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Push — master ( c026c2...632976 )
by Daniel
06:58
created

regenerate_data.regen()   A

↳ Parent: regenerate_data

Complexity

Conditions 3

Size

Total Lines 13
Code Lines 10

Duplication

Lines 0
Ratio 0 %

Importance

Changes 0
Metric Value
eloc 10
dl 0
loc 13
rs 9.9
c 0
b 0
f 0
cc 3
nop 2
1 
import os
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import numpy as np
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import amd
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import pickle
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root = r'tests/data'

            


            
                                                                                                            
                                                                
            
                                    
            
            

                
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def regen(name, generator):

            


            
                                                                        
                            
            
                                    
            
            

                
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    data = []

            


            
                                                                        
                            
            
                                    
            
            

                
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    for s in generator:

            


            
                                                                        
                            
            
                                    
            
            

                
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        pdd = amd.PDD(s, 100)

            


            
                                                                        
                            
            
                                    
            
            

                
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        data.append({'PeriodicSet': s, 'AMD100': amd.PDD_to_AMD(pdd), 'PDD100': pdd})

            


            
                                                                        
                            
            
                                    
            
            

                
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    with open(os.path.join(root, f'{name}.pkl'), 'wb') as f:

            


            
                                                                        
                            
            
                                    
            
            

                
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        pickle.dump(data, f)

            


            
                                                                        
                            
            
                                    
            
            

                
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    pdds = [d['PDD100'] for d in data]

            


            
                                                                        
                            
            
                                    
            
            

                
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    cdm = amd.PDD_pdist(pdds)

            


            
                                                                        
                            
            
                                    
            
            

                
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    np.savez_compressed(os.path.join(root, rf'{name}_cdm.npz'), cdm=cdm)

            


            
                                                                                                            
                            
            
                                    
            
            

                
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def regenerate_from_cifs():

            


            
                                                                                                            
                            
            
                                    
            
            

                
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    filenames = ['cubic', 'T2_experimental']

            


            
                                                                                                            
                            
            
                                    
            
            

                
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    for name in filenames:

            


            
                                                                                                            
                            
            
                                    
            
            

                
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        path = os.path.join(root, name)

            


            
                                                                                                            
                            
            
                                    
            
            

                
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        regen(name, amd.CifReader(path + '.cif', show_warnings=False))

            


            
                                                                                                            
                            
            
                                    
            
            

                
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def regenerate_CSD_families():

            


            
                                                                                                            
                            
            
                                    
            
            

                
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    name = 'CSD_families'

            


            
                                                                                                            
                            
            
                                    
            
            

                
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    csd_families = ['DEBXIT', 'GLYCIN', 'HXACAN', 'ACSALA']

            


            
                                                                                                            
                            
            
                                    
            
            

                
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    generator = amd.CSDReader(csd_families, families=True, show_warnings=False)

            


            
                                                                                                            
                            
            
                                    
            
            

                
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    regen(name, generator)

            


            
                                                                                                            
                            
            
                                    
            
            

                
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if __name__ == '__main__':

            


            
                                                                                                            
                                                                
            
                                    
            
            

                
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    # pass

            


            
                                                        
            
                                    
            
            

                
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    regenerate_CSD_families()