maxtaskperchild, again

@@ -166,7 +166,7 @@ class Chain:
     def __hash__(self):
     def __hash__(self):
         return hash((self.pdb_id, self.pdb_model, self.pdb_chain_id, self.chain_label))
         return hash((self.pdb_id, self.pdb_model, self.pdb_chain_id, self.chain_label))
 
 
-    def extract(self, df, khetatm):
+    def extract(self, df, khetatm) -> None:
         """ Extract the part which is mapped to Rfam from the main CIF file and save it to another file.
         """ Extract the part which is mapped to Rfam from the main CIF file and save it to another file.
         """
         """
         setproctitle(f"RNANet.py {self.chain_label} extract()")
         setproctitle(f"RNANet.py {self.chain_label} extract()")
@@ -192,8 +192,17 @@ class Chain:
 
 
             # Load the whole mmCIF into a Biopython structure object:
             # Load the whole mmCIF into a Biopython structure object:
             mmcif_parser = MMCIFParser()
             mmcif_parser = MMCIFParser()
-            s = mmcif_parser.get_structure(self.pdb_id, path_to_3D_data + "RNAcifs/"+self.pdb_id+".cif")
-            
+            try:
+                s = mmcif_parser.get_structure(self.pdb_id, path_to_3D_data + "RNAcifs/"+self.pdb_id+".cif")
+            except ValueError as e:
+                warn(f"ValueError in {self.chain_label} CIF file: {e}")
+                self.delete_me = True
+                return
+            except IndexError as e:
+                warn(f"IndexError in {self.chain_label} CIF file: {e}")
+                self.delete_me = True
+                return
+
             if self.mapping is not None:
             if self.mapping is not None:
                 valid_set = set(df.old_nt_resnum)
                 valid_set = set(df.old_nt_resnum)
             else:
             else:
@@ -206,7 +215,6 @@ class Chain:
             ioobj = MMCIFIO()
             ioobj = MMCIFIO()
             ioobj.set_structure(s)
             ioobj.set_structure(s)
             ioobj.save(self.file, sel)
             ioobj.save(self.file, sel)
-            
 
 
         notify(status)
         notify(status)
 
 
@@ -1137,7 +1145,7 @@ class Pipeline:
             exit(1)
             exit(1)
     
     
     @trace_unhandled_exceptions
     @trace_unhandled_exceptions
-    def list_available_mappings(self):
+    def list_available_mappings(self) -> None:
         """List 3D chains with available Rfam mappings.
         """List 3D chains with available Rfam mappings.
 
 
         Return a list of Chain() objects with the mappings set up.        
         Return a list of Chain() objects with the mappings set up.        
@@ -1228,7 +1236,7 @@ class Pipeline:
         else:
         else:
             mmcif_list = sorted(set([ c.pdb_id for c in self.update ]))
             mmcif_list = sorted(set([ c.pdb_id for c in self.update ]))
         try:
         try:
-            p = Pool(initializer=init_worker, initargs=(tqdm.get_lock(),), processes=int(coeff_ncores*ncores), maxtasksperchild=1)
+            p = Pool(initializer=init_worker, initargs=(tqdm.get_lock(),), processes=int(coeff_ncores*ncores))
             pbar = tqdm(mmcif_list, maxinterval=1.0, miniters=1, desc="mmCIF files")
             pbar = tqdm(mmcif_list, maxinterval=1.0, miniters=1, desc="mmCIF files")
             for _ in p.imap_unordered(work_mmcif, mmcif_list, chunksize=1): 
             for _ in p.imap_unordered(work_mmcif, mmcif_list, chunksize=1): 
                 pbar.update(1) # Everytime the iteration finishes, update the global progress bar
                 pbar.update(1) # Everytime the iteration finishes, update the global progress bar
@@ -1407,7 +1415,7 @@ class Pipeline:
 
 
         # Start a process pool to dispatch the RNA families,
         # Start a process pool to dispatch the RNA families,
         # over multiple CPUs (one family by CPU)
         # over multiple CPUs (one family by CPU)
-        p = Pool(initializer=init_worker, initargs=(tqdm.get_lock(),), processes=nworkers, maxtasksperchild=1)
+        p = Pool(initializer=init_worker, initargs=(tqdm.get_lock(),), processes=nworkers)
 
 
         try:
         try:
             fam_pbar = tqdm(total=len(self.fam_list), desc="RNA families", position=0, leave=True) 
             fam_pbar = tqdm(total=len(self.fam_list), desc="RNA families", position=0, leave=True) 
@@ -1841,7 +1849,7 @@ def execute_joblist(fulljoblist):
     return results
     return results
 
 
 @trace_unhandled_exceptions
 @trace_unhandled_exceptions
-def work_infer_mappings(update_only, allmappings, codelist):
+def work_infer_mappings(update_only, allmappings, codelist) -> list:
     """Given a list of PDB chains corresponding to an equivalence class from BGSU's NR list, 
     """Given a list of PDB chains corresponding to an equivalence class from BGSU's NR list, 
     build a list of Chain() objects mapped to Rfam families, by expanding available mappings 
     build a list of Chain() objects mapped to Rfam families, by expanding available mappings 
     of any element of the list to all the list elements.
     of any element of the list to all the list elements.