Reordered steps in 3D data extraction + removed inverted numbering support

+#!python3
+import subprocess, os, sys
+
+# Put a list of problematic chains here, they will be properly deleted and recomputed
+problems = [
+"4v7f_1_1_4-3396",
+"4v7f_1_1_1-3167",
+"4v7f_1_1_1-3255",
+"6g90_1_1_1-407",
+"3q3z_1_A_1-74",
+"3q3z_1_V_1-74",
+"4v7f_1_3_1-121"
+]
+
+path_to_3D_data = sys.argv[1]
+path_to_seq_data = sys.argv[2]
+
+for p in problems:
+    print()
+    print()
+    print()
+    print()
+
+    # Remove the datapoints files and 3D files
+    subprocess.run(["rm", '-f', path_to_3D_data + f"/rna_mapped_to_Rfam/{p}.cif"])
+    files = [ f for f in os.listdir(path_to_3D_data + "/datapoints") if p in f ]
+    for f in files:
+        subprocess.run(["rm", '-f', path_to_3D_data + f"/datapoints/{f}"])
+
+    # 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}\";"]
+        print(' '.join(command))
+        subprocess.run(command)
+
+    # 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)
+
+# run statistics

@@ -139,6 +139,7 @@ def reproduce_wadley_results(show=False, carbon=4, sd_range=(1,4)):
         fig.savefig(f"results/figures/wadley_plots/wadley_hist_{angle}_{l}.png")
         fig.savefig(f"results/figures/wadley_plots/wadley_hist_{angle}_{l}.png")
         if show:
         if show:
             fig.show()
             fig.show()
+        fig.close()
 
 
         # Smoothed joint distribution
         # Smoothed joint distribution
         fig = plt.figure()
         fig = plt.figure()
@@ -149,6 +150,7 @@ def reproduce_wadley_results(show=False, carbon=4, sd_range=(1,4)):
         fig.savefig(f"results/figures/wadley_plots/wadley_distrib_{angle}_{l}.png")
         fig.savefig(f"results/figures/wadley_plots/wadley_distrib_{angle}_{l}.png")
         if show:
         if show:
             fig.show()
             fig.show()
+        fig.close()
 
 
         # 2D Wadley plot
         # 2D Wadley plot
         fig = plt.figure(figsize=(5,5))
         fig = plt.figure(figsize=(5,5))
@@ -161,6 +163,7 @@ def reproduce_wadley_results(show=False, carbon=4, sd_range=(1,4)):
         fig.savefig(f"results/figures/wadley_plots/wadley_{angle}_{l}.png")
         fig.savefig(f"results/figures/wadley_plots/wadley_{angle}_{l}.png")
         if show:
         if show:
             fig.show()
             fig.show()
+        fig.close()
     # print(f"[{worker_nbr}]\tComputed joint distribution of angles (C{carbon}) and saved the figures.")
     # print(f"[{worker_nbr}]\tComputed joint distribution of angles (C{carbon}) and saved the figures.")
 
 
 def stats_len():
 def stats_len():
@@ -440,7 +443,7 @@ def to_dist_matrix(f):
     idty = dm.get_distance(al).matrix # list of lists
     idty = dm.get_distance(al).matrix # list of lists
     del al
     del al
     l = len(idty)
     l = len(idty)
-    np.save("data/"+f+".npy", np.array([ idty[i] + [0]*(l-1-i) if i<l-1 else idty[i]  for i in range(l) ]))
+    np.save("data/"+f+".npy", np.array([ idty[i] + [0]*(l-1-i) if i<l-1 else idty[i]  for i in range(l) ], dtype=object))
     del idty
     del idty
     notify(f"Computed {f} distance matrix")
     notify(f"Computed {f} distance matrix")
     return 0
     return 0