Fix: Multiple representatives in no-homology mode

@@ -32,6 +32,8 @@ BUG CORRECTIONS
 TECHNICAL CHANGES
 TECHNICAL CHANGES
     - Switched to DSSR Pro.
     - Switched to DSSR Pro.
     - Switched to esl-alimerge instead of cmalign --merge to merge alignments.
     - Switched to esl-alimerge instead of cmalign --merge to merge alignments.
+    - Tested successfully with Python 3.9.6 + BioPython 1.79. 
+      However, the production server still runs with Python 3.8.1 + BioPython 1.78.
 
 
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 ############################################################################################
 v 1.5 beta, April 2021
 v 1.5 beta, April 2021

@@ -1327,6 +1327,7 @@ class Pipeline:
             conn.execute('pragma journal_mode=wal')
             conn.execute('pragma journal_mode=wal')
             for eq_class, representative, codelist in tqdm(full_structures_list, desc="Eq. classes"):
             for eq_class, representative, codelist in tqdm(full_structures_list, desc="Eq. classes"):
                 codes = codelist.replace('+', ',').split(',')
                 codes = codelist.replace('+', ',').split(',')
+                representatives = representative.replace('+', ',').split(',')
 
 
                 # Simply convert the list of codes to Chain() objects
                 # Simply convert the list of codes to Chain() objects
                 if self.REDUNDANT:
                 if self.REDUNDANT:
@@ -1344,7 +1345,8 @@ class Pipeline:
                         if not len(res) or self.REUSE_ALL:  # the chain is NOT yet in the database, or this is a known issue
                         if not len(res) or self.REUSE_ALL:  # the chain is NOT yet in the database, or this is a known issue
                             self.update.append(Chain(pdb_id, pdb_model, pdb_chain_id, chain_label, eq_class))
                             self.update.append(Chain(pdb_id, pdb_model, pdb_chain_id, chain_label, eq_class))
                 else:
                 else:
-                    nr = representative.split('|')
+                    for rep in representatives:
+                        nr = rep.split('|')
                         pdb_id = nr[0].lower()
                         pdb_id = nr[0].lower()
                         pdb_model = int(nr[1])
                         pdb_model = int(nr[1])
                         pdb_chain_id = nr[2].upper()
                         pdb_chain_id = nr[2].upper()
@@ -2292,7 +2294,7 @@ def execute_joblist(fulljoblist):
                 p.join()
                 p.join()
             except KeyboardInterrupt as e:
             except KeyboardInterrupt as e:
                 warn("KeyboardInterrupt, killing workers (SIGKILL).", error=True)
                 warn("KeyboardInterrupt, killing workers (SIGKILL).", error=True)
-                p.kill()
+                p.terminate()
                 p.join()
                 p.join()
                 raise e
                 raise e
 
 
@@ -2327,7 +2329,7 @@ def work_infer_mappings(update_only, allmappings, fullinference, redundant, code
     # Split the comma-separated list of chain codes into chain codes:
     # Split the comma-separated list of chain codes into chain codes:
     eq_class = codelist[0]
     eq_class = codelist[0]
     codes = codelist[2].replace('+', ',').split(',')
     codes = codelist[2].replace('+', ',').split(',')
-    representative=codelist[1].replace('+', ',').split(',')[0]
+    representative = codelist[1].replace('+', ',').split(',')[0]
     # Search for mappings that apply to an element of this PDB chains list:
     # Search for mappings that apply to an element of this PDB chains list:
     for c in codes:
     for c in codes:
         # search for Rfam mappings with this chain c:
         # search for Rfam mappings with this chain c:

@@ -21,6 +21,6 @@ docker build -t rnanet:latest ..
 rm x3dna-dssr
 rm x3dna-dssr
 
 
 # to run, use something like:
 # to run, use something like:
-# docker run -v /home/persalteas/Data/RNA/3D/:/3D -v /home/persalteas/Data/RNA/sequences/:/sequences -v /home/persalteas/labo/:/runDir persalteas/rnanet [ additional options here ]
+# docker run -v /home/lbecquey/Data/RNA/3D/:/3D -v /home/lbecquey/Data/RNA/sequences/:/sequences -v /home/lbecquey/labo/:/runDir rnanet [ additional options here ]
 # Without additional options, this runs a standard pass with known issues support, log output, and no statistics. The default resolution threshold is 4.0 Angstroms.
 # Without additional options, this runs a standard pass with known issues support, log output, and no statistics. The default resolution threshold is 4.0 Angstroms.