clean up

deeprank/features/BSA.py

@@ -117,19 +117,7 @@ def get_contact_residue_sasa(self, cutoff=5.5):
             # define the xyz key : (chain,x,y,z)
             chain = {'A': 0, 'B': 1}[res[0]]
 
-            # atcenter = 'CB'
-            # if res[2] == 'GLY':
-            #     atcenter = 'CA'
-
-            # try :
-            #     xyz = self.sql.get(
-            #         'x,y,z', resSeq=res[1], chainID=res[0], name=atcenter)[0]
-            # except IndexError :
-            #     warnings.warn('Atom ', atcenter, ' not found for residue ', key[1], \
-            #                    '. Use residue center as feature center')            
-            #     xyz = np.mean(self.sql.get('x,y,z',resSeq=res[1],chainID=res[0]),0)
-            # xyzkey = tuple([chain] + xyz)
-
+            # get the center            
             _, xyz = self.get_residue_center(self.sql, res=res)
             xyzkey = tuple([chain] + xyz[0])
 

deeprank/features/FullPSSM.py

@@ -166,12 +166,6 @@ def get_feature_value(self, cutoff=5.5):
         sql = pdb2sql.interface(self.pdb_file)
 
         # set achors for all residues and get their xyz
-        # xyz_info = sql.get('chainID,resSeq,resName', name='CB')
-        # xyz_info += sql.get('chainID,resSeq,resName', name='CA',
-        #                     resName='GLY')
-        # xyz = sql.get('x,y,z', name='CB')
-        # xyz += sql.get('x,y,z', name='CA', resName='GLY')
-
         xyz_info, xyz = self.get_residue_center(sql)
 
         xyz_dict = {}
@@ -214,15 +208,6 @@ def get_feature_value(self, cutoff=5.5):
                 f" no pssm value:\n {ctc_res_wo_pssm}"
             )
 
-        # elif len(pssm_res_set.difference(ctc_res_set)) > 0:
-        #     # can happen if CA/CB is missing in the res
-        #     pssm_res_wo_ctc = pssm_res_set.difference(ctc_res_set)
-        #     ctc_res_with_pssm = pssm_res_set.intersection(ctc_res_set)
-        #     warnings.warn(
-        #         f"{self.mol_name}: The following interface residues have "
-        #         f" a CA or CB missing :\n {pssm_res_wo_ctc}"
-        #     )
-
         else:
             ctc_res_with_pssm = ctc_res
 

deeprank/features/ResidueDensity.py

@@ -123,21 +123,7 @@ def extract_features(self):
             # total density in raw format
             self.feature_data['RCD_total'][key] = [res.density['total']]
 
-            # # get the type of the center
-            # atcenter = 'CB'
-            # if key[2] == 'GLY':
-            #     atcenter = 'CA'
-
-            # # get the xyz of the center atom
-            # try:
-            #     xyz = self.sql.get(
-            #         'x,y,z', resSeq=key[1], chainID=key[0], name=atcenter)[0]
-            # except IndexError :
-            #     warnings.warn('Atom ', atcenter, ' not found for residue ', key[1], \
-            #                    '. Use residue center as feature center')
-            #     xyz = np.mean(self.sql.get('x,y,z',resSeq=key[1],chainID=key[0]),0).tolist()
-            # xyz_key = tuple([{'A': 0, 'B': 1}[key[0]]] + xyz)
-
+            # get the center
             _, xyz = self.get_residue_center(self.sql, res=key)
             xyz_key = tuple([{'A': 0, 'B': 1}[key[0]]] + xyz[0])
 

deeprank/generate/DataGenerator.py

@@ -251,7 +251,6 @@ def create_database(
 
             # names of the molecule
             mol_name = os.path.splitext(os.path.basename(cplx))[0]
-            #mol_name = mol_name.replace('-', '_')
             mol_aug_name_list = []
 
             try: