Rethink how inferred mappings work

@@ -12,7 +12,6 @@ done
 
 PROCESS_TO_KILL="statistics.py"
 PROCESS_LIST=`ps ax | grep -Ei ${PROCESS_TO_KILL} | grep -Eiv '(grep|vi statistics.py)' | awk ' { print $1;}'`
-KILLED=
 for KILLPID in $PROCESS_LIST; do
   if [ ! -z $KILLPID ];then
     kill -9 $KILLPID

@@ -3,8 +3,8 @@ import subprocess, os, sys
 
 # Put a list of problematic chains here, they will be properly deleted and recomputed
 problems = [
-"4v9n_1_DA_1-2879",
-"4v9n_1_DA_148-2875"
+    "1k73_1_A",
+    "1k73_1_B"
 ]
 
 path_to_3D_data = sys.argv[1]
@@ -15,6 +15,7 @@ for p in problems:
     print()
     print()
     print()
+    homology = ('-' in p)
 
     # Remove the datapoints files and 3D files
     subprocess.run(["rm", '-f', path_to_3D_data + f"/rna_mapped_to_Rfam/{p}.cif"])
@@ -25,16 +26,25 @@ for p in problems:
     # Find more information
     structure = p.split('_')[0]
     chain = p.split('_')[2]
-    families = [ f.split('.')[1] for f in files ] # The RFAM families this chain has been mapped onto
-
-    # Delete the chain from the database, and the associated nucleotides and re_mappings, using foreign keys
-    for fam in families:
-        command = ["sqlite3", "results/RNANet.db", f"PRAGMA foreign_keys=ON; delete from chain where structure_id=\"{structure}\" and chain_name=\"{chain}\" and rfam_acc=\"{fam}\";"]
+    if homology:
+        families = [ f.split('.')[1] for f in files ] # The RFAM families this chain has been mapped onto
+
+        # Delete the chain from the database, and the associated nucleotides and re_mappings, using foreign keys
+        for fam in families:
+            command = ["sqlite3", "results/RNANet.db", f"PRAGMA foreign_keys=ON; delete from chain where structure_id=\"{structure}\" and chain_name=\"{chain}\" and rfam_acc=\"{fam}\";"]
+            print(' '.join(command))
+            subprocess.run(command)
+
+        command = ["python3.8", "RNAnet.py", "--3d-folder", path_to_3D_data, "--seq-folder", path_to_seq_data, "-r", "20.0", "--extract", "--only", p]
+    else:
+        # Delete the chain from the database, and the associated nucleotides and re_mappings, using foreign keys
+        command = ["sqlite3", "results/RNANet.db", f"PRAGMA foreign_keys=ON; delete from chain where structure_id=\"{structure}\" and chain_name=\"{chain}\" and rfam_acc is null;"]
         print(' '.join(command))
         subprocess.run(command)
 
+        command = ["python3.8", "RNAnet.py", "--3d-folder", path_to_3D_data, "--seq-folder", path_to_seq_data, "-r", "20.0", "--no-homology", "--extract", "--only", p]
+
     # Re-run RNANet
-    command = ["python3.8", "RNAnet.py", "--3d-folder", path_to_3D_data, "--seq-folder", path_to_seq_data, "-r", "20.0", "--extract", "--only", p]
     print('\n',' '.join(command),'\n')
     subprocess.run(command)