generated by 'GParser Gaussian.log -S'
-            - C0: list of concentrations needed to calculate A = epsilon x l x c (in mol.L-1)
-            - lambdamin, lambdamax: plot range (x axis)
-            - Amax: y axis graph limit
-            - titles: list of titles (1 per spectrum plot)
-            - linestyles: list of line styles(default = "-", i.e. a continuous line)
-            - annotateP: list of Boolean (annotate lambda max True or False. Default = True)
-            - tP: threshold for finding the peaks (default = 0.1)
-            - resetColors (bool): If True, resets the matplotlib color cycle 
-                                 to the first color. This allows different series 
-                                 (e.g., gas phase vs. solvent) to share the same 
-                                 color coding for each molecule across multiple calls. Default: False
-            - save: saves in a png file (300 dpi) if True (default = False)
-            - filename: saves figure in a 300 dpi png file if not None (default), with filename=full pathway
-        '''
+        
+        Args:
+            datFiles: list of pathway/name to files generated by 'GParser Gaussian.log -S'
+            C0: list of concentrations needed to calculate A = epsilon x l x c (in mol.L-1)
+            lambdamin, lambdamax: plot range (x axis)
+            Amax: y axis graph limit
+            titles: list of titles (1 per spectrum plot)
+            linestyles: list of line styles(default = "-", i.e. a continuous line)
+            annotateP: list of Boolean (annotate lambda max True or False. Default = True)
+            tP: threshold for finding the peaks (default = 0.1)
+            resetColors (bool): If True, resets the matplotlib color cycle 
+                to the first color. This allows different series 
+                (e.g., gas phase vs. solvent) to share the same 
+                color coding for each molecule across multiple calls. Default: False
+            save: saves in a png file (300 dpi) if True (default = False)
+            filename: saves figure in a 300 dpi png file if not None (default), with filename=full pathway
+            
+        """
 
         if self.fig is None:
             fig, graph = self._initializePlot()
@@ -394,11 +412,12 @@ class SpectrumSimulator:
     def plotAbs_lambda_exp(self, csvFiles, C0, lambdamin=200, lambdamax=800,\
                              Amax=2.0, titles=None, linestyles=[], annotateP=[], tP = 0.1,\
                              filename=None):
-        '''
+        """
         Plots an experimental VUV absorbance spectrum read from a csv file between lambdamin and lambdamax
-        input:
+        
+        Args:
             - superpose: False = plots a new graph, otherwise the plot is superposed to a previously created one
-                         (probably with plotAbs_lambda_TDDFT())
+              (probably with plotAbs_lambda_TDDFT())
             - csvfiles: list of pathway/name to experimental csvFiles (see examples for the format)
             - C0: list of experimental concentrations, i.e. for each sample
             - lambdamin, lambdamax: plot range (x axis)
@@ -409,7 +428,8 @@ class SpectrumSimulator:
             - tP: threshold for finding the peaks (default = 0.1)
             - save: saves in a png file (300 dpi) if True (default = False)
             - filename: saves figure in a 300 dpi png file if not None (default), with filename=full pathway
-        '''
+            
+        """
         if linestyles == []: linestyles = len(csvFiles)*['--']
         if annotateP == []: annotateP = len(csvFiles)*[True]