Fix: JSON merging when not using --hrna

@@ -10,6 +10,7 @@ Contents:
 * [Database tables documentation](doc/Database.md)
 * [FAQ](doc/FAQ.md)
 * [Troubleshooting](#troubleshooting)
+* [Known Issues and Feature Requests](doc/KnownIssues.md)
 * [Contact](#contact)
 
 ## 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")
 
 @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.
     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 ]
     concat_jsons(bonds, runDir + "/results/geometry/json/all_atom_distances.json")
     
-
     # All atom torsions
     torsions = ["Alpha", "Beta", "Gamma", "Delta", "Epsilon", "Xhi", "Zeta"]
     torsions = [ runDir + "/results/geometry/json/" + x + ".json" for x in torsions ]
     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
         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 ]
@@ -1772,7 +1779,7 @@ def merge_jsons():
                 concat_jsons(bps, runDir + f"/results/geometry/json/hirerna_{nt1}{nt2}_basepairs.json")
 
         # Delete previous files
-    for f in bonds + torsions + hrnabonds + hrnaangles + hrnators:
+        for f in hrnabonds + hrnaangles + hrnators:
             try:
                 os.remove(f)
             except FileNotFoundError:
@@ -1876,8 +1883,9 @@ def concat_jsons(flist, outfilename):
     
     result = []
     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:
             result.append(json.load(infile))
 

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