Révision f6431316 modules/clustering.py

b/modules/clustering.py
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clustering: Directs the clustering process by calling the relevant functions.
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"""
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import logging
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import warnings
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import hdbscan


  		





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import numpy as np


  		





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logger = logging.getLogger('DockOnSurf')


  		





  
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warnings.filterwarnings("error")


  		





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def get_rmsd(mol_list: list, remove_Hs="c"):


  		





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    exemplars = []


  		





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    for i, mtx in enumerate(clust_affty_mtcs):


  		





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        pref = -1e6 * np.max(np.abs(mtx))


  		





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        af = AffinityPropagation(affinity='precomputed', preference=pref,


  		





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                                 damping=0.95, max_iter=2000,


  		





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                                 random_state=None).fit(mtx)


  		





  
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        try:


  		





  
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            af = AffinityPropagation(affinity='precomputed', preference=pref,


  		





  
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                                     damping=0.95, max_iter=2000,


  		





  
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                                     random_state=None).fit(mtx)


  		





  
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        except UserWarning as w:


  		





  
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            logger.warning(str(w))


  		





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        exemplars.append(clusters[i][af.cluster_centers_indices_[0]])


  		





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    return exemplars


  		





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