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                #! /usr/bin/env python  | 
            
            
                                                                                                            
                            
            
                                    
            
            
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                #  | 
            
            
                                                                                                            
                            
            
                                    
            
            
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                # Copyright (C) 2016 Rich Lewis <[email protected]>  | 
            
            
                                                                                                            
                            
            
                                    
            
            
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                # License: 3-clause BSD  | 
            
            
                                                                                                            
                            
            
                                    
            
            
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                """  | 
            
            
                                                                                                            
                            
            
                                    
            
            
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                # skchem.features.descriptors.autocorrelation  | 
            
            
                                                                                                            
                            
            
                                    
            
            
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                Autocorrelation descriptors for scikit-chem.  | 
            
            
                                                                                                            
                            
            
                                    
            
            
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                """  | 
            
            
                                                                                                            
                            
            
                                    
            
            
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                from functools import partial  | 
            
            
                                                                                                            
                            
            
                                    
            
            
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                from .caching import cache  | 
            
                            
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                from .fundamentals import adjacency_matrix, distance_matrix, atom_props  | 
            
                            
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                import numpy as np  | 
            
                            
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                @cache.inject(distance_matrix, atom_props)  | 
            
            
                                                                                                            
                            
            
                                    
            
            
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                def moreau_broto_autocorrelation(mol, dist_mat, prop, prop_name='atomic_mass',  | 
            
                            
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                                                 c_scaled=False, centred=False,  | 
            
                            
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                                                 ks=range(1, 9)):  | 
            
            
                                                                                                            
                            
            
                                    
            
            
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                    """ The Moreau-Broto autocorrelation.  | 
            
                            
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                    $$ ATS_k = \frac{1}{2} \hdot \sum_{i=1}^A \sum_{j=1}^A $$ | 
            
            
                                                                                                            
                            
            
                                    
            
            
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                    With special case $$ ATS_0 = \sum_{i=1}^A w_i^2. | 
            
            
                                                                                                            
                            
            
                                    
            
            
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                    Where $A$ is the number of atoms, and $w$ is an atomic property.  | 
            
            
                                                                                                            
                            
            
                                    
            
            
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                    Args:  | 
            
            
                                                                                                            
                            
            
                                    
            
            
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                        mol (skchem.Mol):  | 
            
            
                                                                                                            
                            
            
                                    
            
            
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                            The molecule for which to calculate the descriptor.  | 
            
            
                                                                                                            
                            
            
                                    
            
            
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                        prop (str):  | 
            
            
                                                                                                            
                            
            
                                    
            
            
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                            The atomic property.  | 
            
            
                                                                                                            
                            
            
                                    
            
            
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                        c_scaled (bool):  | 
            
            
                                                                                                            
                            
            
                                    
            
            
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                            Whether the properties should be scaled against sp3 carbon.  | 
            
            
                                                                                                            
                            
            
                                    
            
            
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                        centred (bool):  | 
            
            
                                                                                                            
                            
            
                                    
            
            
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                            Whether the descriptor should be divided by the number of  | 
            
            
                                                                                                            
                            
            
                                    
            
            
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                            contributions (avoids dependence on molecular size).  | 
            
            
                                                                                                            
                            
            
                                    
            
            
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                        ks (iterable):  | 
            
            
                                                                                                            
                            
            
                                    
            
            
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                            The lags to calculate the descriptor over.  | 
            
            
                                                                                                            
                            
            
                                    
            
            
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                    Returns:  | 
            
            
                                                                                                            
                            
            
                                    
            
            
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                        float  | 
            
            
                                                                                                            
                            
            
                                    
            
            
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                    Examples:  | 
            
            
                                                                                                            
                            
            
                                    
            
            
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                        >>> import skchem  | 
            
            
                                                                                                            
                            
            
                                    
            
            
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                        >>> m = skchem.Mol.from_smiles('CC(O)CCO') | 
            
            
                                                                                                            
                            
            
                                    
            
            
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                        >>> moreau_broto_autocorrelation(m, centred=False,  | 
            
            
                                                                                                            
                            
            
                                    
            
            
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                        ...                              prop_name='atomic_mass',  | 
            
            
                                                                                                            
                            
            
                                    
            
            
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                        ...                              ks=range(4))  # doctest: +ELLIPSIS  | 
            
            
                                                                                                            
                            
            
                                    
            
            
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                        array([ 1088.99...,   817.12...,   865.02...,   528.59...])  | 
            
            
                                                                                                            
                            
            
                                    
            
            
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                    """  | 
            
            
                                                                                                            
                            
            
                                    
            
            
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                    div = np.array([(dist_mat == k).sum() for k in ks]) if centred else 1  | 
            
                            
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                    return np.array([(1 if k == 0 else 0.5) * prop.dot(dist_mat == k).dot(prop)  | 
            
            
                                                                                                            
                            
            
                                    
            
            
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                                     for k in ks]) / div  | 
            
            
                                                                                                            
                            
            
                                    
            
            
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                @cache.inject(distance_matrix, atom_props)  | 
            
            
                                                                                                            
                            
            
                                    
            
            
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                def moran_coefficient(mol, dist_mat, prop, prop_name='atomic_mass',  | 
            
                            
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                                      c_scaled=False, ks=range(1, 9)):  | 
            
                            
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                    """ Moran coefficient for lags ks.  | 
            
            
                                                                                                            
                            
            
                                    
            
            
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                    Args:  | 
            
            
                                                                                                            
                            
            
                                    
            
            
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                        mol (skchem.Mol):  | 
            
            
                                                                                                            
                            
            
                                    
            
            
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                            The molecule for which to calculate the descriptor.  | 
            
            
                                                                                                            
                            
            
                                    
            
            
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                        prop (str):  | 
            
            
                                                                                                            
                            
            
                                    
            
            
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                            The atomic property.  | 
            
            
                                                                                                            
                            
            
                                    
            
            
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                        c_scaled (bool):  | 
            
            
                                                                                                            
                            
            
                                    
            
            
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                            Whether the properties should be scaled against sp3 carbon.  | 
            
            
                                                                                                            
                            
            
                                    
            
            
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                        centered (bool):  | 
            
            
                                                                                                            
                            
            
                                    
            
            
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                            Whether the descriptor should be divided by the number of  | 
            
            
                                                                                                            
                            
            
                                    
            
            
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                            contributions (avoids dependence on molecular size.  | 
            
            
                                                                                                            
                            
            
                                    
            
            
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                        ks (iterable):  | 
            
            
                                                                                                            
                            
            
                                    
            
            
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                            The lags to calculate the descriptor over.  | 
            
            
                                                                                                            
                            
            
                                    
            
            
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                    Returns:  | 
            
            
                                                                                                            
                            
            
                                    
            
            
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                        float  | 
            
            
                                                                                                            
                            
            
                                    
            
            
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                    """  | 
            
            
                                                                                                            
                            
            
                                    
            
            
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                    prop = prop - prop.mean()  | 
            
            
                                                                                                            
                            
            
                                    
            
            
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                    res = []  | 
            
            
                                                                                                            
                            
            
                                    
            
            
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                    for k in ks:  | 
            
                            
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                        geodesic = dist_mat == k  | 
            
            
                                                                                                            
                            
            
                                    
            
            
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                        num = prop.dot(geodesic).dot(prop) / geodesic.sum()  | 
            
            
                                                                                                            
                            
            
                                    
            
            
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                        denom = (prop ** 2).sum() / len(prop)  | 
            
            
                                                                                                            
                            
            
                                    
            
            
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                        res.append(num / denom)  | 
            
            
                                                                                                            
                            
            
                                    
            
            
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                    return np.array(res)  | 
            
            
                                                                                                            
                            
            
                                    
            
            
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                @cache.inject(distance_matrix, atom_props)  | 
            
            
                                                                                                            
                            
            
                                    
            
            
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                def geary_coefficient(mol, dist_mat, prop, prop_name='atomic_mass',  | 
            
                            
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                                      c_scaled=False, ks=range(1, 9)):  | 
            
                            
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                    """ The geary coefficient for *ks* lags.  | 
            
            
                                                                                                            
                            
            
                                    
            
            
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                    Args:  | 
            
            
                                                                                                            
                            
            
                                    
            
            
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                        mol (skchem.Mol):  | 
            
            
                                                                                                            
                            
            
                                    
            
            
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                            The molecule for which to calculate the descriptor.  | 
            
            
                                                                                                            
                            
            
                                    
            
            
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                        prop (str):  | 
            
            
                                                                                                            
                            
            
                                    
            
            
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                            The atomic property.  | 
            
            
                                                                                                            
                            
            
                                    
            
            
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                        c_scaled (bool):  | 
            
            
                                                                                                            
                            
            
                                    
            
            
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                            Whether the properties should be scaled against sp3 carbon.  | 
            
            
                                                                                                            
                            
            
                                    
            
            
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                        centered (bool):  | 
            
            
                                                                                                            
                            
            
                                    
            
            
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                            Whether the descriptor should be divided by the number of  | 
            
            
                                                                                                            
                            
            
                                    
            
            
                | 
                    126
                 | 
                                    
                                                     | 
                
                 | 
                            contributions (avoids dependence on molecular size.  | 
            
            
                                                                                                            
                            
            
                                    
            
            
                | 
                    127
                 | 
                                    
                                                     | 
                
                 | 
                 | 
            
            
                                                                                                            
                            
            
                                    
            
            
                | 
                    128
                 | 
                                    
                                                     | 
                
                 | 
                        ks (iterable):  | 
            
            
                                                                                                            
                            
            
                                    
            
            
                | 
                    129
                 | 
                                    
                                                     | 
                
                 | 
                            The lags to calculate the descriptor over.  | 
            
            
                                                                                                            
                            
            
                                    
            
            
                | 
                    130
                 | 
                                    
                                                     | 
                
                 | 
                 | 
            
            
                                                                                                            
                            
            
                                    
            
            
                | 
                    131
                 | 
                                    
                                                     | 
                
                 | 
                    Returns:  | 
            
            
                                                                                                            
                            
            
                                    
            
            
                | 
                    132
                 | 
                                    
                                                     | 
                
                 | 
                        float  | 
            
            
                                                                                                            
                            
            
                                    
            
            
                | 
                    133
                 | 
                                    
                                                     | 
                
                 | 
                 | 
            
            
                                                                                                            
                            
            
                                    
            
            
                | 
                    134
                 | 
                                    
                                                     | 
                
                 | 
                    """  | 
            
            
                                                                                                            
                            
            
                                    
            
            
                | 
                    135
                 | 
                                    
                                                     | 
                
                 | 
                 | 
            
            
                                                                                                            
                            
            
                                    
            
            
                | 
                    136
                 | 
                                    
                                                     | 
                
                 | 
                    res = []  | 
            
            
                                                                                                            
                            
            
                                    
            
            
                | 
                    137
                 | 
                                    
                                                     | 
                
                 | 
                    for k in ks:  | 
            
                            
                    | 
                        
                     | 
                     | 
                     | 
                    
                                                                                                    
                        
                         
                                                                                        
                                                                                     
                     | 
                
            
                                                                                                            
                            
            
                                    
            
            
                | 
                    138
                 | 
                                    
                                                     | 
                
                 | 
                        geodesic = dist_mat == k  | 
            
            
                                                                                                            
                            
            
                                    
            
            
                | 
                    139
                 | 
                                    
                                                     | 
                
                 | 
                        num = 0.5 * ((prop - prop[:, np.newaxis]) ** 2 * geodesic).sum() / geodesic.sum()  | 
            
            
                                                                                                            
                            
            
                                    
            
            
                | 
                    140
                 | 
                                    
                                                     | 
                
                 | 
                        denom = ((prop - prop.mean()) ** 2).sum() / (len(prop) - 1)  | 
            
            
                                                                                                            
                            
            
                                    
            
            
                | 
                    141
                 | 
                                    
                                                     | 
                
                 | 
                        res.append(num / denom)  | 
            
            
                                                                                                            
                            
            
                                    
            
            
                | 
                    142
                 | 
                                    
                                                     | 
                
                 | 
                 | 
            
            
                                                                                                            
                            
            
                                    
            
            
                | 
                    143
                 | 
                                    
                                                     | 
                
                 | 
                    return np.array(res)  | 
            
            
                                                                                                            
                            
            
                                    
            
            
                | 
                    144
                 | 
                                    
                                                     | 
                
                 | 
                 | 
            
            
                                                                                                            
                            
            
                                    
            
            
                | 
                    145
                 | 
                                    
                                                     | 
                
                 | 
                 | 
            
            
                                                                                                            
                            
            
                                    
            
            
                | 
                    146
                 | 
                                    
                                                     | 
                
                 | 
                @cache  | 
            
            
                                                                                                            
                            
            
                                    
            
            
                | 
                    147
                 | 
                                    
                                                     | 
                
                 | 
                @cache.inject(adjacency_matrix, distance_matrix)  | 
            
            
                                                                                                            
                            
            
                                    
            
            
                | 
                    148
                 | 
                                    
                                                     | 
                
                 | 
                def galvez_matrix(mol, dist_mat, adj_mat):  | 
            
            
                                                                                                            
                            
            
                                    
            
            
                | 
                    149
                 | 
                                    
                                                     | 
                
                 | 
                 | 
            
            
                                                                                                            
                            
            
                                    
            
            
                | 
                    150
                 | 
                                    
                                                     | 
                
                 | 
                    """ The galvez matrix.  | 
            
            
                                                                                                            
                            
            
                                    
            
            
                | 
                    151
                 | 
                                    
                                                     | 
                
                 | 
                 | 
            
            
                                                                                                            
                            
            
                                    
            
            
                | 
                    152
                 | 
                                    
                                                     | 
                
                 | 
                    Args:  | 
            
            
                                                                                                            
                            
            
                                    
            
            
                | 
                    153
                 | 
                                    
                                                     | 
                
                 | 
                        mol (skchem.Mol):  | 
            
            
                                                                                                            
                            
            
                                    
            
            
                | 
                    154
                 | 
                                    
                                                     | 
                
                 | 
                            The molecule for which to calculate the matrix.  | 
            
            
                                                                                                            
                            
            
                                    
            
            
                | 
                    155
                 | 
                                    
                                                     | 
                
                 | 
                 | 
            
            
                                                                                                            
                            
            
                                    
            
            
                | 
                    156
                 | 
                                    
                                                     | 
                
                 | 
                    Returns:  | 
            
            
                                                                                                            
                            
            
                                    
            
            
                | 
                    157
                 | 
                                    
                                                     | 
                
                 | 
                        np.array  | 
            
            
                                                                                                            
                            
            
                                    
            
            
                | 
                    158
                 | 
                                    
                                                     | 
                
                 | 
                    """  | 
            
            
                                                                                                            
                            
            
                                    
            
            
                | 
                    159
                 | 
                                    
                                                     | 
                
                 | 
                 | 
            
            
                                                                                                            
                            
            
                                    
            
            
                | 
                    160
                 | 
                                    
                                                     | 
                
                 | 
                    temp = dist_mat ** -2  | 
            
            
                                                                                                            
                            
            
                                    
            
            
                | 
                    161
                 | 
                                    
                                                     | 
                
                 | 
                    np.fill_diagonal(temp, 0)  | 
            
            
                                                                                                            
                            
            
                                    
            
            
                | 
                    162
                 | 
                                    
                                                     | 
                
                 | 
                    galvez_mat = temp.dot(adj_mat) + np.diag(mol.atoms.valence_vertex_degree)  | 
            
            
                                                                                                            
                            
            
                                    
            
            
                | 
                    163
                 | 
                                    
                                                     | 
                
                 | 
                    return galvez_mat  | 
            
            
                                                                                                            
                            
            
                                    
            
            
                | 
                    164
                 | 
                                    
                                                     | 
                
                 | 
                 | 
            
            
                                                                                                            
                                                                
            
                                    
            
            
                | 
                    165
                 | 
                                    
                                                     | 
                
                 | 
                 | 
            
            
                                                                        
                            
            
                                    
            
            
                | 
                    166
                 | 
                                    
                                                     | 
                
                 | 
                @cache  | 
            
            
                                                                        
                            
            
                                    
            
            
                | 
                    167
                 | 
                                    
                                                     | 
                
                 | 
                @cache.inject(galvez_matrix)  | 
            
            
                                                                        
                            
            
                                    
            
            
                | 
                    168
                 | 
                                    
                                                     | 
                
                 | 
                def charge_matrix(mol, galvez_mat):  | 
            
            
                                                                        
                            
            
                                    
            
            
                | 
                    169
                 | 
                                    
                                                     | 
                
                 | 
                 | 
            
            
                                                                        
                            
            
                                    
            
            
                | 
                    170
                 | 
                                    
                                                     | 
                
                 | 
                    """ The charge matrix.  | 
            
            
                                                                        
                            
            
                                    
            
            
                | 
                    171
                 | 
                                    
                                                     | 
                
                 | 
                 | 
            
            
                                                                        
                            
            
                                    
            
            
                | 
                    172
                 | 
                                    
                                                     | 
                
                 | 
                    Args:  | 
            
            
                                                                        
                            
            
                                    
            
            
                | 
                    173
                 | 
                                    
                                                     | 
                
                 | 
                        mol (skchem.Mol):  | 
            
            
                                                                        
                            
            
                                    
            
            
                | 
                    174
                 | 
                                    
                                                     | 
                
                 | 
                            The molecule for which to calculate the matrix.  | 
            
            
                                                                        
                            
            
                                    
            
            
                | 
                    175
                 | 
                                    
                                                     | 
                
                 | 
                 | 
            
            
                                                                        
                            
            
                                    
            
            
                | 
                    176
                 | 
                                    
                                                     | 
                
                 | 
                    Returns:  | 
            
            
                                                                        
                            
            
                                    
            
            
                | 
                    177
                 | 
                                    
                                                     | 
                
                 | 
                        np.array  | 
            
            
                                                                        
                            
            
                                    
            
            
                | 
                    178
                 | 
                                    
                                                     | 
                
                 | 
                 | 
            
            
                                                                        
                            
            
                                    
            
            
                | 
                    179
                 | 
                                    
                                                     | 
                
                 | 
                    """  | 
            
            
                                                                        
                            
            
                                    
            
            
                | 
                    180
                 | 
                                    
                                                     | 
                
                 | 
                 | 
            
            
                                                                        
                            
            
                                    
            
            
                | 
                    181
                 | 
                                    
                                                     | 
                
                 | 
                    ct_mat = galvez_mat - galvez_mat.T  | 
            
            
                                                                        
                            
            
                                    
            
            
                | 
                    182
                 | 
                                    
                                                     | 
                
                 | 
                    ct_mat[np.diag_indices_from(ct_mat)] = mol.atoms.depleted_degree  | 
            
            
                                                                        
                            
            
                                    
            
            
                | 
                    183
                 | 
                                    
                                                     | 
                
                 | 
                 | 
            
            
                                                                        
                            
            
                                    
            
            
                | 
                    184
                 | 
                                    
                                                     | 
                
                 | 
                    return ct_mat  | 
            
            
                                                                                                            
                            
            
                                    
            
            
                | 
                    185
                 | 
                                    
                                                     | 
                
                 | 
                 | 
            
            
                                                                                                            
                            
            
                                    
            
            
                | 
                    186
                 | 
                                    
                                                     | 
                
                 | 
                 | 
            
            
                                                                                                            
                            
            
                                    
            
            
                | 
                    187
                 | 
                                    
                                                     | 
                
                 | 
                @cache  | 
            
            
                                                                                                            
                            
            
                                    
            
            
                | 
                    188
                 | 
                                    
                                                     | 
                
                 | 
                @cache.inject(charge_matrix, distance_matrix)  | 
            
            
                                                                                                            
                            
            
                                    
            
            
                | 
                    189
                 | 
                                    
                                                     | 
                
                 | 
                def topological_charge_index(mol, c_mat, dist_mat, ks=range(11)):  | 
            
                            
                    | 
                        
                     | 
                     | 
                     | 
                    
                                                                                                                                                        
                        
                         
                                                                                        
                                                                                            
                                                                                     
                     | 
                
            
                                                                                                            
                            
            
                                    
            
            
                | 
                    190
                 | 
                                    
                                                     | 
                
                 | 
                 | 
            
            
                                                                                                            
                            
            
                                    
            
            
                | 
                    191
                 | 
                                    
                                                     | 
                
                 | 
                    """ The Galvez tologogical charge index for lags ks.  | 
            
            
                                                                                                            
                            
            
                                    
            
            
                | 
                    192
                 | 
                                    
                                                     | 
                
                 | 
                 | 
            
            
                                                                                                            
                            
            
                                    
            
            
                | 
                    193
                 | 
                                    
                                                     | 
                
                 | 
                    Args:  | 
            
            
                                                                                                            
                            
            
                                    
            
            
                | 
                    194
                 | 
                                    
                                                     | 
                
                 | 
                        mol (skchem.Mol):  | 
            
            
                                                                                                            
                            
            
                                    
            
            
                | 
                    195
                 | 
                                    
                                                     | 
                
                 | 
                            The molecule for which to calculate the descriptor.  | 
            
            
                                                                                                            
                            
            
                                    
            
            
                | 
                    196
                 | 
                                    
                                                     | 
                
                 | 
                 | 
            
            
                                                                                                            
                            
            
                                    
            
            
                | 
                    197
                 | 
                                    
                                                     | 
                
                 | 
                        ks (iterable):  | 
            
            
                                                                                                            
                            
            
                                    
            
            
                | 
                    198
                 | 
                                    
                                                     | 
                
                 | 
                            The lags for which to calculate the descriptor.  | 
            
            
                                                                                                            
                            
            
                                    
            
            
                | 
                    199
                 | 
                                    
                                                     | 
                
                 | 
                 | 
            
            
                                                                                                            
                            
            
                                    
            
            
                | 
                    200
                 | 
                                    
                                                     | 
                
                 | 
                    Returns:  | 
            
            
                                                                                                            
                            
            
                                    
            
            
                | 
                    201
                 | 
                                    
                                                     | 
                
                 | 
                        np.array  | 
            
            
                                                                                                            
                            
            
                                    
            
            
                | 
                    202
                 | 
                                    
                                                     | 
                
                 | 
                 | 
            
            
                                                                                                            
                            
            
                                    
            
            
                | 
                    203
                 | 
                                    
                                                     | 
                
                 | 
                    """  | 
            
            
                                                                                                            
                            
            
                                    
            
            
                | 
                    204
                 | 
                                    
                                                     | 
                
                 | 
                    return np.array([0.5 * np.abs(c_mat)[dist_mat == k].sum() for i in ks])  | 
            
                            
                    | 
                        
                     | 
                     | 
                     | 
                    
                                                                                                    
                        
                         
                                                                                        
                                                                                     
                     | 
                
            
                                                                                                            
                            
            
                                    
            
            
                | 
                    205
                 | 
                                    
                                                     | 
                
                 | 
                 | 
            
            
                                                                                                            
                            
            
                                    
            
            
                | 
                    206
                 | 
                                    
                                                     | 
                
                 | 
                 | 
            
            
                                                                                                            
                            
            
                                    
            
            
                | 
                    207
                 | 
                                    
                                                     | 
                
                 | 
                @cache.inject(topological_charge_index)  | 
            
            
                                                                                                            
                            
            
                                    
            
            
                | 
                    208
                 | 
                                    
                                                     | 
                
                 | 
                def mean_topological_charge_index(mol, tci, ks=range(11)):  | 
            
                            
                    | 
                        
                     | 
                     | 
                     | 
                    
                                                                                                                                                        
                        
                         
                                                                                        
                                                                                            
                                                                                     
                     | 
                
            
                                                                                                            
                            
            
                                    
            
            
                | 
                    209
                 | 
                                    
                                                     | 
                
                 | 
                 | 
            
            
                                                                                                            
                            
            
                                    
            
            
                | 
                    210
                 | 
                                    
                                                     | 
                
                 | 
                    """ Mean topological charge index for lags ks.  | 
            
            
                                                                                                            
                            
            
                                    
            
            
                | 
                    211
                 | 
                                    
                                                     | 
                
                 | 
                 | 
            
            
                                                                                                            
                            
            
                                    
            
            
                | 
                    212
                 | 
                                    
                                                     | 
                
                 | 
                    Args:  | 
            
            
                                                                                                            
                            
            
                                    
            
            
                | 
                    213
                 | 
                                    
                                                     | 
                
                 | 
                        mol (skchem.Mol):  | 
            
            
                                                                                                            
                            
            
                                    
            
            
                | 
                    214
                 | 
                                    
                                                     | 
                
                 | 
                            The molecule for which to calculate the descriptor.  | 
            
            
                                                                                                            
                            
            
                                    
            
            
                | 
                    215
                 | 
                                    
                                                     | 
                
                 | 
                 | 
            
            
                                                                                                            
                            
            
                                    
            
            
                | 
                    216
                 | 
                                    
                                                     | 
                
                 | 
                        ks (iterable):  | 
            
            
                                                                                                            
                            
            
                                    
            
            
                | 
                    217
                 | 
                                    
                                                     | 
                
                 | 
                            The lags for which to calculate the descriptor.  | 
            
            
                                                                                                            
                            
            
                                    
            
            
                | 
                    218
                 | 
                                    
                                                     | 
                
                 | 
                 | 
            
            
                                                                                                            
                            
            
                                    
            
            
                | 
                    219
                 | 
                                    
                                                     | 
                
                 | 
                    Returns:  | 
            
            
                                                                                                            
                            
            
                                    
            
            
                | 
                    220
                 | 
                                    
                                                     | 
                
                 | 
                        np.array  | 
            
            
                                                                                                            
                            
            
                                    
            
            
                | 
                    221
                 | 
                                    
                                                     | 
                
                 | 
                    """  | 
            
            
                                                                                                            
                            
            
                                    
            
            
                | 
                    222
                 | 
                                    
                                                     | 
                
                 | 
                 | 
            
            
                                                                                                            
                            
            
                                    
            
            
                | 
                    223
                 | 
                                    
                                                     | 
                
                 | 
                    return tci / (len(mol.atoms) - 1)  | 
            
            
                                                                                                            
                            
            
                                    
            
            
                | 
                    224
                 | 
                                    
                                                     | 
                
                 | 
                 | 
            
            
                                                                                                            
                            
            
                                    
            
            
                | 
                    225
                 | 
                                    
                                                     | 
                
                 | 
                 | 
            
            
                                                                                                            
                            
            
                                    
            
            
                | 
                    226
                 | 
                                    
                                                     | 
                
                 | 
                @cache.inject(topological_charge_index)  | 
            
            
                                                                                                            
                            
            
                                    
            
            
                | 
                    227
                 | 
                                    
                                                     | 
                
                 | 
                def total_charge_index(mol, tci, ks=range(11)):  | 
            
                            
                    | 
                        
                     | 
                     | 
                     | 
                    
                                                                                                                                                                                                            
                        
                         
                                                                                        
                                                                                            
                                                                                            
                                                                                     
                     | 
                
            
                                                                                                            
                            
            
                                    
            
            
                | 
                    228
                 | 
                                    
                                                     | 
                
                 | 
                 | 
            
            
                                                                                                            
                            
            
                                    
            
            
                | 
                    229
                 | 
                                    
                                                     | 
                
                 | 
                    return tci.sum() / (len(mol.atoms) - 1)  | 
            
            
                                                                                                            
                            
            
                                    
            
            
                | 
                    230
                 | 
                                    
                                                     | 
                
                 | 
                 | 
            
            
                                                                                                            
                            
            
                                    
            
            
                | 
                    231
                 | 
                                    
                                                     | 
                
                 | 
                 | 
            
            
                                                                                                            
                            
            
                                    
            
            
                | 
                    232
                 | 
                                    
                                                     | 
                
                 | 
                PROPS = ['atomic_mass', 'van_der_waals_volume', 'sanderson_electronegativity',  | 
            
            
                                                                                                            
                            
            
                                    
            
            
                | 
                    233
                 | 
                                    
                                                     | 
                
                 | 
                         'polarisability', 'ionisation_energy', 'intrinsic_state']  | 
            
            
                                                                                                            
                            
            
                                    
            
            
                | 
                    234
                 | 
                                    
                                                     | 
                
                 | 
                 | 
            
            
                                                                                                            
                            
            
                                    
            
            
                | 
                    235
                 | 
                                    
                                                     | 
                
                 | 
                KS = range(1, 9)  | 
            
            
                                                                                                            
                            
            
                                    
            
            
                | 
                    236
                 | 
                                    
                                                     | 
                
                 | 
                 | 
            
            
                                                                                                            
                            
            
                                    
            
            
                | 
                    237
                 | 
                                    
                                                     | 
                
                 | 
                DESCRIPTORS = [partial(moreau_broto_autocorrelation, k=k, prop=p, centered=c)  | 
            
            
                                                                                                            
                            
            
                                    
            
            
                | 
                    238
                 | 
                                    
                                                     | 
                
                 | 
                               for k in KS for c in (False, True) for p in PROPS]  | 
            
            
                                                                                                            
                            
            
                                    
            
            
                | 
                    239
                 | 
                                    
                                                     | 
                
                 | 
                 | 
            
            
                                                                                                            
                            
            
                                    
            
            
                | 
                    240
                 | 
                                    
                                                     | 
                
                 | 
                FS = (moran_coefficient, geary_coefficient)  | 
            
            
                                                                                                            
                            
            
                                    
            
            
                | 
                    241
                 | 
                                    
                                                     | 
                
                 | 
                 | 
            
            
                                                                                                            
                            
            
                                    
            
            
                | 
                    242
                 | 
                                    
                                                     | 
                
                 | 
                DESCRIPTORS += [partial(f, k=k, prop=p) for f in FS for k in KS for p in PROPS]  | 
            
            
                                                                                                            
                            
            
                                    
            
            
                | 
                    243
                 | 
                                    
                                                     | 
                
                 | 
                 | 
            
            
                                                                                                            
                            
            
                                    
            
            
                | 
                    244
                 | 
                                    
                                                     | 
                
                 | 
                __all__ = ['moreau_broto_autocorrelation', 'moran_coefficient',  | 
            
            
                                                                                                            
                            
            
                                    
            
            
                | 
                    245
                 | 
                                    
                                                     | 
                
                 | 
                           'geary_coefficient', 'topological_charge_index',  | 
            
            
                                                                                                            
                                                                
            
                                    
            
            
                | 
                    246
                 | 
                                    
                                                     | 
                
                 | 
                           'mean_topological_charge_index', 'total_charge_index']  | 
            
            
                                                        
            
                                    
            
            
                | 
                    247
                 | 
                                    
                                                     | 
                
                 | 
                 | 
            
            
                        
This can be caused by one of the following:
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This error could indicate a configuration issue of Pylint. Make sure that your libraries are available by adding the necessary commands.
2. Missing __init__.py files
This error could also result from missing
__init__.pyfiles in your module folders. Make sure that you place one file in each sub-folder.