Fix: JSON merging when not using --hrna

@@ -10,6 +10,7 @@ Contents:
 * [Database tables documentation](doc/Database.md)
 * [Database tables documentation](doc/Database.md)
 * [FAQ](doc/FAQ.md)
 * [FAQ](doc/FAQ.md)
 * [Troubleshooting](#troubleshooting)
 * [Troubleshooting](#troubleshooting)
+* [Known Issues and Feature Requests](doc/KnownIssues.md)
 * [Contact](#contact)
 * [Contact](#contact)
 
 
 ## Cite us
 ## Cite us

@@ -1730,7 +1730,7 @@ def gmm_hrna_basepair_type(type_LW, ntpair, data, scan):
     setproctitle(f"GMM (HiRE-RNA {type_LW} {ntpair} basepairs) finished")
     setproctitle(f"GMM (HiRE-RNA {type_LW} {ntpair} basepairs) finished")
 
 
 @trace_unhandled_exceptions
 @trace_unhandled_exceptions
-def merge_jsons():
+def merge_jsons(do_hrna):
     """
     """
     Reads the tons of JSON files produced by the geometric analyses, and compiles them into fewer files.
     Reads the tons of JSON files produced by the geometric analyses, and compiles them into fewer files.
     It is simple concatenation of the JSONs.
     It is simple concatenation of the JSONs.
@@ -1744,12 +1744,19 @@ def merge_jsons():
     bonds = [ runDir + "/results/geometry/json/" + x + ".json" for x in bonds ]
     bonds = [ runDir + "/results/geometry/json/" + x + ".json" for x in bonds ]
     concat_jsons(bonds, runDir + "/results/geometry/json/all_atom_distances.json")
     concat_jsons(bonds, runDir + "/results/geometry/json/all_atom_distances.json")
     
     
-
     # All atom torsions
     # All atom torsions
     torsions = ["Alpha", "Beta", "Gamma", "Delta", "Epsilon", "Xhi", "Zeta"]
     torsions = ["Alpha", "Beta", "Gamma", "Delta", "Epsilon", "Xhi", "Zeta"]
     torsions = [ runDir + "/results/geometry/json/" + x + ".json" for x in torsions ]
     torsions = [ runDir + "/results/geometry/json/" + x + ".json" for x in torsions ]
     concat_jsons(torsions, runDir + "/results/geometry/json/all_atom_torsions.json")
     concat_jsons(torsions, runDir + "/results/geometry/json/all_atom_torsions.json")
  
  
+    # Delete previous files
+    for f in bonds + torsions:
+        try:
+            os.remove(f)
+        except FileNotFoundError:
+            pass
+
+    if do_hrna:
         # HiRE-RNA distances
         # HiRE-RNA distances
         hrnabonds = [r"P-O5'", r"O5'-C5'", r"C5'-C4'", r"C4'-C1'", r"C1'-B1", r"B1-B2", r"C4'-P"]
         hrnabonds = [r"P-O5'", r"O5'-C5'", r"C5'-C4'", r"C4'-C1'", r"C1'-B1", r"B1-B2", r"C4'-P"]
         hrnabonds = [ runDir + "/results/geometry/json/" + x + ".json" for x in hrnabonds ]
         hrnabonds = [ runDir + "/results/geometry/json/" + x + ".json" for x in hrnabonds ]
@@ -1772,7 +1779,7 @@ def merge_jsons():
                 concat_jsons(bps, runDir + f"/results/geometry/json/hirerna_{nt1}{nt2}_basepairs.json")
                 concat_jsons(bps, runDir + f"/results/geometry/json/hirerna_{nt1}{nt2}_basepairs.json")
 
 
         # Delete previous files
         # Delete previous files
-    for f in bonds + torsions + hrnabonds + hrnaangles + hrnators:
+        for f in hrnabonds + hrnaangles + hrnators:
             try:
             try:
                 os.remove(f)
                 os.remove(f)
             except FileNotFoundError:
             except FileNotFoundError:
@@ -1876,8 +1883,9 @@ def concat_jsons(flist, outfilename):
     
     
     result = []
     result = []
     for f in flist:
     for f in flist:
-        # if not os.path.isfile(f):
-        #     continue:
+        if not os.path.isfile(f):
+            warn("Unable to find "+f)
+            continue
         with open(f, "rb") as infile:
         with open(f, "rb") as infile:
             result.append(json.load(infile))
             result.append(json.load(infile))
 
 

@@ -1536,6 +1536,6 @@ if __name__ == "__main__":
         if DO_WADLEY_ANALYSIS:
         if DO_WADLEY_ANALYSIS:
             joblist.append(Job(function=gmm_pyle, args=(RESCAN_GMM_COMP_NUM, res_thr)))
             joblist.append(Job(function=gmm_pyle, args=(RESCAN_GMM_COMP_NUM, res_thr)))
         process_jobs(joblist)
         process_jobs(joblist)
-        merge_jsons()
+        merge_jsons(DO_HIRE_RNA_MEASURES)